Starting phenix.real_space_refine on Sun Mar 17 05:07:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y8t_33685/03_2024/7y8t_33685.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y8t_33685/03_2024/7y8t_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y8t_33685/03_2024/7y8t_33685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y8t_33685/03_2024/7y8t_33685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y8t_33685/03_2024/7y8t_33685.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y8t_33685/03_2024/7y8t_33685.pdb" } 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 Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B GLU 344": "OE1" <-> "OE2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "B GLU 456": "OE1" <-> "OE2" Residue "B GLU 674": "OE1" <-> "OE2" Residue "B GLU 678": "OE1" <-> "OE2" Residue "B GLU 681": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "A GLU 11": "OE1" <-> "OE2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A GLU 784": "OE1" <-> "OE2" Residue "A PHE 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 943": "OE1" <-> "OE2" Residue "A GLU 944": "OE1" <-> "OE2" Residue "A GLU 972": "OE1" <-> "OE2" Residue "A GLU 1437": "OE1" <-> "OE2" Residue "A GLU 1451": "OE1" <-> "OE2" Residue "A GLU 1496": "OE1" <-> "OE2" Residue "A GLU 1499": "OE1" <-> "OE2" Residue "A GLU 1525": "OE1" <-> "OE2" Residue "A GLU 1589": "OE1" <-> "OE2" Residue "A GLU 1600": "OE1" <-> "OE2" Residue "A PHE 1633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1640": "OE1" <-> "OE2" Residue "A GLU 1650": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.64, 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 - 3.50 Amino acid : False - 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: 5.96 Conformation dependent library (CDL) restraints added in 2.8 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: 5.61 Creating SS restraints... Processing helix chain 'B' and resid 14 through 32 Processing helix chain 'B' and resid 37 through 59 removed outlier: 3.789A pdb=" N LYS B 42 " --> pdb=" O PRO B 38 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS B 43 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 81 removed outlier: 3.774A pdb=" N PHE B 68 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 80 " --> pdb=" O TYR B 76 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 110 removed outlier: 4.069A pdb=" N LYS B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 107 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 136 Processing helix chain 'B' and resid 141 through 155 Processing helix chain 'B' and resid 164 through 177 Processing helix chain 'B' and resid 183 through 190 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 209 through 223 removed outlier: 3.617A pdb=" N LYS B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 230 through 246 removed outlier: 4.261A pdb=" N ASP B 234 " --> pdb=" O HIS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 removed outlier: 4.362A pdb=" N ILE B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS B 267 " --> pdb=" O ARG B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 297 Processing helix chain 'B' and resid 303 through 321 Processing helix chain 'B' and resid 327 through 333 removed outlier: 3.664A pdb=" N LYS B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 359 removed outlier: 3.572A pdb=" N HIS B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE B 345 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LYS B 346 " --> pdb=" O ASN B 342 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 448 Processing helix chain 'B' and resid 454 through 469 removed outlier: 4.006A pdb=" N LEU B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR B 460 " --> pdb=" O GLU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 474 removed outlier: 3.570A pdb=" N CYS B 474 " --> pdb=" O PHE B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 495 removed outlier: 3.760A pdb=" N ARG B 494 " --> pdb=" O PHE B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 removed outlier: 3.792A pdb=" N SER B 500 " --> pdb=" O LEU B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 513 removed outlier: 3.605A pdb=" N ASN B 513 " --> pdb=" O PHE B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 566 through 571 removed outlier: 3.822A pdb=" N LEU B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU B 571 " --> pdb=" O SER B 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 566 through 571' Processing helix chain 'B' and resid 592 through 595 Processing helix chain 'B' and resid 607 through 614 removed outlier: 3.514A pdb=" N LEU B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 631 Processing helix chain 'B' and resid 644 through 651 removed outlier: 3.876A pdb=" N ALA