Starting phenix.real_space_refine on Sun Jun 15 08:13:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y8t_33685/06_2025/7y8t_33685.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y8t_33685/06_2025/7y8t_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_33685/06_2025/7y8t_33685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y8t_33685/06_2025/7y8t_33685.map" model { file = "/net/cci-nas-00/data/ceres_data/7y8t_33685/06_2025/7y8t_33685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y8t_33685/06_2025/7y8t_33685.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'RNA': 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: 9.68, per 1000 atoms: 0.58 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: 3.85 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 4.98 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: 6.47 Time building geometry restraints manager: 4.59 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: 22857 1.80 - 3.59: 429 3.59 - 5.39: 66 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 - 35.70: 10044 35.70 - 71.40: 328 71.40 - 107.10: 29 107.10 - 142.80: 0 142.80 - 178.49: 9 Dihedral angle restraints: 10410 sinusoidal: 4705 harmonic: 5705 Sorted by residual: dihedral pdb=" O4' U D 7 " pdb=" C1' U D 7 " pdb=" N1 U D 7 " pdb=" C2 U D 7 " ideal model delta sinusoidal sigma weight residual 200.00 24.60 175.40 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C D -16 " pdb=" C1' C D -16 " pdb=" N1 C D -16 " pdb=" C2 C D -16 " ideal model delta sinusoidal sigma weight residual 200.00 28.68 171.32 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' C D 1 " pdb=" C1' C D 1 " pdb=" N1 C D 1 " pdb=" C2 C D 1 " ideal model delta sinusoidal sigma weight residual 200.00 35.85 164.15 1 1.50e+01 4.44e-03 8.37e+01 ... (remaining 10407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2491 0.117 - 0.234: 31 0.234 - 0.350: 0 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=" C1' U D 7 " pdb=" O4' U D 7 " pdb=" C2' U D 7 " pdb=" N1 U D 7 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C1' U D -14 " pdb=" O4' U D -14 " pdb=" C2' U D -14 " pdb=" N1 U D -14 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 8.92e-01 ... (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: 3.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 43.750 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.080 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:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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= 0.244 Angle : 0.636 8.987 23395 Z= 0.364 Chirality : 0.043 0.584 2523 Planarity : 0.005 0.101 2881 Dihedral : 16.972 178.494 6742 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.76 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.001 TRP A1685 HIS 0.005 0.001 HIS B 493 PHE 0.027 0.002 PHE A 104 TYR 0.016 0.001 TYR B 277 ARG 0.009 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.19474 ( 581) hydrogen bonds : angle 6.12246 ( 1722) metal coordination : bond 0.00396 ( 16) metal coordination : angle 2.60120 ( 21) covalent geometry : bond 0.00391 (17203) covalent geometry : angle 0.63159 (23374) *********************** 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 : 1.788 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: 1.5017 time to fit residues: 269.2473 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 : 1.975 ------------------------------------------------------------------------------- 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 168 optimal weight: 0.2980 chunk 151 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 102 optimal weight: 0.4980 chunk 80 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 181 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3885 r_free = 0.3885 target = 0.161449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.125518 restraints weight = 19380.273| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.47 r_work: 0.3188 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 17219 Z= 0.115 Angle : 0.558 8.293 23395 Z= 0.295 Chirality : 0.041 0.211 2523 Planarity : 0.005 0.065 2881 Dihedral : 15.603 178.794 2752 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.45 % Favored : 94.40 % Rotamer: Outliers : 1.96 % Allowed : 13.88 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.22 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.19), residues: 1964 helix: 1.93 (0.21), residues: 634 sheet: 0.09 (0.33), residues: 249 loop : -1.71 (0.17), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 278 HIS 0.005 0.001 HIS B 493 PHE 0.013 0.001 PHE B 703 TYR 0.013 0.001 TYR B 704 ARG 0.006 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04597 ( 581) hydrogen bonds : angle 4.50983 ( 1722) metal coordination : bond 