Starting phenix.real_space_refine on Fri Sep 27 23:14:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9g_27261/09_2024/8d9g_27261.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9g_27261/09_2024/8d9g_27261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9g_27261/09_2024/8d9g_27261.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9g_27261/09_2024/8d9g_27261.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9g_27261/09_2024/8d9g_27261.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9g_27261/09_2024/8d9g_27261.cif" } resolution = 2.57 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= 0.055 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 59 5.49 5 S 57 5.16 5 C 10676 2.51 5 N 2981 2.21 5 O 3371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17148 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5516 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 658} Chain breaks: 1 Chain: "B" Number of atoms: 10373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1286, 10373 Classifications: {'peptide': 1286} Link IDs: {'PTRANS': 59, 'TRANS': 1226} Chain breaks: 3 Chain: "C" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 757 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 10, 'rna3p_pur': 5, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 15} Chain: "D" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 498 Classifications: {'RNA': 23} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 13, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 19} Chain: "B" 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 6184 SG CYS B 83 55.509 70.014 21.893 1.00 70.17 S ATOM 6455 SG CYS B 116 56.901 72.883 21.151 1.00 87.17 S ATOM 6501 SG CYS B 122 54.473 74.020 23.376 1.00 69.96 S ATOM 6525 SG CYS B 125 58.265 71.375 24.386 1.00 57.55 S ATOM 9248 SG CYS B 486 47.866 48.591 48.967 1.00 45.05 S ATOM 9316 SG CYS B 496 48.333 49.220 45.654 1.00 40.89 S ATOM 9330 SG CYS B 498 44.875 48.538 47.463 1.00 42.52 S ATOM 9352 SG CYS B 501 48.213 52.200 48.185 1.00 37.30 S ATOM 11336 SG CYS B 747 48.333 32.100 75.440 1.00 55.21 S ATOM 13333 SG CYS B1013 59.273 32.549 110.818 1.00 65.16 S ATOM 13543 SG CYS B1401 59.920 30.605 107.976 1.00 68.33 S ATOM 13594 SG CYS B1409 56.903 30.269 109.626 1.00 59.43 S ATOM 13611 SG CYS B1412 57.239 33.708 108.067 1.00 55.42 S Time building chain proxies: 9.44, per 1000 atoms: 0.55 Number of scatterers: 17148 At special positions: 0 Unit cell: (105.93, 100.58, 162.64, 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 57 16.00 P 59 15.00 O 3371 8.00 N 2981 7.00 C 10676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.02 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1701 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 125 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 116 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 83 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 122 " pdb=" ZN B1702 " pdb="ZN ZN B1702 " - pdb=" SG CYS B 501 " pdb="ZN ZN B1702 " - pdb=" SG CYS B 496 " pdb="ZN ZN B1702 " - pdb=" SG CYS B 486 " pdb="ZN ZN B1702 " - pdb=" SG CYS B 498 " pdb=" ZN B1703 " pdb="ZN ZN B1703 " - pdb=" ND1 HIS B 742 " pdb="ZN ZN B1703 " - pdb=" SG CYS B 747 " pdb=" ZN B1704 " pdb="ZN ZN B1704 " - pdb=" SG CYS B1409 " pdb="ZN ZN B1704 " - pdb=" SG CYS B1401 " pdb="ZN ZN B1704 " - pdb=" SG CYS B1013 " pdb="ZN ZN B1704 " - pdb=" SG CYS B1412 " Number of angles added : 18 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3644 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 22 sheets defined 40.5% alpha, 18.5% beta 14 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 6.59 Creating SS restraints... Processing helix chain 'A' and resid 15 through 33 Processing helix chain 'A' and resid 39 through 59 removed outlier: 4.292A pdb=" N LYS A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 81 removed outlier: 3.700A pdb=" N THR A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.701A pdb=" N LYS A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 136 Processing helix chain 'A' and resid 141 through 155 removed outlier: 3.514A pdb=" N LEU A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 Processing helix chain 'A' and resid 180 through 190 removed outlier: 4.539A pdb=" N ASP A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ASN A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 208 through 223 Processing helix chain 'A' and resid 230 through 247 removed outlier: 4.337A pdb=" N ASP A 234 " --> pdb=" O HIS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 297 removed outlier: 3.559A pdb=" N ASP A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 339 through 357 removed outlier: 3.965A pdb=" N HIS A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 450 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 454 through 469 Processing helix chain 'A' and resid 470 through 474 Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 509 through 514 removed outlier: 3.966A pdb=" N ASN A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 552 removed outlier: 3.701A pdb=" N ASN A 552 " --> pdb=" O GLU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 572 Processing helix chain 'A' and resid 606 through 614 Processing helix chain 'A' and resid 644 through 653 Processing helix chain 'A' and resid 665 through 679 removed outlier: 3.645A pdb=" N THR A 669 " --> pdb=" O ARG A 665 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN A 679 " --> pdb=" O TRP A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 691 removed outlier: 4.190A pdb=" N TRP A 687 " --> pdb=" O LYS A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.761A pdb=" N PHE A 703 " --> pdb=" O HIS A 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 26 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 54 through 72 Processing helix chain 'B' and resid 122 through 128 Processing helix chain 'B' and resid 164 through 167 No H-bonds generated for 'chain 