Starting phenix.real_space_refine on Wed Mar 4 23:53:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d9g_27261/03_2026/8d9g_27261.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d9g_27261/03_2026/8d9g_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 { model { file = "/net/cci-nas-00/data/ceres_data/8d9g_27261/03_2026/8d9g_27261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d9g_27261/03_2026/8d9g_27261.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d9g_27261/03_2026/8d9g_27261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d9g_27261/03_2026/8d9g_27261.map" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.055 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.97, per 1000 atoms: 0.23 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: 1.58 Conformation dependent library (CDL) restraints added in 862.6 milliseconds 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: 2.67 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: 4.02 Time building geometry restraints manager: 2.11 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: 1.410 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.510 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.090 ------------------------------------------------------------------------------- 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 : 0.012 0.487 17666 Z= 0.493 Angle : 0.987 41.917 24103 Z= 0.484 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 : 11.09 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.008 0.001 ARG B 596 TYR 0.021 0.003 TYR A 704 PHE 0.023 0.003 PHE A 594 TRP 0.020 0.003 TRP A 662 HIS 0.007 0.002 HIS B 784 Details of bonding type rmsd covalent geometry : bond 0.01035 (17652) covalent geometry : angle 0.85590 (24085) hydrogen bonds : bond 0.15603 ( 671) hydrogen bonds : angle 6.78837 ( 1938) metal coordination : bond 0.19822 ( 14) metal coordination : angle 17.98042 ( 18) *********************** 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 to be fit. rotamer outliers: 103 poor density : 326 time to evaluate : 0.651 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: 0.7930 (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: 0.6794 time to fit residues: 308.8596 Evaluate side-chains 219 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 541 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 950 ASN ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 ASN B1005 HIS ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1542 HIS B1571 ASN ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1684 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.167216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.115380 restraints weight = 20112.180| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.23 r_work: 0.3332 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17666 Z= 0.142 Angle : 0.642 13.526 24103 Z= 0.329 Chirality : 0.043 0.341 2620 Planarity : 0.004 0.045 2884 Dihedral : 16.618 176.609 3096 Min Nonbonded Distance : 1.530 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.15 % Favored : 95.75 % Rotamer: Outliers : 3.24 % Allowed : 21.69 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.18), residues: 1953 helix: 0.70 (0.19), residues: 715 sheet: -0.47 (0.30), residues: 244 loop : -1.15 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 733 TYR 0.018 0.001 TYR B 13 PHE 0.020 0.002 PHE B 453 TRP 0.012 0.001 TRP B 607 HIS 0.013 0.001 HIS B 742 Details of bonding type rmsd covalent geometry : bond 0.00307 (17652) covalent geometry : angle 0.62473 (24085) hydrogen bonds : bond 0.04133 ( 671) hydrogen bonds : angle 4.61134 ( 1938) metal coordination : bond 0.01161 ( 14) metal coordination : angle 5.43226 ( 18) *********************** 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 265 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 209 time to evaluate : 0.656 Fit side-chains REVERT: A 88 THR cc_start: 0.7037 (p) cc_final: 0.6730 (t) REVERT: A 180 MET cc_start: 0.8777 (mmm) cc_final: 0.8371 (mmm) REVERT: A 216 MET cc_start: 0.7142 (tpt) cc_final: 0.6870 (tpt) REVERT: A 346 LYS cc_start: 0.6403 (tmmt) cc_final: 0.6151 (ttpt) REVERT: A 518 TYR cc_start: 0.7263 (m-80) cc_final: 0.6893 (m-80) REVERT: A 587 GLU cc_start: 0.7029 (pt0) cc_final: 0.6777 (pm20) REVERT: A 686 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7126 (mt-10) REVERT: A 690 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7455 (pp20) REVERT: B 68 GLU cc_start: 0.8252 (tt0) cc_final: 0.7906 (mt-10) REVERT: B 93 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8081 (ttpp) REVERT: B 118 LYS cc_start: 0.7934 (mtmt) cc_final: 0.7675 (mttm) REVERT: B 235 ILE cc_start: 0.8544 (pt) cc_final: 0.8192 (pt) REVERT: B 306 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7351 (mm) REVERT: B 339 LYS cc_start: 0.8017 (mtmt) cc_final: 0.7649 (mttm) REVERT: B 368 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6804 (mp0) REVERT: B 460 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: B 499 LYS cc_start: 0.8486 (mmtm) cc_final: 0.7819 (mtmt) REVERT: B 639 ASP cc_start: 0.8185 (m-30) cc_final: 0.7960 (m-30) REVERT: B 981 ASN cc_start: 0.7144 (OUTLIER) cc_final: 0.6386 (p0) REVERT: B 1469 GLU cc_start: 0.7756 (pm20) cc_final: 0.7479 (pm20) REVERT: B 1597 SER cc_start: 0.8629 (t) cc_final: 0.8342 (t) REVERT: B 1618 ASP cc_start: 0.7831 (t0) cc_final: 0.7339 (t70) REVERT: B 1639 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7298 (pmm-80) outliers start: 56 outliers final: 18 residues processed: 250 average time/residue: 0.7094 time to fit residues: 196.5505 Evaluate