0.00300 ( 16) metal coordination : angle 2.45120 ( 21) covalent geometry : bond 0.00239 (17203) covalent geometry : angle 0.55347 (23374) *********************** 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 186 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 1.884 Fit side-chains revert: symmetry clash REVERT: B 508 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8392 (mmtt) REVERT: B 527 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6796 (mm-30) REVERT: B 686 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6543 (mp0) REVERT: A 6 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7674 (ppp) REVERT: A 125 GLU cc_start: 0.7515 (pp20) cc_final: 0.7313 (pp20) REVERT: A 144 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7897 (mt-10) REVERT: A 240 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8072 (mp) REVERT: A 271 ASP cc_start: 0.7240 (m-30) cc_final: 0.6850 (m-30) REVERT: A 286 GLN cc_start: 0.7871 (tp40) cc_final: 0.7421 (tt0) REVERT: A 288 ASP cc_start: 0.7886 (t0) cc_final: 0.7650 (t0) REVERT: A 697 ARG cc_start: 0.7839 (mtm180) cc_final: 0.7638 (mtm180) REVERT: A 1493 LYS cc_start: 0.7214 (mmtt) cc_final: 0.6920 (tppt) REVERT: A 1580 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7059 (mptt) REVERT: A 1685 TRP cc_start: 0.6492 (OUTLIER) cc_final: 0.4410 (m100) outliers start: 34 outliers final: 16 residues processed: 175 average time/residue: 1.4471 time to fit residues: 280.5227 Evaluate side-chains 165 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 1.864 ------------------------------------------------------------------------------- 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 94 THR 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 529 TYR 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 1468 ILE Chi-restraints excluded: chain A residue 1497 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 1634 LEU 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 154 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3868 r_free = 0.3868 target = 0.159891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.123931 restraints weight = 19435.575| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.55 r_work: 0.3162 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.0820 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= 0.130 Angle : 0.574 8.100 23395 Z= 0.301 Chirality : 0.042 0.217 2523 Planarity : 0.004 0.060 2881 Dihedral : 15.440 177.918 2724 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.75 % Favored : 94.09 % Rotamer: Outliers : 2.94 % Allowed : 13.54 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.19), residues: 1964 helix: 1.86 (0.21), residues: 645 sheet: -0.02 (0.32), residues: 260 loop : -1.67 (0.17), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 612 HIS 0.006 0.001 HIS B 493 PHE 0.016 0.001 PHE B 703 TYR 0.022 0.001 TYR B 277 ARG 0.005 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04650 ( 581) hydrogen bonds : angle 4.29068 ( 1722) metal coordination : bond 0.00345 ( 16) metal coordination : angle 2.38278 ( 21) covalent geometry : bond 0.00289 (17203) covalent geometry : angle 0.56994 (23374) *********************** 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 203 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 152 time to evaluate : 1.999 Fit side-chains revert: symmetry clash REVERT: B 527 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6737 (mm-30) REVERT: B 618 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7060 (ttmm) REVERT: B 686 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: A 6 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7446 (ppp) REVERT: A 240 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8108 (mp) REVERT: A 271 ASP cc_start: 0.7188 (m-30) cc_final: 0.6721 (m-30) REVERT: A 286 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: A 288 ASP cc_start: 0.7922 (t0) cc_final: 0.7660 (t0) REVERT: A 885 MET cc_start: 0.1941 (mmm) cc_final: 0.1716 (mmt) REVERT: A 913 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7088 (mp10) REVERT: A 1496 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8030 (pt0) REVERT: A 1580 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7044 (mptt) REVERT: A 1685 TRP cc_start: 0.6211 (OUTLIER) cc_final: 0.4341 (m100) outliers start: 51 outliers final: 17 residues processed: 186 average time/residue: 1.4761 time to fit residues: 303.6284 Evaluate side-chains 168 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 452 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 94 THR 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 529 TYR 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 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 1618 VAL Chi-restraints excluded: chain A residue 1662 THR 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 197 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 0.0270 chunk 116 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 128 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 187 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 193 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3884 r_free = 0.3884 target = 0.161258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.125649 restraints weight = 19400.218| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.50 r_work: 0.3171 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1000 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= 0.108 Angle : 0.537 7.980 23395 Z= 0.283 Chirality : 0.041 0.214 2523 Planarity : 0.004 0.058 2881 Dihedral : 15.359 178.470 2722 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.50 % Favored : 94.35 % Rotamer: Outliers : 2.71 % Allowed : 14.17 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.19), residues: 1964 helix: 1.96 (0.21), residues: 652 sheet: 0.20 (0.33), residues: 249 loop : -1.62 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 612 HIS 0.004 0.001 HIS B 493 PHE 0.012 0.001 PHE B 491 TYR 0.020 0.001 TYR B 277 ARG 0.007 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 581) hydrogen bonds : angle 4.08896 ( 1722) metal coordination : bond 0.00272 ( 16) metal coordination : angle 2.18349 ( 21) covalent geometry : bond 0.00226 (17203) covalent geometry : angle 0.53304 (23374) *********************** 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: 47 poor density : 152 time to evaluate : 1.869 Fit side-chains revert: symmetry clash REVERT: B 109 ASN cc_start: 0.6810 (m-40) cc_final: 0.6556 (m-40) REVERT: B 527 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6714 (mm-30) REVERT: B 618 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.6954 (ttmm) REVERT: A 6 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7484 (ppp) REVERT: A 144 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: A 240 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8054 (mp) REVERT: A 271 ASP cc_start: 0.7209 (m-30) cc_final: 0.6699 (m-30) REVERT: A 286 GLN cc_start: 0.7828 (tp40) cc_final: 0.7468 (tt0) REVERT: A 288 ASP cc_start: 0.7812 (t0) cc_final: 0.7536 (t0) REVERT: A 808 TYR cc_start: 0.7649 (m-80) cc_final: 0.7224 (t80) REVERT: A 842 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7952 (mt) REVERT: A 913 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7022 (mp10) REVERT: A 1496 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8059 (pt0) REVERT: A 1580 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.6809 (mptt) REVERT: A 1685 TRP cc_start: 0.6136 (OUTLIER) cc_final: 0.4382 (m100) outliers start: 47 outliers final: 21 residues processed: 182 average time/residue: 1.4347 time to fit residues: 289.4463 Evaluate side-chains 172 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 GLU 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 A residue 6 MET Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 94 THR 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 529 TYR Chi-restraints excluded: chain A residue 548 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 1 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 178 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 592 ASN B 621 GLN 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 = 0.3810 r_free = 0.3810 target = 0.154455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118199 restraints weight = 19362.629| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.57 r_work: 0.3071 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17219 Z= 0.250 Angle : 0.748 10.067 23395 Z= 0.387 Chirality : 0.048 0.242 2523 Planarity : 0.006 0.063 2881 Dihedral : 15.694 178.474 2722 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.98 % Favored : 92.77 % Rotamer: Outliers : 3.80 % Allowed : 14.06 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.22 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.18), residues: 1964 helix: 1.43 (0.21), residues: 651 sheet: 0.06 (0.32), residues: 254 loop : -1.84 (0.17), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1685 HIS 0.009 0.002 HIS B 493 PHE 0.022 0.002 PHE B 703 TYR 0.036 0.002 TYR B 277 ARG 0.008 0.001 ARG A1523 Details of bonding type rmsd hydrogen bonds : bond 0.06819 ( 581) hydrogen bonds : angle 4.47995 ( 1722) metal coordination : bond 0.00736 ( 16) metal coordination : angle 3.26484 ( 21) covalent geometry : bond 0.00600 (17203) covalent geometry : angle 0.74195 (23374) *********************** 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 214 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 148 time to evaluate : 1.905 Fit side-chains