'B' and resid 164 through 167' Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.596A pdb=" N ALA B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 282 removed outlier: 3.554A pdb=" N ASN B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 removed outlier: 4.093A pdb=" N ILE B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 302 removed outlier: 4.502A pdb=" N GLY B 302 " --> pdb=" O ARG B 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 299 through 302' Processing helix chain 'B' and resid 303 through 308 Processing helix chain 'B' and resid 333 through 345 Processing helix chain 'B' and resid 349 through 369 Processing helix chain 'B' and resid 429 through 433 Processing helix chain 'B' and resid 466 through 483 Processing helix chain 'B' and resid 498 through 505 Processing helix chain 'B' and resid 564 through 574 Processing helix chain 'B' and resid 612 through 620 Processing helix chain 'B' and resid 621 through 623 No H-bonds generated for 'chain 'B' and resid 621 through 623' Processing helix chain 'B' and resid 625 through 631 Processing helix chain 'B' and resid 633 through 637 Processing helix chain 'B' and resid 649 through 652 Processing helix chain 'B' and resid 653 through 659 Processing helix chain 'B' and resid 682 through 688 Processing helix chain 'B' and resid 718 through 735 Processing helix chain 'B' and resid 749 through 754 Processing helix chain 'B' and resid 771 through 775 Processing helix chain 'B' and resid 826 through 842 Processing helix chain 'B' and resid 850 through 854 Processing helix chain 'B' and resid 868 through 878 removed outlier: 3.801A pdb=" N THR B 878 " --> pdb=" O MET B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1011 removed outlier: 3.702A pdb=" N LEU B 998 " --> pdb=" O PRO B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1389 through 1394 Processing helix chain 'B' and resid 1395 through 1399 Processing helix chain 'B' and resid 1409 through 1415 Processing helix chain 'B' and resid 1481 through 1488 removed outlier: 3.722A pdb=" N ILE B1485 " --> pdb=" O GLY B1481 " (cutoff:3.500A) Processing helix chain 'B' and resid 1488 through 1496 Processing helix chain 'B' and resid 1523 through 1535 Processing helix chain 'B' and resid 1547 through 1551 Processing helix chain 'B' and resid 1578 through 1598 removed outlier: 3.770A pdb=" N GLY B1598 " --> pdb=" O ILE B1594 " (cutoff:3.500A) Processing helix chain 'B' and resid 1610 through 1613 removed outlier: 3.727A pdb=" N VAL B1613 " --> pdb=" O GLN B1610 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1610 through 1613' Processing helix chain 'B' and resid 1614 through 1624 Processing helix chain 'B' and resid 1668 through 1678 Processing sheet with id=AA1, first strand: chain 'A' and resid 425 through 431 removed outlier: 6.629A pdb=" N VAL A 401 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A 487 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 403 " --> pdb=" O VAL A 487 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 540 removed outlier: 7.080A pdb=" N VAL A 537 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU A 583 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 539 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU A 580 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY A 625 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 582 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR A 660 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 146 through 148 removed outlier: 6.529A pdb=" N SER B 51 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG B 14 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N TRP B 39 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL B 16 " --> pdb=" O TRP B 39 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N TRP B 41 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP B 190 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N GLU B 17 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 13.336A pdb=" N ARG B 188 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP B 185 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 162 through 163 removed outlier: 3.915A pdb=" N LEU B 162 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER B 51 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AA6, first strand: chain 'B' and resid 105 through 106 removed outlier: 6.034A pdb=" N THR B 105 " --> pdb=" O VAL B 400 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 374 through 375 Processing sheet with id=AA8, first strand: chain 'B' and resid 507 through 509 removed outlier: 6.533A pdb=" N GLU B 410 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU B 606 " --> pdb=" O GLU B 410 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 412 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE B 604 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 414 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE B 602 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 507 through 509 removed outlier: 6.533A pdb=" N GLU B 410 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU B 606 " --> pdb=" O GLU B 410 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 412 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE B 604 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 414 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE B 602 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 426 through 427 removed outlier: 4.182A pdb=" N ASN B 454 " --> pdb=" O VAL B 427 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 464 through 465 Processing sheet with id=AB3, first strand: chain 'B' and resid 521 through 528 removed outlier: 10.144A pdb=" N GLU B 521 " --> pdb=" O ASP B 542 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N ASP B 542 " --> pdb=" O GLU B 521 " (cutoff:3.500A) removed outlier: 11.103A pdb=" N ARG B 523 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 9.851A pdb=" N LEU B 