side-chains 189 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 598 LEU Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 690 GLU 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 306 ILE Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 368 GLU 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 1639 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 83 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 86 optimal weight: 0.2980 chunk 54 optimal weight: 0.0770 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 553 ASN ** 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** ** B1666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.164926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.112764 restraints weight = 20329.174| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.22 r_work: 0.3295 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17666 Z= 0.126 Angle : 0.580 12.662 24103 Z= 0.297 Chirality : 0.042 0.332 2620 Planarity : 0.004 0.044 2884 Dihedral : 16.146 175.063 3057 Min Nonbonded Distance : 1.606 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.56 % Favored : 95.39 % Rotamer: Outliers : 3.53 % Allowed : 22.73 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.19), residues: 1953 helix: 1.35 (0.20), residues: 724 sheet: 0.20 (0.31), residues: 227 loop : -0.89 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 841 TYR 0.017 0.001 TYR B1585 PHE 0.012 0.001 PHE B 10 TRP 0.016 0.001 TRP A 675 HIS 0.004 0.001 HIS B 979 Details of bonding type rmsd covalent geometry : bond 0.00273 (17652) covalent geometry : angle 0.56577 (24085) hydrogen bonds : bond 0.03737 ( 671) hydrogen bonds : angle 4.24351 ( 1938) metal coordination : bond 0.00761 ( 14) metal coordination : angle 4.74210 ( 18) *********************** 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 250 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 189 time to evaluate : 0.608 Fit side-chains REVERT: A 88 THR cc_start: 0.7119 (p) cc_final: 0.6865 (t) REVERT: A 180 MET cc_start: 0.8751 (mmm) cc_final: 0.8498 (mmm) REVERT: A 189 LYS cc_start: 0.8370 (tmtt) cc_final: 0.8132 (tmmm) REVERT: A 216 MET cc_start: 0.7162 (tpt) cc_final: 0.6913 (tpt) REVERT: A 574 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6545 (mpp-170) REVERT: A 686 GLU cc_start: 0.7322 (mt-10) cc_final: 0.7054 (mt-10) REVERT: A 697 LYS cc_start: 0.7130 (ptpp) cc_final: 0.6911 (pmtt) REVERT: B 68 GLU cc_start: 0.8310 (tt0) cc_final: 0.7973 (mt-10) REVERT: B 93 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8068 (ttpp) REVERT: B 118 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7502 (mttm) REVERT: B 119 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7623 (mm-30) REVERT: B 235 ILE cc_start: 0.8552 (pt) cc_final: 0.8148 (pp) REVERT: B 309 ASP cc_start: 0.7657 (m-30) cc_final: 0.7433 (m-30) REVERT: B 339 LYS cc_start: 0.8003 (mtmt) cc_final: 0.7710 (mttm) REVERT: B 499 LYS cc_start: 0.8474 (mmtm) cc_final: 0.7998 (mmmt) REVERT: B 639 ASP cc_start: 0.8377 (m-30) cc_final: 0.7611 (t70) REVERT: B 649 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: B 745 CYS cc_start: 0.5744 (p) cc_final: 0.5205 (p) REVERT: B 756 GLU cc_start: 0.7855 (mp0) cc_final: 0.7564 (mm-30) REVERT: B 837 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8296 (tt) REVERT: B 981 ASN cc_start: 0.7384 (OUTLIER) cc_final: 0.6512 (p0) REVERT: B 1396 LYS cc_start: 0.8058 (tppt) cc_final: 0.7483 (ttpp) REVERT: B 1569 SER cc_start: 0.6704 (OUTLIER) cc_final: 0.6156 (p) REVERT: B 1610 GLN cc_start: 0.8319 (mm-40) cc_final: 0.8075 (mm-40) REVERT: B 1618 ASP cc_start: 0.7752 (t0) cc_final: 0.7253 (t70) REVERT: B 1639 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7054 (pmm-80) outliers start: 61 outliers final: 16 residues processed: 231 average time/residue: 0.7047 time to fit residues: 180.9795 Evaluate side-chains 193 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 574 ARG Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 591 SER 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 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 1502 VAL Chi-restraints excluded: chain B residue 1569 SER 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 140 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 131 optimal weight: 0.2980 chunk 98 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 194 optimal weight: 8.9990 chunk 127 optimal weight: 0.8980 chunk 190 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 476 ASN A 592 ASN A 602 ASN B 155 HIS ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.163048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.112867 restraints weight = 20443.981| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.36 r_work: 0.3263 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17666 Z= 0.125 Angle : 0.564 11.115 24103 Z= 0.290 Chirality : 0.041 0.325 2620 Planarity : 0.004 0.047 2884 Dihedral : 16.016 174.993 3052 Min Nonbonded Distance : 1.609 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.20 % Favored : 95.