revert: symmetry clash REVERT: B 40 ASP cc_start: 0.8051 (m-30) cc_final: 0.7791 (m-30) REVERT: B 109 ASN cc_start: 0.6742 (m-40) cc_final: 0.6537 (m-40) REVERT: B 527 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6814 (mm-30) REVERT: B 618 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7095 (ttmm) REVERT: A 6 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7976 (ppp) REVERT: A 125 GLU cc_start: 0.7555 (pp20) cc_final: 0.7228 (mm-30) REVERT: A 147 LYS cc_start: 0.8391 (ttmt) cc_final: 0.7870 (ttpp) REVERT: A 271 ASP cc_start: 0.7251 (m-30) cc_final: 0.6750 (m-30) REVERT: A 286 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7666 (tt0) REVERT: A 288 ASP cc_start: 0.8066 (t0) cc_final: 0.7743 (t0) REVERT: A 808 TYR cc_start: 0.7665 (m-80) cc_final: 0.7363 (t80) REVERT: A 913 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7097 (mp10) REVERT: A 932 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7112 (tmtt) REVERT: A 959 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: A 1499 GLU cc_start: 0.8134 (tt0) cc_final: 0.7924 (tt0) REVERT: A 1580 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.6775 (mttm) REVERT: A 1682 THR cc_start: 0.9054 (t) cc_final: 0.8512 (m) REVERT: A 1685 TRP cc_start: 0.6901 (OUTLIER) cc_final: 0.5517 (m100) outliers start: 66 outliers final: 30 residues processed: 197 average time/residue: 1.4843 time to fit residues: 322.4361 Evaluate side-chains 182 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 138 GLU 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 A residue 6 MET Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 387 THR 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 698 ASP 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 959 GLU Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 980 ASN 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 1490 ILE Chi-restraints excluded: chain A residue 1580 LYS Chi-restraints excluded: chain A residue 1582 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 19 optimal weight: 0.6980 chunk 188 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 chunk 150 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 199 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3848 r_free = 0.3848 target = 0.157980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.122173 restraints weight = 19314.779| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.52 r_work: 0.3118 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1272 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= 0.130 Angle : 0.585 7.902 23395 Z= 0.307 Chirality : 0.042 0.227 2523 Planarity : 0.004 0.062 2881 Dihedral : 15.495 179.201 2722 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.30 % Favored : 94.50 % Rotamer: Outliers : 3.17 % Allowed : 15.50 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.19), residues: 1964 helix: 1.80 (0.21), residues: 644 sheet: 0.05 (0.32), residues: 260 loop : -1.72 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 612 HIS 0.004 0.001 HIS B 493 PHE 0.014 0.001 PHE B 254 TYR 0.023 0.001 TYR B 277 ARG 0.006 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04588 ( 581) hydrogen bonds : angle 4.19369 ( 1722) metal coordination : bond 0.00341 ( 16) metal coordination : angle 2.64910 ( 21) covalent geometry : bond 0.00288 (17203) covalent geometry : angle 0.58024 (23374) *********************** 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 202 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 147 time to evaluate : 1.936 Fit side-chains revert: symmetry clash REVERT: B 109 ASN cc_start: 0.6712 (m-40) cc_final: 0.6491 (m-40) REVERT: B 527 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6742 (mm-30) REVERT: B 618 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7026 (ttmm) REVERT: B 686 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: A 6 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.8019 (ppp) REVERT: A 147 LYS cc_start: 0.8148 (ttmt) cc_final: 0.7613 (ttpp) REVERT: A 271 ASP cc_start: 0.7257 (m-30) cc_final: 0.6741 (m-30) REVERT: A 286 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: A 288 ASP cc_start: 0.7867 (t0) cc_final: 0.7539 (t0) REVERT: A 808 TYR cc_start: 0.7625 (m-80) cc_final: 0.7283 (t80) REVERT: A 913 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7054 (mp10) REVERT: A 932 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7196 (tmtt) REVERT: A 1499 GLU cc_start: 0.8124 (tt0) cc_final: 0.7916 (tt0) REVERT: A 1580 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.6838 (mptt) REVERT: A 1682 THR cc_start: 0.8850 (t) cc_final: 0.8285 (m) REVERT: A 1685 TRP cc_start: 0.6630 (OUTLIER) cc_final: 0.4706 (m100) outliers start: 55 outliers final: 26 residues processed: 183 average time/residue: 