B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 679 removed outlier: 3.873A pdb=" N THR B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN B 679 " --> pdb=" O TRP B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 691 removed outlier: 3.793A pdb=" N TRP B 687 " --> pdb=" O LYS B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.636A pdb=" N PHE B 703 " --> pdb=" O HIS B 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 31 removed outlier: 3.592A pdb=" N LYS A 30 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 59 through 77 removed outlier: 3.920A pdb=" N VAL A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 216 through 226 removed outlier: 3.571A pdb=" N ALA A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 287 removed outlier: 3.901A pdb=" N ASN A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 291 removed outlier: 6.410A pdb=" N GLU A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 288 through 291' Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 303 through 307 removed outlier: 4.664A pdb=" N GLY A 307 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.658A pdb=" N SER A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 488 removed outlier: 3.562A pdb=" N LEU A 475 " --> pdb=" O PRO A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 removed outlier: 3.710A pdb=" N GLU A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 579 removed outlier: 3.736A pdb=" N SER A 573 " --> pdb=" O PRO A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 625 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 630 through 636 removed outlier: 3.643A pdb=" N GLU A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 removed outlier: 3.934A pdb=" N LEU A 642 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 667 No H-bonds generated for 'chain 'A' and resid 665 through 667' Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 723 through 740 removed outlier: 3.624A pdb=" N PHE A 731 " --> pdb=" O HIS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 744 Processing helix chain 'A' and resid 752 through 759 Processing helix chain 'A' and resid 776 through 780 removed outlier: 3.544A pdb=" N GLU A 779 " --> pdb=" O ASN A 776 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 780 " --> pdb=" O GLY A 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 776 through 780' Processing helix chain 'A' and resid 833 through 847 Processing helix chain 'A' and resid 855 through 859 removed outlier: 3.683A pdb=" N GLY A 859 " --> pdb=" O GLY A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 883 Processing helix chain 'A' and resid 908 through 914 removed outlier: 3.930A pdb=" N LYS A 912 " --> pdb=" O HIS A 908 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1016 removed outlier: 3.880A pdb=" N LEU A1003 " --> pdb=" O PRO A 999 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1399 removed outlier: 3.524A pdb=" N LEU A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1404 removed outlier: 3.514A pdb=" N HIS A1404 " --> pdb=" O LYS A1401 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1421 Processing helix chain 'A' and resid 1486 through 1494 removed outlier: 4.050A pdb=" N ILE A1490 " --> pdb=" O GLY A1486 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN A1492 " --> pdb=" O ARG A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1540 removed outlier: 3.512A pdb=" N ASP A1540 " --> pdb=" O LEU A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1556 Processing helix chain 'A' and resid 1583 through 1602 removed outlier: 4.063A pdb=" N GLU A1589 " --> pdb=" O SER A1585 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1618 Processing helix chain 'A' and resid 1619 through 1629 removed outlier: 3.512A pdb=" N LYS A1627 " --> pdb=" O ASP A1623 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A1628 " --> pdb=" O LYS A1624 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A1629 " --> pdb=" O LEU A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1673 through 1682 Processing sheet with id=AA1, first strand: chain 'B' and resid 425 through 431 removed outlier: 3.521A pdb=" N SER B 425 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 431 " --> pdb=" O GLY B 414 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 401 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL B 487 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 403 " --> pdb=" O VAL B 487 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 536 through 540 removed outlier: 6.569A pdb=" N LEU B 580 " --> pdb=" O ILE B 623 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THR B 660 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 659 " --> pdb=" O ARG B 710 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 585 through 587 removed