540 " --> pdb=" O ARG B 523 " (cutoff:3.500A) removed outlier: 10.435A pdb=" N ARG B 525 " --> pdb=" O GLY B 538 " (cutoff:3.500A) removed outlier: 9.557A pdb=" N GLY B 538 " --> pdb=" O ARG B 525 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA B 527 " --> pdb=" O GLU B 536 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 698 through 699 removed outlier: 5.791A pdb=" N PHE B 715 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 698 through 699 removed outlier: 5.791A pdb=" N PHE B 715 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLN B 668 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ILE B 863 " --> pdb=" O GLN B 668 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR B 670 " --> pdb=" O ILE B 861 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE B 861 " --> pdb=" O THR B 670 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU B 672 " --> pdb=" O ALA B 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 680 through 681 removed outlier: 3.626A pdb=" N ILE B 695 " --> pdb=" O ASP B 681 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AB8, first strand: chain 'B' and resid 782 through 787 removed outlier: 6.020A pdb=" N ALA B 798 " --> pdb=" O ALA B 786 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 915 through 916 Processing sheet with id=AC1, first strand: chain 'B' and resid 919 through 922 Processing sheet with id=AC2, first strand: chain 'B' and resid 986 through 987 removed outlier: 6.614A pdb=" N LEU B 991 " --> pdb=" O TYR B1431 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ALA B1429 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ASP B1516 " --> pdb=" O ALA B1429 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N TYR B1431 " --> pdb=" O SER B1514 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER B1514 " --> pdb=" O TYR B1431 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN B1433 " --> pdb=" O VAL B1512 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B1512 " --> pdb=" O THR B 955 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR B 955 " --> pdb=" O VAL B1512 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N SER B1514 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU B 953 " --> pdb=" O SER B1514 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASP B1516 " --> pdb=" O CYS B 951 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N CYS B 951 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ARG B1518 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE B 949 " --> pdb=" O ARG B1518 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLU B1520 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY B 947 " --> pdb=" O GLU B1520 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N SER B 946 " --> pdb=" O THR B1564 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR B1564 " --> pdb=" O SER B 946 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS B 948 " --> pdb=" O LEU B1562 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU B1562 " --> pdb=" O LYS B 948 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASN B 950 " --> pdb=" O ASP B1560 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1424 through 1426 removed outlier: 6.862A pdb=" N VAL B1512 " --> pdb=" O THR B 955 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR B 955 " --> pdb=" O VAL B1512 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N SER B1514 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU B 953 " --> pdb=" O SER B1514 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASP B1516 " --> pdb=" O CYS B 951 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N CYS B 951 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ARG B1518 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE B 949 " --> pdb=" O ARG B1518 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLU B1520 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY B 947 " --> pdb=" O GLU B1520 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N SER B 946 " --> pdb=" O THR B1564 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR B1564 " --> pdb=" O SER B 946 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS B 948 " --> pdb=" O LEU B1562 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU B1562 " --> pdb=" O LYS B 948 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASN B 950 " --> pdb=" O ASP B1560 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 980 through 982 removed outlier: 6.197A pdb=" N LYS B 980 " --> pdb=" O THR B1503 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N GLU B1505 " --> pdb=" O LYS B 980 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N TYR B 982 " --> pdb=" O GLU B1505 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 7.99 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3379 1.32 - 1.45: 4563 1.45 - 1.57: 9514 1.57 - 1.69: 116 1.69 - 1.82: 80 Bond restraints: 17652 Sorted by residual: bond pdb=" CA ASN B 73 " pdb=" C ASN B 73 " ideal model delta sigma weight residual 1.523 1.494 0.030 1.56e-02 4.11e+03 3.62e+00 bond pdb=" C PHE A 714 " pdb=" N PRO A 715 " ideal model delta sigma weight residual 1.335 1.319 0.016 8.70e-03 1.32e+04 3.29e+00 bond pdb=" CD1 TYR B 365 " pdb=" CE1 TYR B 365 " ideal model delta sigma weight residual 1.382 1.331 0.051 3.00e-02 1.11e+03 2.90e+00 bond pdb=" CD1 TYR B 558 " pdb=" CE1 TYR B 558 " ideal model delta sigma weight residual 1.382 1.331 0.051 3.00e-02 1.11e+03 2.86e+00 bond pdb=" CB LEU A 598 " pdb=" CG LEU A 598 " ideal model delta sigma weight residual 1.530 1.563 -0.033 2.00e-02 2.50e+03 2.77e+00 ... (remaining 17647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 23455 2.26 - 4.52: 575 4.52 - 6.78: 46 6.78 - 9.03: 7 9.03 - 11.29: 2 Bond angle restraints: 24085 Sorted by residual: angle pdb=" C PRO A 335 " pdb=" N LYS A 336 " pdb=" CA LYS A 336 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" O4' G C 40 " pdb=" C1' G C 40 " pdb=" N9 G C 40 " ideal model delta sigma