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.19), residues: 1953 helix: 1.54 (0.20), residues: 723 sheet: 0.37 (0.33), residues: 228 loop : -0.85 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 140 TYR 0.020 0.001 TYR A 607 PHE 0.020 0.001 PHE B 453 TRP 0.021 0.001 TRP A 675 HIS 0.007 0.001 HIS B 903 Details of bonding type rmsd covalent geometry : bond 0.00274 (17652) covalent geometry : angle 0.55221 (24085) hydrogen bonds : bond 0.03537 ( 671) hydrogen bonds : angle 4.10003 ( 1938) metal coordination : bond 0.00687 ( 14) metal coordination : angle 4.14922 ( 18) *********************** 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 249 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 192 time to evaluate : 0.672 Fit side-chains REVERT: A 88 THR cc_start: 0.7241 (p) cc_final: 0.7014 (t) REVERT: A 180 MET cc_start: 0.8755 (mmm) cc_final: 0.8327 (mmm) REVERT: A 189 LYS cc_start: 0.8286 (tmtt) cc_final: 0.7999 (tmmm) REVERT: A 216 MET cc_start: 0.7169 (tpt) cc_final: 0.6937 (tpt) REVERT: A 331 MET cc_start: 0.4673 (tpt) cc_final: 0.3173 (tpt) REVERT: A 353 VAL cc_start: 0.5192 (t) cc_final: 0.4961 (t) REVERT: A 630 ASP cc_start: 0.7470 (t0) cc_final: 0.6893 (t0) REVERT: A 686 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7087 (mt-10) REVERT: A 697 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6885 (pmtt) REVERT: B 93 LYS cc_start: 0.8621 (mmmt) cc_final: 0.8068 (ttpp) REVERT: B 118 LYS cc_start: 0.8040 (mtmt) cc_final: 0.7752 (mtpt) REVERT: B 207 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7930 (mpt-90) REVERT: B 235 ILE cc_start: 0.8740 (pt) cc_final: 0.8375 (pp) REVERT: B 309 ASP cc_start: 0.7642 (m-30) cc_final: 0.7395 (m-30) REVERT: B 339 LYS cc_start: 0.8086 (mtmt) cc_final: 0.7833 (mttm) REVERT: B 368 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: B 460 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8594 (mm-30) REVERT: B 499 LYS cc_start: 0.8478 (mmtm) cc_final: 0.8053 (mmmt) REVERT: B 615 GLU cc_start: 0.8048 (mp0) cc_final: 0.7794 (mp0) REVERT: B 625 LYS cc_start: 0.8360 (mtmm) cc_final: 0.7727 (mttm) REVERT: B 639 ASP cc_start: 0.8460 (m-30) cc_final: 0.7667 (t70) REVERT: B 649 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: B 745 CYS cc_start: 0.5877 (p) cc_final: 0.5157 (p) REVERT: B 756 GLU cc_start: 0.7847 (mp0) cc_final: 0.7597 (mm-30) REVERT: B 915 ILE cc_start: 0.7479 (mt) cc_final: 0.7144 (mp) REVERT: B 981 ASN cc_start: 0.7653 (OUTLIER) cc_final: 0.7155 (p0) REVERT: B 1396 LYS cc_start: 0.8080 (tppt) cc_final: 0.7507 (ttpp) REVERT: B 1469 GLU cc_start: 0.7702 (pm20) cc_final: 0.7461 (pm20) REVERT: B 1470 ILE cc_start: 0.8588 (mm) cc_final: 0.8381 (mp) REVERT: B 1502 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7639 (t) REVERT: B 1610 GLN cc_start: 0.8322 (mm-40) cc_final: 0.8099 (mm-40) REVERT: B 1639 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7006 (pmm-80) outliers start: 57 outliers final: 17 residues processed: 233 average time/residue: 0.6821 time to fit residues: 176.9736 Evaluate side-chains 190 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 456 GLU Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 697 LYS 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 270 LYS Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 460 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 981 ASN Chi-restraints excluded: chain B residue 1002 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 1 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 155 optimal weight: 0.0170 chunk 19 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 HIS ** B 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 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** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1591 GLN B1630 ASN B1684 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.158886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105701 restraints weight = 20216.004| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.21 r_work: 0.3197 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17666 Z= 0.185 Angle : 0.610 11.945 24103 Z= 0.313 Chirality : 0.043 0.334 2620 Planarity : 0.004 0.043 2884 Dihedral : 16.015 175.719 3050 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.47 % Allowed : 22.15 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.19), residues: 1953 helix: 1.41 (0.19), residues: 730 sheet: 0.01 (0.32), residues: 258 loop : -0.82 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 140 TYR 0.020 0.002 TYR A 607 PHE 0.015 0.002 PHE B 187 TRP 0.019 0.001 TRP A 675 HIS 0.005 0.001 HIS B 742 Details of bonding type rmsd covalent geometry : bond 0.00427 (17652) covalent geometry : angle 0.59570 (24085) hydrogen bonds : bond 0.04045 ( 671) hydrogen bonds : angle 4.29638 ( 1938) metal coordination : bond 0.00842 ( 14) metal coordination : angle 4.82776 ( 18) *********************** 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 to be fit. rotamer outliers: 60 poor density : 179 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 88 THR cc_start: 0.7137 (p) cc_final: 0.6832 (t) REVERT: A 180 MET cc_start: 0.8745 (mmm) cc_final: 0.8310 (mmm) REVERT: A 189 LYS cc_start: 0.8295 (tmtt) cc_final: 0.7936 (pttp) REVERT: A 216 MET cc_start: 0.7220 (tpt) cc_final: 0.6890 (tpt) REVERT: A 331 MET cc_start: 0.4758 (tpt) cc_final: 0.4176 (tpt) REVERT: A 578 ARG cc_start: 0.6686 (ttm-80) cc_final: 0.6470 (ttt-90) REVERT: A 630 ASP cc_start: 0.7623 (t0) cc_final: 0.7023 (t0) REVERT: A 686 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7210 (mt-10) REVERT: A 697 LYS cc_start: 0.7307 (ptpp) cc_final: 0.7071 (pmtt) REVERT: B 90 ASP cc_start: 0.8062 (p0) cc_final: 0.7856 (p0) REVERT: B 93 LYS cc_start: 0.8660 (mmmt) cc_final: 0.8013 (ttpp) REVERT: B 118 LYS cc_start: 0.7949 (mtmt) cc_final: 0.7564 (tppt) REVERT: B 235 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8447 (pp) REVERT: B 309 ASP cc_start: 0.7666 (m-30) cc_final: 0.7365 (m-30) REVERT: B 339 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7805 (mttp) REVERT: B 340 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7201 (tt0) REVERT: B 368 