outlier: 4.247A pdb=" N HIS B 585 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 605 " --> pdb=" O LEU B 598 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.596A pdb=" N LEU A 211 " --> pdb=" O MET A 6 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET A 6 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 20 through 22 removed outlier: 4.394A pdb=" N LEU A 167 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA8, first strand: chain 'A' and resid 110 through 111 removed outlier: 5.937A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 173 through 181 removed outlier: 4.859A pdb=" N ARG A 180 " --> pdb=" O ASP A 190 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASP A 190 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.691A pdb=" N GLY A 565 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 417 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG A 421 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP A 606 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS A 423 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU A 604 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 589 " --> pdb=" O PHE A 602 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.691A pdb=" N GLY A 565 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 417 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG A 421 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP A 606 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS A 423 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU A 604 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.505A pdb=" N SER A 517 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 526 through 530 removed outlier: 3.537A pdb=" N GLU A 526 " --> pdb=" O VAL A 550 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 703 through 704 removed outlier: 6.202A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 703 through 704 removed outlier: 6.202A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLN A 673 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE A 868 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR A 675 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE A 866 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU A 677 " --> pdb=" O ALA A 864 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB9, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AC1, first strand: chain 'A' and resid 991 through 992 removed outlier: 6.811A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL A1517 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS A 956 " --> pdb=" O PHE A1520 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A1524 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 3.555A pdb=" N CYS A 956 " --> pdb=" O PHE A1520 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A1524 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS A1571 " --> pdb=" O LYS A1578 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LYS A1578 " --> pdb=" O LYS A1571 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1453 through 1455 removed outlier: 3.634A pdb=" N THR A1509 " --> pdb=" O LEU A1454 " (cutoff:3.500A) 613 hydrogen bonds defined for protein. 1722 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 6.64 Time building geometry restraints manager: 6.48 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: 99.90 - 106.72: 660 106.72 - 113.54: 9188 113.54 - 120.37: 6546 120.37 - 127.19: 6716 127.19 - 134.01: 264 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 2.520 nonbonded pdb=" NH1 ARG A 737 " pdb=" O HIS A 942 " model vdw 2.231 2.520 nonbonded pdb=" N GLU A 948 " pdb=" OE1 GLU A 948 " model vdw 2.237 2.520 nonbonded pdb=" N GLU A1529 " pdb=" OE1 GLU A1529 " model vdw 2.239 2.520 nonbonded pdb=" OG SER B 65 " pdb=" ND2 ASN B 112 " model vdw 2.248 2.520 ... (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 ========== 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 14.370 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 52.420 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.210 ------------------------------------------------------------------------------- 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 17203 Z= 0.278 Angle : 0.632 8.987 23374 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 *********************** 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 fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 1.537 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: 1.4629 time to fit residues: 261.6664 Evaluate side-chains 156 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.958 ------------------------------------------------------------------------------- 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: 0.9990 chunk 151 