weight residual 108.20 114.22 -6.02 1.50e+00 4.44e-01 1.61e+01 angle pdb=" O4' A C 28 " pdb=" C1' A C 28 " pdb=" N9 A C 28 " ideal model delta sigma weight residual 108.20 114.05 -5.85 1.50e+00 4.44e-01 1.52e+01 angle pdb=" N GLU B1436 " pdb=" CA GLU B1436 " pdb=" CB GLU B1436 " ideal model delta sigma weight residual 114.17 109.80 4.37 1.14e+00 7.69e-01 1.47e+01 angle pdb=" N GLN B 34 " pdb=" CA GLN B 34 " pdb=" C GLN B 34 " ideal model delta sigma weight residual 111.75 116.56 -4.81 1.28e+00 6.10e-01 1.41e+01 ... (remaining 24080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 10201 35.32 - 70.64: 446 70.64 - 105.95: 42 105.95 - 141.27: 1 141.27 - 176.59: 5 Dihedral angle restraints: 10695 sinusoidal: 5026 harmonic: 5669 Sorted by residual: dihedral pdb=" O4' C C 22 " pdb=" C1' C C 22 " pdb=" N1 C C 22 " pdb=" C2 C C 22 " ideal model delta sinusoidal sigma weight residual 200.00 23.97 176.03 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C D 21 " pdb=" C1' C D 21 " pdb=" N1 C D 21 " pdb=" C2 C D 21 " ideal model delta sinusoidal sigma weight residual -160.00 -11.80 -148.20 1 1.50e+01 4.44e-03 7.89e+01 dihedral pdb=" O4' U C 15 " pdb=" C1' U C 15 " pdb=" N1 U C 15 " pdb=" C2 U C 15 " ideal model delta sinusoidal sigma weight residual 232.00 55.41 176.59 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 10692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2062 0.061 - 0.121: 491 0.121 - 0.182: 59 0.182 - 0.243: 6 0.243 - 0.303: 2 Chirality restraints: 2620 Sorted by residual: chirality pdb=" C1' A C 28 " pdb=" O4' A C 28 " pdb=" C2' A C 28 " pdb=" N9 A C 28 " both_signs ideal model delta sigma weight residual False 2.44 2.13 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C1' G C 40 " pdb=" O4' G C 40 " pdb=" C2' G C 40 " pdb=" N9 G C 40 " both_signs ideal model delta sigma weight residual False 2.44 2.15 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1' C D 38 " pdb=" O4' C D 38 " pdb=" C2' C D 38 " pdb=" N1 C D 38 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2617 not shown) Planarity restraints: 2884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C C 38 " 0.045 2.00e-02 2.50e+03 2.29e-02 1.18e+01 pdb=" N1 C C 38 " -0.048 2.00e-02 2.50e+03 pdb=" C2 C C 38 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C C 38 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C C 38 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C C 38 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C C 38 " 0.015 2.00e-02 2.50e+03 pdb=" C5 C C 38 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C C 38 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 28 " 0.033 2.00e-02 2.50e+03 1.73e-02 8.26e+00 pdb=" N9 A C 28 " -0.045 2.00e-02 2.50e+03 pdb=" C8 A C 28 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A C 28 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A C 28 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A C 28 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A C 28 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A C 28 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A C 28 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A C 28 " -0.008 2.00e-02 2.50e+03 pdb=" C4 A C 28 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 40 " 0.033 2.00e-02 2.50e+03 1.63e-02 7.94e+00 pdb=" N9 G C 40 " -0.044 2.00e-02 2.50e+03 pdb=" C8 G C 40 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G C 40 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G C 40 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G C 40 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G C 40 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G C 40 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G C 40 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G C 40 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G C 40 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G C 40 " -0.006 2.00e-02 2.50e+03 ... (remaining 2881 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 241 2.61 - 3.18: 15249 3.18 - 3.75: 27244 3.75 - 4.33: 40035 4.33 - 4.90: 63007 Nonbonded interactions: 145776 Sorted by model distance: nonbonded pdb=" O ASP B 796 " pdb=" O2' C D 26 " model vdw 2.036 3.040 nonbonded pdb=" O PHE A 122 " pdb=" OG SER A 126 " model vdw 2.100 3.040 nonbonded pdb=" OD2 ASP B 681 " pdb=" OG SER B 684 " model vdw 2.115 3.040 nonbonded pdb=" O GLU B1455 " pdb=" O2' C C 42 " model vdw 2.131 3.040 nonbonded pdb=" NH1 ARG B 299 " pdb=" OE2 GLU B 355 " model vdw 2.160 3.120 ... (remaining 145771 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 48.820 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.010 0.079 17652 Z= 0.670 Angle : 0.856 11.293 24085 Z= 0.475 Chirality : 0.053 0.303 2620 Planarity : 0.005 0.043 2884 Dihedral : 18.989 176.590 7051 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.01 % Favored : 92.78 % Rotamer: Outliers : 5.96 % Allowed : 16.83 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.52 (0.16), residues: 1953 helix: -1.38 (0.16), residues: 717 sheet: -1.04 (0.29), residues: 253 loop : -2.06 (0.17), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 662 HIS 0.007 0.002 HIS B 784 PHE 0.023 0.003 PHE A 594 TYR 0.021 0.003 TYR A 704 ARG 0.008 0.001 ARG B 596 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 326 time to evaluate : 1.840 Fit side-chains REVERT: A 715 PRO cc_start: 0.7130 (Cg_endo) cc_final: 0.6804 (Cg_exo) REVERT: B 68 GLU cc_start: 0.7582 (tt0) cc_final: 0.7258 (mt-10) REVERT: B 93 LYS cc_start: 0.8210 (mmmt) cc_final: 0.7190 (mptp) REVERT: B 118 LYS cc_start: 0.7899 (mtmt) cc_final: 0.7518 (mtpp) REVERT: B 162 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8533 (tp) REVERT: B 235 ILE cc_start: 0.8010 (pt) cc_final: 0.7703 (pt) REVERT: B 416 ARG cc_start: 0.8154 (mtp85) cc_final: 0.7931 (mtp180) REVERT: B 639 ASP cc_start: 0.7709 (m-30) cc_final: 0.7384 (t70) REVERT: B 1456 SER cc_start: 0.8511 (OUTLIER) cc_final: 0.8236 (p) REVERT: B 1618 ASP cc_start: 0.7793 (t0) cc_final: 0.7265 (t0) REVERT: B 1637 ASP cc_start: 0.7386 (t70) cc_final: 0.6892 (t0) outliers start: 103 outliers final: 37 residues processed: 410 average time/residue: 1.2569 time to fit residues: 573.8292 Evaluate side-chains 219 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 180 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 675 SER Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1456 SER Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1514 SER Chi-restraints excluded: chain B residue 1535 ASP 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: 0.9980 chunk 84 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 133 ASN A 183 HIS A 476 ASN A 551 GLN A 552 ASN A 553 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS B 155 HIS B 345 ASN B 360 ASN B 614 ASN B 896 ASN ** B 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 ASN B1005 HIS ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1571 ASN ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1684 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17652 Z= 0.209 Angle : 0.631 10.931 24085 Z= 0.333 Chirality : 0.043 0.338 2620 Planarity : 0.004 0.043 2884 Dihedral : 16.671 176.302 3096 Min Nonbonded Distance : 1.520 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.45 % Favored : 95.49 % Rotamer: Outliers : 3.30 % Allowed : 22.04 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.65 (0.18), residues: 1953 helix: 0.62 (0.19), residues: 713 sheet: -0.45 (0.30), residues: 242 loop : -1.21 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 607 HIS 0.013 0.001 HIS B 742 PHE 0.015 0.002 PHE B 453 TYR 0.018 0.001 TYR B1656 ARG 0.007 0.001 ARG B 733 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 201 time to evaluate : 1.969 Fit side-chains REVERT: A 686 GLU cc_start: 0.7237 (mt-10) cc_final: 0.7026 (mt-10) REVERT: B 68 GLU cc_start: 0.7489 (tt0) cc_final: 0.7226 (mt-10) REVERT: B 93 LYS cc_start: 0.8453 (mmmt) cc_final: 0.8245 (ttpp) REVERT: B 235 ILE cc_start: 0.8208 (pt) cc_final: 0.7853 (pt) REVERT: B 270 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8233 (mtpt) REVERT: B 460 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: B 499 LYS cc_start: 0.8083 (mmtm) cc_final: 0.7870 (mtmt) REVERT: B 639 ASP cc_start: 0.7798 (m-30) cc_final: 0.7596 (m-30) REVERT: B 981 ASN cc_start: 0.7284 (OUTLIER) cc_final: 0.6652 (p0) REVERT: B 1516 ASP cc_start: 0.7751 (m-30) cc_final: 0.7453 (m-30) REVERT: B 1569 SER cc_start: 0.6351 (OUTLIER) cc_final: 0.5824 (p) REVERT: B 1597 SER cc_start: 0.8634 (t) cc_final: 0.8339 (t) REVERT: B 1618 ASP cc_start: 0.7677 (t0) cc_final: 0.7135 (t70) REVERT: B 1639 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7466 (pmm-80) outliers start: 57 outliers final: 20 residues processed: 245 average time/residue: 1.3955 time to fit residues: 380.2744 Evaluate side-chains 192 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1569 SER Chi-restraints excluded: chain B residue 1639 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 181 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 541 ASN A 553 ASN A 585 HIS ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN B 155 HIS B 450 HIS ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1542 HIS B1630 ASN ** B1666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17652 Z= 0.223 Angle : 0.599 11.435 24085 Z= 0.313 Chirality : 0.043 0.330 2620 Planarity : 0.004 0.047 2884 Dihedral : 16.174 177.178 3060 Min Nonbonded Distance : 1.582 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.61 % Favored : 95.34 % Rotamer: Outliers : 3.76 % Allowed : 22.21 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.01 (0.19), residues: 1953 helix: 1.27 (0.19), residues: 721 sheet: -0.14 (0.31), residues: 248 loop : -0.90 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 675 HIS 0.005 0.001 HIS B 784 PHE 0.018 0.002 PHE A 594 TYR 0.018 0.001 TYR B1585 ARG 0.005 0.000 ARG A 595 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 189 time to evaluate : 1.870 Fit side-chains REVERT: A 534 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6808 (t0) REVERT: A 597 MET cc_start: 0.2515 (mtm) cc_final: 0.2047 (ptp) REVERT: B 31 MET cc_start: 0.8752 (mmm) cc_final: 0.8398 (mmp) REVERT: B 235 ILE cc_start: 0.8448 (pt) cc_final: 0.8103 (pp) REVERT: B 499 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7924 (mmmt) REVERT: B 625 LYS cc_start: 0.8442 (mtmm) cc_final: 0.7996 (mttm) REVERT: B 639 ASP cc_start: 0.8061 (m-30) cc_final: 0.7566 (t70) REVERT: B 649 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: B 837 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8473 (tt) REVERT: B 981 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7310 (p0) REVERT: B 1396 LYS cc_start: 0.8314 (tppt) cc_final: 0.7890 (ttpp) REVERT: B 1469 GLU cc_start: 0.7821 (pm20) cc_final: 0.7560 (pm20) REVERT: B 1618 ASP cc_start: 0.7791 (t0) cc_final: 0.7152 (t70) REVERT: B 1639 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7343 (pmm-80) outliers start: 65 outliers final: 18 residues processed: 235 average time/residue: 1.3801 time to fit residues: 360.5833 Evaluate side-chains 186 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 163 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1024 SER Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1629 LEU Chi-restraints excluded: chain B residue 1639 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 551 GLN A 592 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17652 Z= 0.312 Angle : 0.621 10.398 24085 Z= 0.326 Chirality : 0.044 0.329 2620 Planarity : 0.004 0.052 2884 Dihedral : 16.149 175.786 3052 Min Nonbonded Distance : 1.599 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.81 % Favored : 95.14 % Rotamer: Outliers : 3.70 % Allowed : 22.79 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.00 (0.19), residues: 1953 helix: 1.24 (0.19), residues: 722 sheet: -0.04 (0.32), residues: 