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.7013 (mm-30) REVERT: B 375 ARG cc_start: 0.7777 (ttm110) cc_final: 0.7473 (mtm-85) REVERT: B 404 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7698 (tp30) REVERT: B 437 LYS cc_start: 0.7543 (mppt) cc_final: 0.7252 (mptt) REVERT: B 499 LYS cc_start: 0.8485 (mmtm) cc_final: 0.8074 (mmmt) REVERT: B 504 MET cc_start: 0.9248 (mmm) cc_final: 0.8943 (mmm) REVERT: B 615 GLU cc_start: 0.8203 (mp0) cc_final: 0.7988 (mp0) REVERT: B 625 LYS cc_start: 0.8397 (mtmm) cc_final: 0.7814 (mttm) REVERT: B 639 ASP cc_start: 0.8630 (m-30) cc_final: 0.7814 (t70) REVERT: B 649 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: B 743 GLU cc_start: 0.5469 (OUTLIER) cc_final: 0.4436 (tm-30) REVERT: B 756 GLU cc_start: 0.8047 (mp0) cc_final: 0.7778 (mm-30) REVERT: B 1396 LYS cc_start: 0.7869 (tppt) cc_final: 0.7312 (ttpp) REVERT: B 1502 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.7930 (t) REVERT: B 1610 GLN cc_start: 0.8234 (mm-40) cc_final: 0.8012 (mm-40) REVERT: B 1619 LYS cc_start: 0.7362 (mtpp) cc_final: 0.7155 (mttp) REVERT: B 1637 ASP cc_start: 0.8021 (t70) cc_final: 0.7383 (t0) REVERT: B 1670 LYS cc_start: 0.8409 (mttp) cc_final: 0.7664 (mppt) outliers start: 60 outliers final: 28 residues processed: 221 average time/residue: 0.6953 time to fit residues: 170.0889 Evaluate side-chains 199 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 591 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 742 HIS Chi-restraints excluded: chain B residue 743 GLU 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 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 89 optimal weight: 0.6980 chunk 194 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 199 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 0.0980 chunk 171 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS B 155 HIS B 429 GLN B 691 ASN ** B 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** B1487 GLN ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.158487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.106655 restraints weight = 20270.323| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.38 r_work: 0.3170 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17666 Z= 0.162 Angle : 0.580 10.120 24103 Z= 0.299 Chirality : 0.042 0.322 2620 Planarity : 0.004 0.042 2884 Dihedral : 15.967 175.084 3048 Min Nonbonded Distance : 1.606 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.41 % Allowed : 22.96 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 1953 helix: 1.50 (0.19), residues: 722 sheet: 0.22 (0.32), residues: 253 loop : -0.80 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 140 TYR 0.016 0.001 TYR A 704 PHE 0.028 0.002 PHE B 453 TRP 0.021 0.001 TRP A 675 HIS 0.004 0.001 HIS B 784 Details of bonding type rmsd covalent geometry : bond 0.00371 (17652) covalent geometry : angle 0.56763 (24085) hydrogen bonds : bond 0.03793 ( 671) hydrogen bonds : angle 4.20832 ( 1938) metal coordination : bond 0.00772 ( 14) metal coordination : angle 4.42345 ( 18) *********************** 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 238 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 179 time to evaluate : 0.626 Fit side-chains REVERT: A 88 THR cc_start: 0.7106 (p) cc_final: 0.6821 (t) REVERT: A 180 MET cc_start: 0.8723 (mmm) cc_final: 0.8281 (mmm) REVERT: A 189 LYS cc_start: 0.8259 (tmtt) cc_final: 0.8036 (tmmm) REVERT: A 216 MET cc_start: 0.7236 (tpt) cc_final: 0.6922 (tpt) REVERT: A 331 MET cc_start: 0.4535 (tpt) cc_final: 0.4245 (mmp) REVERT: A 597 MET cc_start: 0.2622 (mtt) cc_final: 0.1967 (ptp) REVERT: A 630 ASP cc_start: 0.7454 (t0) cc_final: 0.6972 (t0) REVERT: A 686 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7259 (mt-10) REVERT: A 697 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.7023 (pmtt) REVERT: B 29 SER cc_start: 0.8028 (OUTLIER) cc_final: 0.7813 (m) REVERT: B 90 ASP cc_start: 0.8069 (p0) cc_final: 0.7840 (p0) REVERT: B 93 LYS cc_start: 0.8673 (mmmt) cc_final: 0.7946 (ttpp) REVERT: B 118 LYS cc_start: 0.7981 (mtmt) cc_final: 0.7571 (tptt) REVERT: B 127 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8132 (mp) REVERT: B 184 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8205 (pmtt) REVERT: B 193 ASP cc_start: 0.8373 (t0) cc_final: 0.8157 (t0) REVERT: B 235 ILE cc_start: 0.8816 (pt) cc_final: 0.8432 (pp) REVERT: B 309 ASP cc_start: 0.7715 (m-30) cc_final: 0.7397 (m-30) REVERT: B 339 LYS cc_start: 0.8042 (mtmt) cc_final: 0.7773 (mttp) REVERT: B 340 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7233 (tt0) REVERT: B 368 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7186 (mm-30) REVERT: B 375 ARG cc_start: 0.7834 (ttm110) cc_final: 0.7549 (mtm-85) REVERT: B 404 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7733 (tp30) REVERT: B 437 LYS cc_start: 0.7548 (mppt) cc_final: 0.7263 (mptt) REVERT: B 504 MET cc_start: 0.9253 (mmm) cc_final: 0.8899 (mmm) REVERT: B 615 GLU cc_start: 0.8224 (mp0) cc_final: 0.7933 (mp0) REVERT: B 625 LYS cc_start: 0.8344 (mtmm) cc_final: 0.7769 (mttm) REVERT: B 639 ASP cc_start: 0.8616 (m-30) cc_final: 0.7772 (t0) REVERT: B 649 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: B 743 GLU cc_start: 0.5312 (OUTLIER) cc_final: 0.4121 (tm-30) REVERT: B 745 CYS cc_start: 0.6630 (p) cc_final: 0.6133 (p) REVERT: B 756 GLU cc_start: 0.8018 (mp0) cc_final: 0.7721 (mm-30) REVERT: B 954 GLU cc_start: 0.8280 (tt0) cc_final: 0.7930 (tt0) REVERT: B 1396 LYS cc_start: 0.7865 (tppt) cc_final: 0.7327 (ttpp) REVERT: B 1447 ARG cc_start: 0.8126 (ttp-170) cc_final: 0.7834 (ttp-170) REVERT: B 1483 