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 51 optimal weight: 0.0870 chunk 102 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 181 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN A 328 HIS ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 17203 Z= 0.158 Angle : 0.544 8.366 23374 Z= 0.289 Chirality : 0.041 0.210 2523 Planarity : 0.004 0.065 2881 Dihedral : 15.597 178.529 2752 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.70 % Favored : 94.09 % Rotamer: Outliers : 2.48 % Allowed : 13.88 % Favored : 83.64 % 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: -0.33 (0.19), residues: 1964 helix: 1.94 (0.21), residues: 633 sheet: 0.07 (0.33), residues: 250 loop : -1.73 (0.17), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1685 HIS 0.005 0.001 HIS B 493 PHE 0.013 0.001 PHE B 703 TYR 0.013 0.001 TYR B 704 ARG 0.005 0.000 ARG A 382 *********************** 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 191 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 148 time to evaluate : 1.940 Fit side-chains revert: symmetry clash REVERT: A 6 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7454 (ppp) REVERT: A 240 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8076 (mp) REVERT: A 271 ASP cc_start: 0.7115 (m-30) cc_final: 0.6775 (m-30) REVERT: A 286 GLN cc_start: 0.7936 (tp40) cc_final: 0.7540 (tt0) REVERT: A 697 ARG cc_start: 0.7770 (mtm180) cc_final: 0.7552 (mtm180) REVERT: A 980 ASN cc_start: 0.6629 (OUTLIER) cc_final: 0.6424 (m110) REVERT: A 1493 LYS cc_start: 0.7556 (mmtt) cc_final: 0.7195 (tppt) REVERT: A 1580 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7325 (mptt) REVERT: A 1685 TRP cc_start: 0.6074 (OUTLIER) cc_final: 0.4291 (m100) outliers start: 43 outliers final: 15 residues processed: 178 average time/residue: 1.4777 time to fit residues: 290.9569 Evaluate side-chains 160 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain A residue 6 MET 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 500 LEU 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 980 ASN Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1544 ASN Chi-restraints excluded: chain A residue 1580 LYS Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1685 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 162 optimal weight: 0.2980 chunk 180 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 145 optimal weight: 0.1980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN B 592 ASN A 328 HIS A 712 ASN ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17203 Z= 0.192 Angle : 0.566 8.150 23374 Z= 0.298 Chirality : 0.042 0.214 2523 Planarity : 0.004 0.062 2881 Dihedral : 15.429 177.403 2725 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.01 % Favored : 93.79 % Rotamer: Outliers : 3.51 % Allowed : 13.59 % Favored : 82.89 % 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: -0.34 (0.19), residues: 1964 helix: 1.91 (0.21), residues: 639 sheet: 0.01 (0.33), residues: 256 loop : -1.74 (0.17), residues: 1069 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 0.002 PHE B 703 TYR 0.024 0.001 TYR B 277 ARG 0.005 0.000 ARG B 137 *********************** 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 208 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 147 time to evaluate : 2.042 Fit side-chains revert: symmetry clash REVERT: B 618 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7211 (ttmm) REVERT: B 686 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6640 (mp0) REVERT: A 6 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7310 (ppp) REVERT: A 240 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8173 (mp) REVERT: A 271 ASP cc_start: 0.7102 (m-30) cc_final: 0.6704 (m-30) REVERT: A 286 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: A 288 ASP cc_start: 0.7716 (t0) cc_final: 0.7494 (t0) REVERT: A 808 TYR cc_start: 0.7555 (m-80) cc_final: 0.7249 (t80) REVERT: A 913 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7257 (mp10) REVERT: A 1407 THR cc_start: 0.8810 (t) cc_final: 0.8522 (t) REVERT: A 1580 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7335 (mptt) REVERT: A 1685 TRP cc_start: 0.6260 (OUTLIER) cc_final: 0.4577 (m100) outliers start: 61 outliers final: 23 residues processed: 184 average time/residue: 1.4667 time to fit residues: 298.1169 Evaluate side-chains 172 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 569 ASP 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 517 SER 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 698 ASP Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 900 ASN 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 1490 ILE Chi-restraints excluded: chain A residue 1544 ASN Chi-restraints excluded: chain A residue 1580 LYS Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1685 