249 loop : -0.93 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 675 HIS 0.006 0.001 HIS A 457 PHE 0.019 0.002 PHE B1565 TYR 0.021 0.002 TYR A 704 ARG 0.007 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 179 time to evaluate : 2.065 Fit side-chains REVERT: A 231 ARG cc_start: 0.7646 (ptm160) cc_final: 0.7273 (ptp90) REVERT: A 331 MET cc_start: 0.5429 (tpt) cc_final: 0.4219 (mmt) REVERT: A 476 ASN cc_start: 0.7830 (OUTLIER) cc_final: 0.7241 (m-40) REVERT: A 630 ASP cc_start: 0.7763 (t0) cc_final: 0.7407 (t0) REVERT: B 31 MET cc_start: 0.8916 (mmm) cc_final: 0.8698 (mmm) REVERT: B 118 LYS cc_start: 0.8072 (mttm) cc_final: 0.7199 (tppt) REVERT: B 235 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8219 (pp) REVERT: B 340 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6446 (tt0) REVERT: B 368 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7189 (mm-30) REVERT: B 625 LYS cc_start: 0.8508 (mtmm) cc_final: 0.8083 (mttm) REVERT: B 639 ASP cc_start: 0.8157 (m-30) cc_final: 0.7647 (t70) REVERT: B 649 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: B 745 CYS cc_start: 0.5159 (p) cc_final: 0.4743 (p) REVERT: B 837 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8489 (tt) REVERT: B 1396 LYS cc_start: 0.8152 (tppt) cc_final: 0.7708 (ttpp) REVERT: B 1447 ARG cc_start: 0.8395 (ttp-170) cc_final: 0.8177 (ttp-170) REVERT: B 1502 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8229 (t) REVERT: B 1670 LYS cc_start: 0.8452 (mttp) cc_final: 0.7911 (mppt) outliers start: 64 outliers final: 29 residues processed: 224 average time/residue: 1.3730 time to fit residues: 341.9206 Evaluate side-chains 193 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 157 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 698 LYS Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1504 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 79 optimal weight: 0.4980 chunk 164 optimal weight: 0.8980 chunk 133 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 0.0670 chunk 173 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 429 GLN ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1684 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17652 Z= 0.260 Angle : 0.586 9.928 24085 Z= 0.308 Chirality : 0.043 0.326 2620 Planarity : 0.004 0.048 2884 Dihedral : 16.074 175.327 3050 Min Nonbonded Distance : 1.611 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.56 % Favored : 95.39 % Rotamer: Outliers : 3.82 % Allowed : 23.19 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.13 (0.19), residues: 1953 helix: 1.37 (0.19), residues: 721 sheet: -0.05 (0.31), residues: 259 loop : -0.85 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 675 HIS 0.005 0.001 HIS B 742 PHE 0.016 0.002 PHE B1565 TYR 0.017 0.002 TYR A 704 ARG 0.005 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 173 time to evaluate : 2.021 Fit side-chains REVERT: A 231 ARG cc_start: 0.7659 (ptm160) cc_final: 0.7302 (ptp90) REVERT: A 331 MET cc_start: 0.5342 (tpt) cc_final: 0.4736 (tpt) REVERT: A 476 ASN cc_start: 0.7365 (OUTLIER) cc_final: 0.6866 (m110) REVERT: A 630 ASP cc_start: 0.7509 (t0) cc_final: 0.7296 (t0) REVERT: B 31 MET cc_start: 0.8904 (mmm) cc_final: 0.8667 (mmm) REVERT: B 118 LYS cc_start: 0.7953 (mttm) cc_final: 0.7138 (tppt) REVERT: B 184 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7704 (pmtt) REVERT: B 207 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.7951 (mtt90) REVERT: B 235 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8249 (pp) REVERT: B 368 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7148 (mm-30) REVERT: B 375 ARG cc_start: 0.7683 (ttm110) cc_final: 0.7390 (mtm-85) REVERT: B 504 MET cc_start: 0.8909 (mmm) cc_final: 0.8579 (mmm) REVERT: B 612 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7501 (mtpp) REVERT: B 625 LYS cc_start: 0.8491 (mtmm) cc_final: 0.8104 (mttm) REVERT: B 639 ASP cc_start: 0.8108 (m-30) cc_final: 0.7638 (t70) REVERT: B 649 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7828 (mp0) REVERT: B 745 CYS cc_start: 0.5180 (p) cc_final: 0.4845 (p) REVERT: B 837 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8505 (tt) REVERT: B 1396 LYS cc_start: 0.8140 (tppt) cc_final: 0.7743 (ttpp) REVERT: B 1502 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8168 (t) REVERT: B 1569 SER cc_start: 0.6357 (OUTLIER) cc_final: 0.5736 (p) REVERT: B 1670 LYS cc_start: 0.8503 (mttp) cc_final: 0.7943 (mppt) outliers start: 66 outliers final: 32 residues processed: 222 average time/residue: 1.3510 time to fit residues: 335.6113 Evaluate side-chains 196 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 155 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 698 LYS Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1569 SER Chi-restraints excluded: chain B residue 1629 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 160 optimal weight: 0.0670 chunk 89 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 0.3980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 480 ASN A 553 ASN A 602 ASN B 155 HIS ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 17652 Z= 0.155 Angle : 0.544 10.033 24085 Z= 0.286 Chirality : 0.041 0.314 2620 Planarity : 0.004 0.049 2884 Dihedral : 15.948 174.790 3050 Min Nonbonded Distance : 1.649 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.12 % Allowed : 24.29 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.37 (0.19), residues: 1953 helix: 1.60 (0.20), residues: 723 sheet: 0.35 (0.32), residues: 241 loop : -0.81 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 675 HIS 0.004 0.001 HIS A 457 PHE 0.014 0.001 PHE B 800 TYR 0.018 0.001 TYR A 607 ARG 0.006 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 180 time to evaluate : 1.789 Fit side-chains REVERT: A 331 MET cc_start: 0.5319 (tpt) cc_final: 0.5101 (mmt) REVERT: A 590 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6702 (ttm) REVERT: B 31 MET cc_start: 0.8869 (mmm) cc_final: 