1.5136 time to fit residues: 306.1308 Evaluate side-chains 171 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 2.000 ------------------------------------------------------------------------------- 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 6 MET Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 286 GLN 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 529 TYR 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 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 918 LYS 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 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 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 22 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 190 optimal weight: 0.2980 chunk 105 optimal weight: 0.0270 chunk 124 optimal weight: 3.9990 chunk 175 optimal weight: 0.0050 chunk 60 optimal weight: 0.0170 chunk 96 optimal weight: 2.9990 overall best weight: 0.4692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 514 HIS B 592 ASN A 328 HIS A1617 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.160336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.124823 restraints weight = 19332.407| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.49 r_work: 0.3149 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1275 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= 0.110 Angle : 0.553 8.400 23395 Z= 0.290 Chirality : 0.041 0.238 2523 Planarity : 0.004 0.060 2881 Dihedral : 15.405 176.852 2722 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.60 % Favored : 94.20 % Rotamer: Outliers : 2.36 % Allowed : 16.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.19), residues: 1964 helix: 1.95 (0.21), residues: 651 sheet: 0.17 (0.33), residues: 256 loop : -1.63 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 278 HIS 0.006 0.001 HIS A1547 PHE 0.015 0.001 PHE B 254 TYR 0.025 0.001 TYR B 277 ARG 0.008 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 581) hydrogen bonds : angle 4.03594 ( 1722) metal coordination : bond 0.00265 ( 16) metal coordination : angle 2.18354 ( 21) covalent geometry : bond 0.00231 (17203) covalent geometry : angle 0.54902 (23374) *********************** 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 189 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 1.955 Fit side-chains revert: symmetry clash REVERT: B 109 ASN cc_start: 0.6818 (m-40) cc_final: 0.6573 (m-40) REVERT: B 686 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: A 124 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: A 147 LYS cc_start: 0.8095 (ttmt) cc_final: 0.7559 (ttpp) REVERT: A 271 ASP cc_start: 0.7243 (m-30) cc_final: 0.6733 (m-30) REVERT: A 286 GLN cc_start: 0.7931 (tp40) cc_final: 0.7523 (tt0) REVERT: A 288 ASP cc_start: 0.7822 (t0) cc_final: 0.7507 (t0) REVERT: A 808 TYR cc_start: 0.7548 (m-80) cc_final: 0.7280 (t80) REVERT: A 913 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7093 (mp10) REVERT: A 932 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7202 (tmtt) REVERT: A 1499 GLU cc_start: 0.8115 (tt0) cc_final: 0.7904 (tt0) REVERT: A 1580 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.6813 (mptt) REVERT: A 1682 THR cc_start: 0.8527 (t) cc_final: 0.7949 (m) REVERT: A 1685 TRP cc_start: 0.6299 (OUTLIER) cc_final: 0.4451 (m100) outliers start: 41 outliers final: 22 residues processed: 177 average time/residue: 1.4255 time to fit residues: 280.0612 Evaluate side-chains 168 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.908 ------------------------------------------------------------------------------- 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 682 TYR Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 124 GLU 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 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 918 LYS 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 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 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 25 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 150 optimal weight: 0.6980 chunk 128 optimal weight: 0.4980 chunk 116 optimal weight: 0.0570 chunk 107 optimal weight: 0.3980 chunk 179 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 589 ASN ** 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 = 0.3875 r_free = 0.3875 target = 0.160591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.124772 restraints weight = 19349.122| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.53 r_work: 0.3175 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 17219 Z= 0.108 Angle : 0.549 8.197 23395 Z= 0.287 Chirality : 0.041 0.249 2523 Planarity : 0.004 0.059 2881 Dihedral : 15.344 178.072 2722 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.35 % Favored : 94.50 % Rotamer: Outliers : 2.36 % Allowed : 17.34 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.19), residues: 1964 helix: 2.08 (0.21), residues: 651 sheet: 0.35 (0.33), residues: 250 loop : -1.57 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 612 HIS 0.004 0.001 HIS B 493 PHE 0.014 0.001 PHE B 491 TYR 0.021 0.001 TYR B 277 ARG 0.008 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 581) hydrogen bonds : angle 3.94234 ( 1722) metal coordination : bond 0.00222 ( 16) metal coordination : angle 2.03237 ( 21) covalent geometry : bond 0.00231 (17203) covalent geometry : angle 0.54545 (23374) *********************** 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 191 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: B 109 ASN cc_start: 0.6821 (m-40) cc_final: 0.6577 (m-40) REVERT: B 618 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.6909 (ttmm) REVERT: B 686 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: A 124 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: A 147 LYS cc_start: 0.8052 (ttmt) cc_final: 0.7529 (ttpp) REVERT: A 271 ASP cc_start: 0.7250 (m-30) cc_final: 0.6754 (m-30) REVERT: A 286 GLN cc_start: 0.7925 (tp40) cc_final: 0.7481 (tt0) REVERT: A 288 ASP cc_start: 0.7804 (t0) cc_final: 0.7539 (t0) REVERT: A 808 TYR cc_start: 0.7585 (m-80) cc_final: 0.7265 (t80) REVERT: A 913 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7148 (mp10) REVERT: A 932 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7250 (tmtt) REVERT: A 1499 GLU cc_start: 0.8147 (tt0) cc_final: 0.7937 (tt0) REVERT: A 1580 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.6915 (mptt) REVERT: A 1685 TRP cc_start: 0.6239 (OUTLIER) cc_final: 0.4331 (m100) outliers start: 41 outliers final: 23 residues processed: 181 average time/residue: 1.4443 time to fit residues: 289.7717 Evaluate side-chains 173 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ILE 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 94 THR Chi-restraints excluded: chain A residue 124 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 640 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 849 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 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 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 112 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 182 optimal weight: 0.0970 chunk 46 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3873 r_free = 0.3873 target = 0.160295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.124614 restraints weight = 19358.244| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.52 r_work: 0.3146 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1348 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= 0.119 Angle : 0.572 9.865 23395 Z= 0.298 Chirality : 0.042 0.271 2523 Planarity : 0.004 0.059 2881 Dihedral : 15.349 177.863 2722 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.70 % Favored : 94.14 % Rotamer: Outliers : 2.30 % Allowed : 17.34 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.19), residues: 1964 helix: 2.12 (0.21), residues: 646 sheet: 0.35 (0.33), residues: 250 loop : -1.57 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1685 HIS 0.005 0.001 HIS B 493 PHE 0.016 0.001 PHE B 254 TYR 0.023 0.001 TYR B 277 ARG 0.009 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 581) hydrogen bonds : angle 3.96287 ( 1722) metal coordination : bond 0.00254 ( 16) metal coordination : angle 2.12200 ( 21) covalent geometry : bond 0.00265 (17203) covalent geometry : angle 0.56913 (23374) *********************** 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 185 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 1.847 Fit side-chains revert: symmetry clash REVERT: B 109 ASN cc_start: 0.6820 (m-40) cc_final: 0.6557 (m-40) REVERT: B 686 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: A 147 LYS cc_start: 0.8026 (ttmt) cc_final: 0.7494 (ttpp) REVERT: A 240 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8122 (mp) REVERT: A 271 ASP cc_start: 0.7250 (m-30) cc_final: 0.6744 (m-30) REVERT: A 286 GLN cc_start: 0.7925 (tp40) cc_final: 0.7479 (tt0) REVERT: A 808 TYR cc_start: 0.7633 (m-80) cc_final: 0.7266 (t80) REVERT: A 913 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7114 (mp10) REVERT: A 932 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7166 (tmtt) REVERT: A 1499 GLU cc_start: 0.8149 (tt0) cc_final: 0.7930 (tt0) REVERT: A 1580 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6923 (mptt) REVERT: A 1664 LYS cc_start: 0.8497 (mttt) cc_final: 0.8055 (pttt) REVERT: A 1685 TRP cc_start: 0.6094 (OUTLIER) cc_final: 0.4244 (m100) outliers start: 40 outliers final: 28 residues processed: 175 average time/residue: 1.3744 time to fit residues: 268.1783 Evaluate side-chains 