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 122 optimal weight: 0.1980 chunk 182 optimal weight: 3.9990 chunk 193 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN B 592 ASN A 328 HIS ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17203 Z= 0.169 Angle : 0.547 8.166 23374 Z= 0.288 Chirality : 0.041 0.212 2523 Planarity : 0.004 0.061 2881 Dihedral : 15.382 177.446 2724 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.91 % Favored : 93.89 % Rotamer: Outliers : 3.23 % Allowed : 14.63 % Favored : 82.14 % 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: -0.24 (0.19), residues: 1964 helix: 1.95 (0.21), residues: 644 sheet: 0.08 (0.33), residues: 256 loop : -1.67 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 612 HIS 0.005 0.001 HIS B 493 PHE 0.014 0.001 PHE B 703 TYR 0.022 0.001 TYR B 277 ARG 0.005 0.000 ARG B 137 *********************** 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 204 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 148 time to evaluate : 1.936 Fit side-chains revert: symmetry clash REVERT: B 618 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7203 (ttmm) REVERT: B 686 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: A 6 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7301 (ppp) REVERT: A 125 GLU cc_start: 0.7448 (pp20) cc_final: 0.7208 (mt-10) REVERT: A 271 ASP cc_start: 0.7111 (m-30) cc_final: 0.6675 (m-30) REVERT: A 286 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: A 288 ASP cc_start: 0.7757 (t0) cc_final: 0.7539 (t0) REVERT: A 808 TYR cc_start: 0.7625 (m-80) cc_final: 0.7300 (t80) REVERT: A 913 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7181 (mp10) REVERT: A 1407 THR cc_start: 0.8763 (t) cc_final: 0.8455 (t) REVERT: A 1580 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7168 (mptt) REVERT: A 1636 ASP cc_start: 0.5496 (OUTLIER) cc_final: 0.5158 (p0) REVERT: A 1685 TRP cc_start: 0.6205 (OUTLIER) cc_final: 0.4531 (m100) outliers start: 56 outliers final: 28 residues processed: 184 average time/residue: 1.3857 time to fit residues: 282.8544 Evaluate side-chains 178 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 569 ASP 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 500 LEU Chi-restraints excluded: chain A residue 517 SER 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 698 ASP Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 900 ASN 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 1544 ASN Chi-restraints excluded: chain A residue 1580 LYS Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1636 ASP 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 161 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 173 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN B 592 ASN A 328 HIS ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17203 Z= 0.257 Angle : 0.622 8.327 23374 Z= 0.326 Chirality : 0.044 0.220 2523 Planarity : 0.005 0.063 2881 Dihedral : 15.514 179.213 2724 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.62 % Favored : 93.13 % Rotamer: Outliers : 4.09 % Allowed : 14.57 % 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: -0.39 (0.19), residues: 1964 helix: 1.74 (0.21), residues: 650 sheet: 0.07 (0.32), residues: 260 loop : -1.74 (0.17), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1685 HIS 0.006 0.001 HIS B 493 PHE 0.019 0.002 PHE B 703 TYR 0.027 0.002 TYR B 277 ARG 0.006 0.000 ARG B 137 *********************** 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 218 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 147 time to evaluate : 1.988 Fit side-chains revert: symmetry clash REVERT: B 618 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7308 (ttmm) REVERT: B 686 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: A 6 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7343 (ppp) REVERT: A 125 GLU cc_start: 0.7568 (pp20) cc_final: 0.7312 (mt-10) REVERT: A 144 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: A 147 LYS cc_start: 0.8123 (ttmt) cc_final: 0.7576 (ttpp) REVERT: A 271 ASP cc_start: 0.7129 (m-30) cc_final: 0.6662 (m-30) REVERT: A 286 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: A 808 TYR cc_start: 0.7642 (m-80) cc_final: 0.7348 (t80) REVERT: A 913 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7199 (mp10) REVERT: A 1407 THR cc_start: 0.8785 (t) cc_final: 0.8471 (t) REVERT: A 1580 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7125 (mptt) REVERT: A 1636 ASP cc_start: 0.5572 (OUTLIER) cc_final: 0.5233 (p0) REVERT: A 1685 TRP cc_start: 0.6555 (OUTLIER) cc_final: 0.4855 (m100) outliers start: 71 outliers final: 34 residues processed: 194 average time/residue: 1.4068 time to fit residues: 302.4143 Evaluate side-chains 185 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 