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6487 (mtt180) REVERT: B 1499 GLU cc_start: 0.8444 (pm20) cc_final: 0.8199 (pm20) REVERT: B 1502 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.7836 (t) REVERT: B 1569 SER cc_start: 0.6860 (OUTLIER) cc_final: 0.6219 (p) REVERT: B 1583 ARG cc_start: 0.7783 (mpt180) cc_final: 0.7238 (mmt180) REVERT: B 1619 LYS cc_start: 0.7337 (mtpp) cc_final: 0.7062 (mttp) REVERT: B 1670 LYS cc_start: 0.8428 (mttp) cc_final: 0.7667 (mppt) outliers start: 59 outliers final: 23 residues processed: 219 average time/residue: 0.6870 time to fit residues: 166.3608 Evaluate side-chains 201 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 225 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 697 LYS 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 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 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 743 GLU 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 1483 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 123 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 0.0770 chunk 91 optimal weight: 1.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN A 480 ASN B 155 HIS ** B 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** 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 = 0.3948 r_free = 0.3948 target = 0.160909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.108207 restraints weight = 20194.504| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.23 r_work: 0.3235 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17666 Z= 0.110 Angle : 0.542 9.063 24103 Z= 0.279 Chirality : 0.040 0.314 2620 Planarity : 0.004 0.042 2884 Dihedral : 15.871 174.893 3048 Min Nonbonded Distance : 1.646 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.49 % Allowed : 24.18 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 1953 helix: 1.68 (0.20), residues: 723 sheet: 0.41 (0.33), residues: 236 loop : -0.70 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 733 TYR 0.017 0.001 TYR A 607 PHE 0.013 0.001 PHE B 800 TRP 0.028 0.001 TRP A 675 HIS 0.004 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00240 (17652) covalent geometry : angle 0.53302 (24085) hydrogen bonds : bond 0.03373 ( 671) hydrogen bonds : angle 4.03244 ( 1938) metal coordination : bond 0.00594 ( 14) metal coordination : angle 3.62897 ( 18) *********************** 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 226 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 88 THR cc_start: 0.7204 (p) cc_final: 0.6977 (t) REVERT: A 180 MET cc_start: 0.8674 (mmm) cc_final: 0.8254 (mmm) REVERT: A 189 LYS cc_start: 0.8184 (tmtt) cc_final: 0.7949 (tmmm) REVERT: A 225 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.7336 (m-80) REVERT: A 590 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6488 (ttm) REVERT: A 597 MET cc_start: 0.2657 (OUTLIER) cc_final: 0.1822 (ptp) REVERT: A 630 ASP cc_start: 0.7171 (t0) cc_final: 0.6799 (t0) REVERT: A 639 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6849 (ptm) REVERT: A 686 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7190 (mt-10) REVERT: A 697 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.7006 (pmtt) REVERT: B 29 SER cc_start: 0.7991 (OUTLIER) cc_final: 0.7781 (m) REVERT: B 68 GLU cc_start: 0.8361 (tt0) cc_final: 0.7969 (mt-10) REVERT: B 90 ASP cc_start: 0.7987 (p0) cc_final: 0.7759 (p0) REVERT: B 93 LYS cc_start: 0.8670 (mmmt) cc_final: 0.7978 (ttpp) REVERT: B 118 LYS cc_start: 0.8002 (mtmt) cc_final: 0.7611 (tptt) REVERT: B 127 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8135 (mp) REVERT: B 213 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8503 (tttt) REVERT: B 235 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8559 (pt) REVERT: B 293 ASP cc_start: 0.8228 (m-30) cc_final: 0.7959 (m-30) REVERT: B 309 ASP cc_start: 0.7727 (m-30) cc_final: 0.7444 (m-30) REVERT: B 339 LYS cc_start: 0.8052 (mtmt) cc_final: 0.7791 (mttp) REVERT: B 368 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.7105 (mm-30) REVERT: B 375 ARG cc_start: 0.7839 (ttm110) cc_final: 0.7569 (mtm-85) REVERT: B 404 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7678 (tp30) REVERT: B 437 LYS cc_start: 0.7431 (mppt) cc_final: 0.7162 (mptt) REVERT: B 615 GLU cc_start: 0.8209 (mp0) cc_final: 0.7940 (mp0) REVERT: B 625 LYS cc_start: 0.8236 (mtmm) cc_final: 0.7676 (mttm) REVERT: B 639 ASP cc_start: 0.8576 (m-30) cc_final: 0.7696 (t0) REVERT: B 649 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7759 (mp0) REVERT: B 745 CYS cc_start: 0.6596 (p) cc_final: 0.6030 (p) REVERT: B 756 GLU cc_start: 0.7942 (mp0) cc_final: 0.7586 (mm-30) REVERT: B 954 GLU cc_start: 0.8201 (tt0) cc_final: 0.7892 (tm-30) REVERT: B 1396 LYS cc_start: 0.7831 (tppt) cc_final: 0.7305 (ttpp) REVERT: B 1499 GLU cc_start: 0.8381 (pm20) cc_final: 0.8105 (pm20) REVERT: B 1502 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.7951 (t) REVERT: B 1583 ARG cc_start: 0.7816 (mpt180) cc_final: 0.7289 (mmt180) REVERT: B 1619 LYS cc_start: 0.7285 (mtpp) cc_final: 0.7027 (mttp) REVERT: B 1670 LYS cc_start: 0.8406 (mttp) cc_final: 0.7642 (mppt) outliers start: 43 outliers final: 19 residues processed: 212 average time/residue: 0.7065 time to fit residues: 166.0551 Evaluate side-chains 207 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 225 TYR Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 597 MET Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 697 LYS 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 213 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 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 