0.8623 (mmm) REVERT: B 93 LYS cc_start: 0.8650 (mptp) cc_final: 0.8396 (mptp) REVERT: B 118 LYS cc_start: 0.7935 (mttm) cc_final: 0.7162 (tppt) REVERT: B 207 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7956 (mpt-90) REVERT: B 235 ILE cc_start: 0.8578 (pt) cc_final: 0.8318 (pt) REVERT: B 368 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7234 (mm-30) REVERT: B 404 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6920 (tp30) REVERT: B 499 LYS cc_start: 0.8118 (mmmt) cc_final: 0.7843 (mmtm) REVERT: B 625 LYS cc_start: 0.8382 (mtmm) cc_final: 0.7947 (mttm) REVERT: B 639 ASP cc_start: 0.8063 (m-30) cc_final: 0.7586 (t70) REVERT: B 649 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: B 745 CYS cc_start: 0.4986 (p) cc_final: 0.4534 (p) REVERT: B 927 LYS cc_start: 0.8149 (ttpp) cc_final: 0.7833 (tmtt) REVERT: B 1396 LYS cc_start: 0.8095 (tppt) cc_final: 0.7699 (ttpp) REVERT: B 1502 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8193 (t) REVERT: B 1670 LYS cc_start: 0.8472 (mttp) cc_final: 0.7934 (mppt) outliers start: 54 outliers final: 20 residues processed: 220 average time/residue: 1.3589 time to fit residues: 332.9859 Evaluate side-chains 186 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1569 SER 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: 10.0000 chunk 110 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 162 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 HIS B 691 ASN ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1487 GLN B1591 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17652 Z= 0.185 Angle : 0.558 9.840 24085 Z= 0.293 Chirality : 0.041 0.317 2620 Planarity : 0.004 0.050 2884 Dihedral : 15.905 175.112 3048 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.37 % Allowed : 25.22 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.42 (0.19), residues: 1953 helix: 1.62 (0.19), residues: 725 sheet: 0.39 (0.33), residues: 236 loop : -0.77 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 675 HIS 0.004 0.001 HIS B 784 PHE 0.021 0.001 PHE A 184 TYR 0.018 0.001 TYR A 607 ARG 0.004 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 170 time to evaluate : 1.917 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.6838 (m-30) cc_final: 0.6509 (m-30) REVERT: A 331 MET cc_start: 0.5208 (tpt) cc_final: 0.4995 (mmt) REVERT: A 590 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6739 (ttm) REVERT: A 683 LYS cc_start: 0.7740 (mmtt) cc_final: 0.7532 (mmtt) REVERT: B 68 GLU cc_start: 0.7638 (tt0) cc_final: 0.7352 (mt-10) REVERT: B 118 LYS cc_start: 0.7954 (mttm) cc_final: 0.7190 (tppt) REVERT: B 207 ARG cc_start: 0.8171 (ttm-80) cc_final: 0.7961 (mpt-90) REVERT: B 235 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8325 (pt) REVERT: B 368 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7257 (mm-30) REVERT: B 404 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6932 (tp30) REVERT: B 499 LYS cc_start: 0.8148 (mmmt) cc_final: 0.7871 (mmtm) REVERT: B 625 LYS cc_start: 0.8404 (mtmm) cc_final: 0.7952 (mttm) REVERT: B 639 ASP cc_start: 0.8071 (m-30) cc_final: 0.7613 (t70) REVERT: B 649 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: B 745 CYS cc_start: 0.5178 (p) cc_final: 0.4763 (p) REVERT: B 1396 LYS cc_start: 0.8104 (tppt) cc_final: 0.7712 (ttpp) REVERT: B 1502 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8293 (t) REVERT: B 1639 ARG cc_start: 0.7946 (mtp180) cc_final: 0.7586 (pmm-80) REVERT: B 1670 LYS cc_start: 0.8487 (mttp) cc_final: 0.7946 (mppt) outliers start: 41 outliers final: 19 residues processed: 196 average time/residue: 1.4567 time to fit residues: 318.0240 Evaluate side-chains 184 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1569 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 95 optimal weight: 0.0270 chunk 17 optimal weight: 8.9990 chunk 151 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN A 575 ASN B 155 HIS ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1591 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17652 Z= 0.161 Angle : 0.541 9.853 24085 Z= 0.283 Chirality : 0.040 0.314 2620 Planarity : 0.004 0.043 2884 Dihedral : 15.843 174.853 3048 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.31 % Allowed : 25.62 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.55 (0.19), residues: 1953 helix: 1.72 (0.20), residues: 726 sheet: 0.39 (0.32), residues: 248 loop : -0.68 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 675 HIS 0.004 0.001 HIS A 457 PHE 0.020 0.001 PHE B 453 TYR 0.018 0.001 TYR A 607 ARG 0.004 0.000 ARG A 574 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 177 time to evaluate : 2.047 Fit side-chains REVERT: A 166 ASP cc_start: 0.6842 (m-30) cc_final: 0.6523 (m-30) REVERT: A 590 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6839 (ttm) REVERT: A 683 LYS cc_start: 0.7694 (mmtt) cc_final: 0.7492 (mmtm) REVERT: B 68 GLU cc_start: 0.7638 (tt0) cc_final: 0.7349 (mt-10) REVERT: B 118 LYS cc_start: 0.7982 (mttm) cc_final: 0.7229 (tppt) REVERT: B 127 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8112 (mp) REVERT: B 235 ILE cc_start: 0.8583 (pt) cc_final: 0.8344 (pt) REVERT: B 368 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7242 (mm-30) REVERT: B 404 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6921 (tp30) REVERT: B 499 LYS cc_start: 0.8138 (mmmt) cc_final: 0.7859 (mmtm) REVERT: B 625 LYS cc_start: 0.8342 (mtmm) cc_final: 0.7982 (mttm) REVERT: B 639 ASP cc_start: 0.8087 (m-30) cc_final: 0.7630 (t70) REVERT: B 649 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: B 1396 LYS cc_start: 0.8064 (tppt) cc_final: 0.7697 (ttpp) REVERT: B 1502 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8295 (t) REVERT: B 1639 ARG cc_start: 0.7920 (mtp180) cc_final: 0.7552 (pmm-80) REVERT: B 1670 LYS cc_start: 0.8477 (mttp) cc_final: 0.7925 (mppt) outliers start: 40 outliers final: 20 residues processed: 205 average time/residue: 1.3738 time to fit residues: 314.0096 