142 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 569 ASP 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 7 ASN Chi-restraints excluded: chain A residue 52 THR 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 286 GLN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 517 SER 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 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 986 ASN 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 1618 VAL Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1636 ASP Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1682 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 65 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 193 optimal weight: 0.3980 chunk 160 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 HIS B 432 GLN A 328 HIS ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17203 Z= 0.214 Angle : 0.589 8.226 23374 Z= 0.310 Chirality : 0.043 0.219 2523 Planarity : 0.005 0.063 2881 Dihedral : 15.478 178.744 2724 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.01 % Favored : 93.74 % Rotamer: Outliers : 3.92 % Allowed : 15.44 % Favored : 80.65 % 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: -0.34 (0.19), residues: 1964 helix: 1.84 (0.21), residues: 644 sheet: 0.09 (0.32), residues: 260 loop : -1.73 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 612 HIS 0.005 0.001 HIS B 493 PHE 0.017 0.002 PHE B 703 TYR 0.027 0.001 TYR B 277 ARG 0.006 0.000 ARG B 137 *********************** 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 213 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 145 time to evaluate : 1.835 Fit side-chains revert: symmetry clash REVERT: B 392 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: B 618 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7297 (ttmm) REVERT: B 686 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6682 (mp0) REVERT: A 6 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7777 (ppp) REVERT: A 122 ASP cc_start: 0.7798 (p0) cc_final: 0.7078 (p0) REVERT: A 124 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: A 144 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: A 147 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7765 (ttpp) REVERT: A 271 ASP cc_start: 0.7137 (m-30) cc_final: 0.6660 (m-30) REVERT: A 286 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7620 (tt0) REVERT: A 288 ASP cc_start: 0.7815 (t0) cc_final: 0.7578 (t0) REVERT: A 808 TYR cc_start: 0.7664 (m-80) cc_final: 0.7383 (t80) REVERT: A 913 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7198 (mp10) REVERT: A 959 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: A 1407 THR cc_start: 0.8793 (t) cc_final: 0.8462 (t) REVERT: A 1580 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7132 (mptt) REVERT: A 1636 ASP cc_start: 0.5650 (OUTLIER) cc_final: 0.5249 (p0) REVERT: A 1685 TRP cc_start: 0.6508 (OUTLIER) cc_final: 0.4762 (m100) outliers start: 68 outliers final: 37 residues processed: 191 average time/residue: 1.3896 time to fit residues: 294.2973 Evaluate side-chains 195 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 146 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 569 ASP 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 7 ASN Chi-restraints excluded: chain A residue 52 THR 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 144 GLU Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 517 SER 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 836 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1445 THR Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1544 ASN Chi-restraints excluded: chain A residue 1580 LYS Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1636 ASP Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1682 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 186 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN A 328 HIS ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17203 Z= 0.188 Angle : 0.571 8.262 23374 Z= 0.300 Chirality : 0.042 0.251 2523 Planarity : 0.004 0.062 2881 Dihedral : 15.431 177.916 2724 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.96 % Favored : 93.84 % Rotamer: Outliers : 3.57 % Allowed : 16.07 % 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: -0.26 (0.19), residues: 1964 helix: 1.93 (0.21), residues: 643 sheet: 0.09 (0.32), residues: 261 loop : -1.69 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 612 HIS 0.005 0.001 HIS B 493 PHE 0.015 0.001 PHE B 254 TYR 0.026 0.001 TYR B 277 ARG 0.007 0.000 ARG B 137 *********************** 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 209 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 147 time to evaluate : 2.045 Fit side-chains revert: symmetry clash REVERT: B 392 