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 1569 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 575 ASN B 155 HIS ** B 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** 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 = 0.159458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.107491 restraints weight = 20270.056| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.45 r_work: 0.3202 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 0.003 0.073 17666 Z= 0.140 Angle : 0.564 9.216 24103 Z= 0.290 Chirality : 0.041 0.318 2620 Planarity : 0.004 0.042 2884 Dihedral : 15.870 175.261 3048 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.37 % Allowed : 24.52 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 1953 helix: 1.64 (0.19), residues: 720 sheet: 0.26 (0.32), residues: 260 loop : -0.68 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 733 TYR 0.017 0.001 TYR A 607 PHE 0.018 0.001 PHE A 254 TRP 0.030 0.001 TRP A 675 HIS 0.004 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00321 (17652) covalent geometry : angle 0.55336 (24085) hydrogen bonds : bond 0.03660 ( 671) hydrogen bonds : angle 4.12120 ( 1938) metal coordination : bond 0.00676 ( 14) metal coordination : angle 4.05762 ( 18) *********************** 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 222 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.669 Fit side-chains REVERT: A 88 THR cc_start: 0.7204 (p) cc_final: 0.6977 (t) REVERT: A 180 MET cc_start: 0.8674 (mmm) cc_final: 0.8256 (mmm) REVERT: A 216 MET cc_start: 0.7472 (tpt) cc_final: 0.7144 (tpt) REVERT: A 225 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: A 534 ASP cc_start: 0.6893 (t0) cc_final: 0.6646 (m-30) REVERT: A 574 ARG cc_start: 0.6946 (mpp-170) cc_final: 0.6695 (mpp-170) REVERT: A 583 LEU cc_start: 0.6426 (mp) cc_final: 0.5816 (mt) REVERT: A 590 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6522 (ttm) REVERT: A 597 MET cc_start: 0.2893 (OUTLIER) cc_final: 0.2630 (mtt) REVERT: A 630 ASP cc_start: 0.7289 (t0) cc_final: 0.6897 (t0) REVERT: A 639 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6812 (ptm) REVERT: A 683 LYS cc_start: 0.6606 (mmtt) cc_final: 0.6166 (mmtm) REVERT: A 686 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7274 (mt-10) REVERT: A 697 LYS cc_start: 0.7221 (ptpp) cc_final: 0.6988 (pmtt) REVERT: B 29 SER cc_start: 0.7999 (OUTLIER) cc_final: 0.7794 (m) REVERT: B 68 GLU cc_start: 0.8376 (tt0) cc_final: 0.7987 (mt-10) REVERT: B 90 ASP cc_start: 0.8018 (p0) cc_final: 0.7780 (p0) REVERT: B 93 LYS cc_start: 0.8669 (mmmt) cc_final: 0.7978 (ttpp) REVERT: B 118 LYS cc_start: 0.8030 (mtmt) cc_final: 0.7636 (tptt) REVERT: B 184 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8130 (pmtt) REVERT: B 213 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8518 (tttt) REVERT: B 235 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8579 (pt) REVERT: B 293 ASP cc_start: 0.8262 (m-30) cc_final: 0.8026 (m-30) REVERT: B 309 ASP cc_start: 0.7720 (m-30) cc_final: 0.7358 (m-30) REVERT: B 339 LYS cc_start: 0.8058 (mtmt) cc_final: 0.7746 (mttp) REVERT: B 368 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.7012 (mm-30) REVERT: B 375 ARG cc_start: 0.7842 (ttm110) cc_final: 0.7580 (mtm-85) REVERT: B 404 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7713 (tp30) REVERT: B 437 LYS cc_start: 0.7407 (mppt) cc_final: 0.7132 (mptt) REVERT: B 499 LYS cc_start: 0.8486 (mmtm) cc_final: 0.8012 (mmmt) REVERT: B 504 MET cc_start: 0.9236 (mmm) cc_final: 0.8896 (mmm) REVERT: B 615 GLU cc_start: 0.8260 (mp0) cc_final: 0.7898 (mp0) REVERT: B 625 LYS cc_start: 0.8227 (mtmm) cc_final: 0.7627 (mttm) REVERT: B 639 ASP cc_start: 0.8658 (m-30) cc_final: 0.7804 (t0) REVERT: B 649 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: B 743 GLU cc_start: 0.5260 (OUTLIER) cc_final: 0.4087 (tm-30) REVERT: B 745 CYS cc_start: 0.6796 (p) cc_final: 0.6271 (p) REVERT: B 756 GLU cc_start: 0.8014 (mp0) cc_final: 0.7695 (mm-30) REVERT: B 909 ASP cc_start: 0.5297 (OUTLIER) cc_final: 0.5097 (p0) REVERT: B 954 GLU cc_start: 0.8240 (tt0) cc_final: 0.7927 (tm-30) REVERT: B 1396 LYS cc_start: 0.7836 (tppt) cc_final: 0.7351 (ttpp) REVERT: B 1499 GLU cc_start: 0.8373 (pm20) cc_final: 0.8112 (pm20) REVERT: B 1502 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.7960 (t) REVERT: B 1583 ARG cc_start: 0.7795 (mpt180) cc_final: 0.7256 (mmt180) REVERT: B 1619 LYS cc_start: 0.7299 (mtpp) cc_final: 0.7044 (mttp) REVERT: B 1639 ARG cc_start: 0.8032 (mtp180) cc_final: 0.7539 (pmm-80) REVERT: B 1670 LYS cc_start: 0.8430 (mttp) cc_final: 0.7669 (mppt) outliers start: 41 outliers final: 20 residues processed: 210 average time/residue: 0.7500 time to fit residues: 173.9442 Evaluate side-chains 198 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 590 MET Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 597 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 184 LYS Chi-restraints excluded: chain B residue 213 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 446 VAL 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 743 GLU 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 909 ASP 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 1507 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 145 optimal weight: 0.0170 chunk 105 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 575 ASN A 585 HIS ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** 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 = 0.3928 r_free = 0.3928 target = 0.160368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.107951 restraints weight = 