Evaluate side-chains 183 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 158 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1504 THR Chi-restraints excluded: chain B residue 1569 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 5.9990 chunk 168 optimal weight: 0.0670 chunk 179 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 55 optimal weight: 0.0070 chunk 162 optimal weight: 0.8980 chunk 169 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 189 optimal weight: 0.0970 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 230 HIS A 575 ASN A 585 HIS B 155 HIS ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 17652 Z= 0.142 Angle : 0.541 9.729 24085 Z= 0.282 Chirality : 0.040 0.313 2620 Planarity : 0.004 0.043 2884 Dihedral : 15.761 174.756 3048 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.79 % Allowed : 26.49 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.66 (0.19), residues: 1953 helix: 1.84 (0.20), residues: 724 sheet: 0.47 (0.32), residues: 251 loop : -0.64 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 675 HIS 0.006 0.001 HIS B 900 PHE 0.019 0.001 PHE A 184 TYR 0.014 0.001 TYR A 607 ARG 0.004 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 177 time to evaluate : 2.090 Fit side-chains REVERT: A 575 ASN cc_start: 0.7511 (m-40) cc_final: 0.7157 (t0) REVERT: A 590 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6593 (ttm) REVERT: B 68 GLU cc_start: 0.7669 (tt0) cc_final: 0.7379 (mt-10) REVERT: B 118 LYS cc_start: 0.8009 (mttm) cc_final: 0.7261 (tppt) REVERT: B 235 ILE cc_start: 0.8568 (pt) cc_final: 0.8322 (pt) REVERT: B 368 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7217 (mm-30) REVERT: B 625 LYS cc_start: 0.8307 (mtmm) cc_final: 0.7948 (mttm) REVERT: B 639 ASP cc_start: 0.8073 (m-30) cc_final: 0.7625 (t70) REVERT: B 649 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: B 745 CYS cc_start: 0.5085 (p) cc_final: 0.4359 (p) REVERT: B 1396 LYS cc_start: 0.8058 (tppt) cc_final: 0.7708 (ttpp) REVERT: B 1502 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8398 (t) REVERT: B 1639 ARG cc_start: 0.7819 (mtp180) cc_final: 0.7502 (pmm-80) REVERT: B 1670 LYS cc_start: 0.8480 (mttp) cc_final: 0.7873 (mppt) outliers start: 31 outliers final: 16 residues processed: 197 average time/residue: 1.3699 time to fit residues: 300.6298 Evaluate side-chains 181 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 161 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1569 SER Chi-restraints excluded: chain B residue 1629 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 chunk 199 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 122 optimal weight: 0.2980 chunk 97 optimal weight: 0.0010 chunk 126 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 230 HIS A 585 HIS A 688 GLN B 914 ASN ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17652 Z= 0.163 Angle : 0.552 9.633 24085 Z= 0.289 Chirality : 0.040 0.316 2620 Planarity : 0.004 0.043 2884 Dihedral : 15.694 174.978 3046 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.68 % Allowed : 26.95 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.68 (0.19), residues: 1953 helix: 1.83 (0.20), residues: 724 sheet: 0.58 (0.32), residues: 246 loop : -0.63 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 675 HIS 0.012 0.001 HIS B 910 PHE 0.016 0.001 PHE A 184 TYR 0.015 0.001 TYR A 607 ARG 0.006 0.000 ARG A 574 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 1.863 Fit side-chains REVERT: A 131 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7363 (tt0) REVERT: A 575 ASN cc_start: 0.7538 (m-40) cc_final: 0.7217 (t0) REVERT: A 583 LEU cc_start: 0.7123 (mp) cc_final: 0.6687 (mt) REVERT: A 590 MET cc_start: 0.6873 (OUTLIER) cc_final: 0.6591 (ttm) REVERT: B 68 GLU cc_start: 0.7652 (tt0) cc_final: 0.7374 (mt-10) REVERT: B 118 LYS cc_start: 0.8018 (mttm) cc_final: 0.7268 (tppt) REVERT: B 235 ILE cc_start: 0.8581 (pt) cc_final: 0.8333 (pt) REVERT: B 277 GLU cc_start: 0.7199 (pp20) cc_final: 0.6990 (pp20) REVERT: B 368 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7228 (mm-30) REVERT: B 625 LYS cc_start: 0.8296 (mtmm) cc_final: 0.7928 (mttm) REVERT: B 639 ASP cc_start: 0.8085 (m-30) cc_final: 0.7650 (t70) REVERT: B 649 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: B 1396 LYS cc_start: 0.8070 (tppt) cc_final: 0.7722 (ttpp) REVERT: B 1490 LEU cc_start: 0.8216 (mp) cc_final: 0.7951 (mm) REVERT: B 1502 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8421 (t) REVERT: B 1597 SER cc_start: 0.8663 (t) cc_final: 0.8454 (p) REVERT: B 1639 ARG cc_start: 0.7809 (mtp180) cc_final: 0.7492 (pmm-80) REVERT: B 1670 LYS cc_start: 0.8449 (mttp) cc_final: 0.7842 (mppt) outliers start: 29 outliers final: 19 residues processed: 186 average time/residue: 1.4132 time to fit residues: 293.0966 Evaluate side-chains 184 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1569 SER Chi-restraints excluded: chain B residue 1629 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 230 HIS A 585 HIS ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.160556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.107940 restraints weight = 19992.923| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.45 r_work: 0.3207 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17652 Z= 0.173 Angle : 0.559 9.530 24085 Z= 0.291 Chirality : 0.041 0.317 2620 Planarity : 0.004 0.047 2884 Dihedral : 15.672 175.105 3046 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.56 % Allowed : 26.95 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.66 (0.19), residues: 1953 helix: 1.81 (0.20), residues: 725 sheet: 0.58 (0.32), residues: 251 loop : -0.65 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 675 HIS 0.005 0.001 HIS A 230 PHE 0.017 0.001 PHE A 184 TYR 0.016 0.001 TYR A 607 ARG 0.007 0.000 ARG A 574 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6619.04 seconds wall clock time: 116 minutes 58.59 seconds (7018.59 seconds total)