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: B 618 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7212 (ttmm) REVERT: B 686 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6714 (mp0) REVERT: A 6 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7784 (ppp) REVERT: A 124 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: A 144 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7707 (mt-10) REVERT: A 147 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7574 (ttpp) REVERT: A 271 ASP cc_start: 0.7118 (m-30) cc_final: 0.6638 (m-30) REVERT: A 286 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7601 (tt0) REVERT: A 288 ASP cc_start: 0.7857 (t0) cc_final: 0.7656 (t0) REVERT: A 808 TYR cc_start: 0.7638 (m-80) cc_final: 0.7384 (t80) REVERT: A 913 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7260 (mp10) REVERT: A 1407 THR cc_start: 0.8777 (t) cc_final: 0.8454 (t) REVERT: A 1580 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7242 (mptt) REVERT: A 1685 TRP cc_start: 0.6544 (OUTLIER) cc_final: 0.4781 (m100) outliers start: 62 outliers final: 37 residues processed: 188 average time/residue: 1.4194 time to fit residues: 294.8019 Evaluate side-chains 187 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 140 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 569 ASP 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 7 ASN Chi-restraints excluded: chain A residue 52 THR 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 144 GLU Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 517 SER 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 698 ASP Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 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 1618 VAL Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1682 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 119 optimal weight: 0.7980 chunk 76 optimal weight: 0.0170 chunk 115 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 37 optimal weight: 0.0970 chunk 122 optimal weight: 0.3980 chunk 131 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 175 optimal weight: 10.0000 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN B 514 HIS ** B 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1544 ASN A1617 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 17203 Z= 0.148 Angle : 0.530 8.438 23374 Z= 0.278 Chirality : 0.041 0.250 2523 Planarity : 0.004 0.062 2881 Dihedral : 15.315 178.045 2724 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.70 % Favored : 94.09 % Rotamer: Outliers : 2.71 % Allowed : 17.28 % Favored : 80.01 % 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: -0.08 (0.19), residues: 1964 helix: 2.08 (0.21), residues: 646 sheet: 0.28 (0.33), residues: 250 loop : -1.60 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 612 HIS 0.004 0.001 HIS B 493 PHE 0.015 0.001 PHE B 491 TYR 0.021 0.001 TYR B 277 ARG 0.008 0.000 ARG B 137 *********************** 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 192 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 145 time to evaluate : 1.887 Fit side-chains revert: symmetry clash REVERT: B 392 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: B 618 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7197 (ttmm) REVERT: B 686 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6686 (mp0) REVERT: A 124 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: A 147 LYS cc_start: 0.8004 (ttmt) cc_final: 0.7504 (ttpp) REVERT: A 271 ASP cc_start: 0.7103 (m-30) cc_final: 0.6619 (m-30) REVERT: A 286 GLN cc_start: 0.7935 (tp40) cc_final: 0.7572 (tt0) REVERT: A 913 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7274 (mp10) REVERT: A 1407 THR cc_start: 0.8777 (t) cc_final: 0.8446 (t) REVERT: A 1580 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7222 (mptt) REVERT: A 1685 TRP cc_start: 0.6149 (OUTLIER) cc_final: 0.4636 (m100) outliers start: 47 outliers final: 26 residues processed: 176 average time/residue: 1.4213 time to fit residues: 277.0313 Evaluate side-chains 170 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 2.003 ------------------------------------------------------------------------------- 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 161 ASP Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 505 THR 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 7 ASN Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 318 ASP 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 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 956 CYS Chi-restraints excluded: chain A residue 986 ASN 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 1634 LEU Chi-restraints excluded: chain A residue 1682 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 184 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 