20078.782| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.50 r_work: 0.3179 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 17666 Z= 0.109 Angle : 0.540 8.916 24103 Z= 0.278 Chirality : 0.040 0.312 2620 Planarity : 0.004 0.043 2884 Dihedral : 15.801 174.931 3048 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.31 % Allowed : 24.99 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 1953 helix: 1.73 (0.19), residues: 722 sheet: 0.34 (0.32), residues: 246 loop : -0.64 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 140 TYR 0.017 0.001 TYR A 607 PHE 0.020 0.001 PHE A 254 TRP 0.033 0.001 TRP A 675 HIS 0.004 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00241 (17652) covalent geometry : angle 0.53121 (24085) hydrogen bonds : bond 0.03351 ( 671) hydrogen bonds : angle 4.00777 ( 1938) metal coordination : bond 0.00554 ( 14) metal coordination : angle 3.55852 ( 18) *********************** 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 227 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 1.056 Fit side-chains REVERT: A 88 THR cc_start: 0.7193 (p) cc_final: 0.6986 (t) REVERT: A 180 MET cc_start: 0.8673 (mmm) cc_final: 0.8273 (mmm) REVERT: A 225 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.7246 (m-80) REVERT: A 574 ARG cc_start: 0.6961 (mpp-170) cc_final: 0.6562 (mpp-170) REVERT: A 575 ASN cc_start: 0.7854 (m-40) cc_final: 0.7083 (t0) REVERT: A 578 ARG cc_start: 0.6693 (ttm-80) cc_final: 0.6404 (ttt-90) REVERT: A 583 LEU cc_start: 0.6396 (mp) cc_final: 0.5784 (mt) REVERT: A 590 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6546 (ttm) REVERT: A 597 MET cc_start: 0.2663 (OUTLIER) cc_final: 0.2165 (mtm) REVERT: A 630 ASP cc_start: 0.7021 (t0) cc_final: 0.6725 (t0) REVERT: A 639 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6705 (ptm) REVERT: A 683 LYS cc_start: 0.6514 (mmtt) cc_final: 0.6071 (mmtm) REVERT: A 686 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7235 (mt-10) REVERT: A 697 LYS cc_start: 0.7351 (ptpp) cc_final: 0.7077 (pmtt) REVERT: B 68 GLU cc_start: 0.8385 (tt0) cc_final: 0.8033 (mt-10) REVERT: B 90 ASP cc_start: 0.7948 (p0) cc_final: 0.7659 (p0) REVERT: B 93 LYS cc_start: 0.8664 (mmmt) cc_final: 0.7927 (ttpp) REVERT: B 118 LYS cc_start: 0.7960 (mtmt) cc_final: 0.7577 (tptt) REVERT: B 127 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8119 (mp) REVERT: B 184 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8177 (pmtt) REVERT: B 207 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7900 (mtt90) REVERT: B 213 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8516 (tttt) REVERT: B 235 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8563 (pt) REVERT: B 293 ASP cc_start: 0.8134 (m-30) cc_final: 0.7878 (m-30) REVERT: B 309 ASP cc_start: 0.7639 (m-30) cc_final: 0.7295 (m-30) REVERT: B 339 LYS cc_start: 0.7993 (mtmt) cc_final: 0.7654 (mttp) REVERT: B 375 ARG cc_start: 0.7731 (ttm110) cc_final: 0.7406 (mtm-85) REVERT: B 404 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7764 (tp30) REVERT: B 437 LYS cc_start: 0.7271 (mppt) cc_final: 0.7009 (mptt) REVERT: B 499 LYS cc_start: 0.8451 (mmtm) cc_final: 0.7957 (mmmt) REVERT: B 612 LYS cc_start: 0.8099 (mmtp) cc_final: 0.7859 (mtpp) REVERT: B 615 GLU cc_start: 0.8170 (mp0) cc_final: 0.7731 (mp0) REVERT: B 625 LYS cc_start: 0.8142 (mtmm) cc_final: 0.7486 (mttm) REVERT: B 639 ASP cc_start: 0.8597 (m-30) cc_final: 0.7664 (t0) REVERT: B 649 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: B 743 GLU cc_start: 0.5209 (OUTLIER) cc_final: 0.3910 (tm-30) REVERT: B 756 GLU cc_start: 0.7916 (mp0) cc_final: 0.7565 (mm-30) REVERT: B 909 ASP cc_start: 0.5343 (OUTLIER) cc_final: 0.5133 (p0) REVERT: B 954 GLU cc_start: 0.8175 (tt0) cc_final: 0.7852 (tm-30) REVERT: B 1396 LYS cc_start: 0.7767 (tppt) cc_final: 0.7250 (ttpp) REVERT: B 1499 GLU cc_start: 0.8385 (pm20) cc_final: 0.8061 (pm20) REVERT: B 1502 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.7885 (t) REVERT: B 1583 ARG cc_start: 0.7750 (mpt180) cc_final: 0.7217 (mmt180) REVERT: B 1619 LYS cc_start: 0.7287 (mtpp) cc_final: 0.7030 (mttp) REVERT: B 1639 ARG cc_start: 0.8045 (mtp180) cc_final: 0.7567 (pmm-80) REVERT: B 1670 LYS cc_start: 0.8403 (mttp) cc_final: 0.7639 (mppt) outliers start: 40 outliers final: 17 residues processed: 215 average time/residue: 0.7228 time to fit residues: 171.3574 Evaluate side-chains 200 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 590 MET Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 597 MET Chi-restraints excluded: chain A residue 639 MET 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 213 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 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 698 LYS Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 909 ASP 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 1507 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 63 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 192 optimal weight: 0.2980 chunk 32 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 189 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 167 optimal weight: 0.3980 chunk 143 optimal weight: 0.6980 chunk 166 optimal weight: 0.6980 chunk 47 optimal weight: 0.0270 overall best weight: 0.4038 ------------------------------------------------------------------------------- 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 342 ASN B 914 ASN ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.162860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.109213 restraints weight = 19884.740| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.29 