174 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 161 ASP 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 682 TYR Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 240 ILE 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 640 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 849 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 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 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 22 optimal weight: 0.7980 chunk 193 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 155 optimal weight: 0.0010 chunk 138 optimal weight: 0.0470 overall best weight: 0.5686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3865 r_free = 0.3865 target = 0.159711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.123776 restraints weight = 19380.065| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.60 r_work: 0.3160 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17219 Z= 0.130 Angle : 0.755 59.180 23395 Z= 0.431 Chirality : 0.042 0.359 2523 Planarity : 0.004 0.059 2881 Dihedral : 15.350 177.865 2722 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.65 % Favored : 94.20 % Rotamer: Outliers : 2.19 % Allowed : 17.57 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.19), residues: 1964 helix: 2.13 (0.21), residues: 646 sheet: 0.35 (0.33), residues: 250 loop : -1.57 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1685 HIS 0.005 0.001 HIS B 493 PHE 0.015 0.001 PHE B 254 TYR 0.022 0.001 TYR B 277 ARG 0.008 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 581) hydrogen bonds : angle 3.96329 ( 1722) metal coordination : bond 0.00241 ( 16) metal coordination : angle 2.12202 ( 21) covalent geometry : bond 0.00273 (17203) covalent geometry : angle 0.75289 (23374) ********************** 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 178 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 2.077 Fit side-chains revert: symmetry clash REVERT: B 109 ASN cc_start: 0.6830 (m-40) cc_final: 0.6568 (m-40) REVERT: B 686 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6689 (mp0) REVERT: A 124 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: A 147 LYS cc_start: 0.8038 (ttmt) cc_final: 0.7521 (ttpp) REVERT: A 240 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8127 (mp) REVERT: A 271 ASP cc_start: 0.7257 (m-30) cc_final: 0.6771 (m-30) REVERT: A 286 GLN cc_start: 0.7940 (tp40) cc_final: 0.7500 (tt0) REVERT: A 808 TYR cc_start: 0.7648 (m-80) cc_final: 0.7291 (t80) REVERT: A 913 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7134 (mp10) REVERT: A 932 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7181 (tmtt) REVERT: A 1499 GLU cc_start: 0.8147 (tt0) cc_final: 0.7932 (tt0) REVERT: A 1580 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.6966 (mptt) REVERT: A 1685 TRP cc_start: 0.6133 (OUTLIER) cc_final: 0.4285 (m100) outliers start: 38 outliers final: 28 residues processed: 168 average time/residue: 1.4327 time to fit residues: 267.4912 Evaluate side-chains 175 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 161 ASP 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 682 TYR Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 240 ILE 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 640 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 849 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 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 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 102 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS ** A1544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.160268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124327 restraints weight = 19276.820| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.51 r_work: 0.3166 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17219 Z= 0.130 Angle : 0.755 59.180 23395 Z= 0.431 Chirality : 0.042 0.359 2523 Planarity : 0.004 0.059 2881 Dihedral : 15.350 177.865 2722 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.65 % Favored : 94.20 % Rotamer: Outliers : 2.07 % Allowed : 17.68 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.19), residues: 1964 helix: 2.13 (0.21), residues: 646 sheet: 0.35 (0.33), residues: 250 loop : -1.57 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1685 HIS 0.005 0.001 HIS B 493 PHE 0.015 0.001 PHE B 254 TYR 0.022 0.001 TYR B 277 ARG 0.008 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 581) hydrogen bonds : angle 3.96329 ( 1722) metal coordination : bond 0.00241 ( 16) metal coordination : angle 2.12202 ( 21) covalent geometry : bond 0.00273 (17203) covalent geometry : angle 0.75289 (23374) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10435.07 seconds wall clock time: 179 minutes 4.88 seconds (10744.88 seconds total)