108 optimal weight: 0.0970 chunk 78 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 169 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 189 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN A 328 HIS ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1544 ASN A1617 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 17203 Z= 0.163 Angle : 0.548 8.817 23374 Z= 0.287 Chirality : 0.041 0.266 2523 Planarity : 0.004 0.062 2881 Dihedral : 15.305 178.082 2723 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.21 % Favored : 93.58 % Rotamer: Outliers : 2.53 % Allowed : 17.68 % Favored : 79.78 % 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: -0.05 (0.19), residues: 1964 helix: 2.11 (0.21), residues: 647 sheet: 0.33 (0.33), residues: 250 loop : -1.59 (0.17), residues: 1067 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 0.017 0.001 PHE B 254 TYR 0.020 0.001 TYR B 277 ARG 0.009 0.000 ARG B 137 *********************** 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 186 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 142 time to evaluate : 1.817 Fit side-chains revert: symmetry clash REVERT: B 392 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7409 (mp0) REVERT: B 618 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7197 (ttmm) REVERT: B 686 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: A 124 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: A 147 LYS cc_start: 0.7987 (ttmt) cc_final: 0.7589 (ttpm) REVERT: A 271 ASP cc_start: 0.7108 (m-30) cc_final: 0.6635 (m-30) REVERT: A 286 GLN cc_start: 0.7947 (tp40) cc_final: 0.7576 (tt0) REVERT: A 697 ARG cc_start: 0.7427 (mtm180) cc_final: 0.6696 (mtt-85) REVERT: A 913 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7295 (mp10) REVERT: A 1407 THR cc_start: 0.8775 (t) cc_final: 0.8444 (t) REVERT: A 1580 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7259 (mptt) REVERT: A 1685 TRP cc_start: 0.6156 (OUTLIER) cc_final: 0.4653 (m100) outliers start: 44 outliers final: 31 residues processed: 173 average time/residue: 1.4348 time to fit residues: 275.5937 Evaluate side-chains 175 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 2.032 ------------------------------------------------------------------------------- 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 283 VAL Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 569 ASP 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 7 ASN Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 318 ASP 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 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 956 CYS Chi-restraints excluded: chain A residue 986 ASN 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 1682 THR Chi-restraints excluded: chain A residue 1685 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.2087 > 50: distance: 70 - 89: 8.393 distance: 77 - 97: 8.182 distance: 82 - 101: 10.652 distance: 85 - 89: 7.150 distance: 89 - 90: 4.112 distance: 90 - 93: 3.420 distance: 91 - 92: 6.469 distance: 91 - 97: 3.959 distance: 93 - 94: 6.614 distance: 94 - 95: 3.312 distance: 94 - 96: 4.282 distance: 97 - 98: 8.138 distance: 98 - 99: 6.013 distance: 99 - 100: 3.996 distance: 99 - 101: 4.537 distance: 101 - 102: 3.902 distance: 102 - 103: 4.696 distance: 102 - 105: 3.924 distance: 103 - 104: 3.679 distance: 103 - 112: 7.680 distance: 106 - 107: 3.447 distance: 106 - 108: 3.567 distance: 107 - 109: 4.457 distance: 108 - 110: 3.965 distance: 109 - 111: 5.462 distance: 112 - 113: 4.577 distance: 113 - 114: 4.208 distance: 113 - 116: 3.732 distance: 114 - 115: 7.302 distance: 114 - 119: 5.157 distance: 116 - 117: 9.632 distance: 116 - 118: 6.361 distance: 119 - 120: 15.393 distance: 120 - 121: 6.999 distance: 120 - 123: 19.678 distance: 121 - 122: 4.687 distance: 121 - 127: 13.317 distance: 123 - 124: 16.710 distance: 124 - 125: 19.515 distance: 124 - 126: 8.783 distance: 128 - 129: 6.489 distance: 128 - 131: 11.251 distance: 129 - 136: 7.934 distance: 131 - 132: 11.447 distance: 132 - 133: 20.817 distance: 133 - 134: 5.431 distance: 134 - 135: 11.501 distance: 136 - 137: 16.557 distance: 136 - 157: 17.171 distance: 137 - 138: 5.967 distance: 137 - 140: 3.630 distance: 138 - 139: 3.526 distance: 138 - 144: 4.939 distance: 139 - 154: 5.807 distance: 140 - 141: 5.268 distance: 141 - 142: 13.312 distance: 141 - 143: 13.088 distance: 144 - 145: 21.754 distance: 145 - 146: 22.366 distance: 145 - 148: 18.619 distance: 146 - 147: 8.354 distance: 146 - 150: 22.223 distance: 148 - 149: 20.601 distance: 150 - 151: 10.490 distance: 151 - 152: 12.102 distance: 152 - 153: 11.207 distance: 152 - 154: 7.566 distance: 154 - 155: 5.637 distance: 155 - 156: 6.440 distance: 155 - 158: 10.268 distance: 156 - 157: 5.922