r_work: 0.3236 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 17666 Z= 0.098 Angle : 0.528 9.095 24103 Z= 0.272 Chirality : 0.039 0.314 2620 Planarity : 0.004 0.045 2884 Dihedral : 15.677 174.604 3048 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.68 % Allowed : 25.56 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.19), residues: 1953 helix: 1.80 (0.20), residues: 725 sheet: 0.51 (0.32), residues: 249 loop : -0.52 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 140 TYR 0.016 0.001 TYR A 607 PHE 0.018 0.001 PHE A 254 TRP 0.044 0.001 TRP A 675 HIS 0.004 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00214 (17652) covalent geometry : angle 0.52109 (24085) hydrogen bonds : bond 0.03118 ( 671) hydrogen bonds : angle 3.90019 ( 1938) metal coordination : bond 0.00489 ( 14) metal coordination : angle 3.17644 ( 18) ********************** 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 224 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.649 Fit side-chains REVERT: A 61 ASP cc_start: 0.7635 (m-30) cc_final: 0.7076 (t0) REVERT: A 180 MET cc_start: 0.8622 (mmm) cc_final: 0.8218 (mmm) REVERT: A 225 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.7191 (m-80) REVERT: A 573 ILE cc_start: 0.7104 (mm) cc_final: 0.6826 (mm) REVERT: A 574 ARG cc_start: 0.6921 (mpp-170) cc_final: 0.6440 (mpp-170) REVERT: A 575 ASN cc_start: 0.7875 (m-40) cc_final: 0.7182 (t0) REVERT: A 583 LEU cc_start: 0.6335 (mp) cc_final: 0.5779 (mt) REVERT: A 590 MET cc_start: 0.6732 (OUTLIER) cc_final: 0.6389 (ttm) REVERT: A 683 LYS cc_start: 0.6402 (mmtt) cc_final: 0.5957 (mmtm) REVERT: A 686 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7150 (mt-10) REVERT: A 689 LYS cc_start: 0.7323 (ttpp) cc_final: 0.6921 (ptmt) REVERT: A 697 LYS cc_start: 0.7265 (ptpp) cc_final: 0.7019 (pmtt) REVERT: B 68 GLU cc_start: 0.8394 (tt0) cc_final: 0.8044 (mt-10) REVERT: B 90 ASP cc_start: 0.7919 (p0) cc_final: 0.7620 (p0) REVERT: B 93 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8074 (ttpp) REVERT: B 118 LYS cc_start: 0.7955 (mtmt) cc_final: 0.7581 (tptt) REVERT: B 184 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8081 (pmtt) REVERT: B 207 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7884 (mpt-90) REVERT: B 213 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8495 (tttt) REVERT: B 235 ILE cc_start: 0.8756 (pt) cc_final: 0.8498 (pt) REVERT: B 293 ASP cc_start: 0.8003 (m-30) cc_final: 0.7797 (m-30) REVERT: B 309 ASP cc_start: 0.7610 (m-30) cc_final: 0.7288 (m-30) REVERT: B 339 LYS cc_start: 0.7963 (mtmt) cc_final: 0.7609 (mttp) REVERT: B 375 ARG cc_start: 0.7731 (ttm110) cc_final: 0.7494 (mtm-85) REVERT: B 404 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7717 (tp30) REVERT: B 499 LYS cc_start: 0.8437 (mmtm) cc_final: 0.7959 (mmmt) REVERT: B 612 LYS cc_start: 0.8093 (mmtp) cc_final: 0.7875 (mtpp) REVERT: B 615 GLU cc_start: 0.8150 (mp0) cc_final: 0.7774 (mp0) REVERT: B 625 LYS cc_start: 0.8106 (mtmm) cc_final: 0.7558 (mttm) REVERT: B 639 ASP cc_start: 0.8572 (m-30) cc_final: 0.7640 (t0) REVERT: B 649 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: B 756 GLU cc_start: 0.7824 (mp0) cc_final: 0.7507 (mm-30) REVERT: B 909 ASP cc_start: 0.5194 (OUTLIER) cc_final: 0.4988 (p0) REVERT: B 954 GLU cc_start: 0.8173 (tt0) cc_final: 0.7850 (tm-30) REVERT: B 1396 LYS cc_start: 0.7731 (tppt) cc_final: 0.7248 (ttpp) REVERT: B 1499 GLU cc_start: 0.8527 (pm20) cc_final: 0.8116 (pm20) REVERT: B 1502 VAL cc_start: 0.8285 (OUTLIER) cc_final: 0.7942 (t) REVERT: B 1583 ARG cc_start: 0.7823 (mpt180) cc_final: 0.7273 (mmt180) REVERT: B 1619 LYS cc_start: 0.7217 (mtpp) cc_final: 0.6968 (mttp) REVERT: B 1639 ARG cc_start: 0.8040 (mtp180) cc_final: 0.7624 (pmm-80) REVERT: B 1670 LYS cc_start: 0.8367 (mttp) cc_final: 0.7543 (mppt) outliers start: 29 outliers final: 13 residues processed: 210 average time/residue: 0.7351 time to fit residues: 170.1254 Evaluate side-chains 195 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 590 MET Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 597 MET Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 270 LYS 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 909 ASP 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 81 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 B 343 GLN ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** 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 = 0.3886 r_free = 0.3886 target = 0.156601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102041 restraints weight = 20114.428| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.27 r_work: 0.3144 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 17666 Z= 0.219 Angle : 0.624 11.419 24103 Z= 0.320 Chirality : 0.044 0.330 2620 Planarity : 0.004 0.044 2884 Dihedral : 15.769 175.598 3043 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.62 % Allowed : 26.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.19), residues: 1953 helix: 1.50 (0.19), residues: 728 sheet: 0.18 (0.32), residues: 260 loop : -0.68 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 140 TYR 0.024 0.002 TYR A 704 PHE 0.020 0.002 PHE A 254 TRP 0.046 0.002 TRP A 675 HIS 0.005 0.001 HIS B 903 Details of bonding type rmsd covalent geometry : bond 0.00511 (17652) covalent geometry : angle 0.60890 (24085) hydrogen bonds : bond 0.04121 ( 671) hydrogen bonds : angle 4.27875 ( 1938) metal coordination : bond 0.00792 ( 14) metal coordination : angle 4.99550 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7884.05 seconds wall clock time: 134 minutes 47.52 seconds (8087.52 seconds total)