Starting phenix.real_space_refine on Sat Sep 12 17:57:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d9g_27261/09_2026/8d9g_27261.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d9g_27261/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d9g_27261/09_2026/8d9g_27261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d9g_27261/09_2026/8d9g_27261.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8d9g_27261/09_2026/8d9g_27261.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d9g_27261/09_2026/8d9g_27261.cif" model { file = "/net/cci-nas-00/data/ceres_data/8d9g_27261/09_2026/8d9g_27261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d9g_27261/09_2026/8d9g_27261.cif" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: 3.61, per 1000 atoms: 0.21 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: 1.61 Conformation dependent library (CDL) restraints added in 718.3 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: 2.23 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: 3.96 Time building geometry restraints manager: 2.09 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: 23260 2.26 - 4.52: 719 4.52 - 6.78: 96 6.78 - 9.03: 8 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=" 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 angle pdb=" C LEU A 598 " pdb=" N LYS A 599 " pdb=" CA LYS A 599 " ideal model delta sigma weight residual 121.54 128.47 -6.93 1.91e+00 2.74e-01 1.32e+01 angle pdb=" O3' A C 28 " pdb=" C3' A C 28 " pdb=" C2' A C 28 " ideal model delta sigma weight residual 113.80 106.78 7.02 2.00e+00 2.50e-01 1.23e+01 ... (remaining 24080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 8761 17.71 - 35.41: 1224 35.41 - 53.12: 336 53.12 - 70.83: 133 70.83 - 88.53: 35 Dihedral angle restraints: 10489 sinusoidal: 4820 harmonic: 5669 Sorted by residual: dihedral pdb=" C4' A C 33 " pdb=" C3' A C 33 " pdb=" C2' A C 33 " pdb=" C1' A C 33 " ideal model delta sinusoidal sigma weight residual 36.34 -40.02 76.37 1 3.10e+00 1.04e-01 7.64e+02 dihedral pdb=" C4' G C 26 " pdb=" C3' G C 26 " pdb=" C2' G C 26 " pdb=" C1' G C 26 " ideal model delta sinusoidal sigma weight residual 36.34 -39.46 75.81 1 3.10e+00 1.04e-01 7.54e+02 dihedral pdb=" C4' A C 28 " pdb=" C3' A C 28 " pdb=" C2' A C 28 " pdb=" C1' A C 28 " ideal model delta sinusoidal sigma weight residual 36.34 -39.24 75.58 1 3.10e+00 1.04e-01 7.50e+02 ... (remaining 10486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2126 0.073 - 0.146: 374 0.146 - 0.218: 58 0.218 - 0.291: 46 0.291 - 0.364: 16 Chirality restraints: 2620 Sorted by residual: chirality pdb=" C2' C C 38 " pdb=" C3' C C 38 " pdb=" O2' C C 38 " pdb=" C1' C C 38 " both_signs ideal model delta sigma weight residual False -2.79 -2.43 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" C3' A C 28 " pdb=" C4' A C 28 " pdb=" O3' A C 28 " pdb=" C2' A C 28 " both_signs ideal model delta sigma weight residual False -2.50 -2.84 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C3' G C 40 " pdb=" C4' G C 40 " pdb=" O3' G C 40 " pdb=" C2' G C 40 " both_signs ideal model delta sigma weight residual False -2.50 -2.84 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 2617 not shown) Planarity restraints: 2884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C C 38 " 0.045 2.00e-02 2.50e+03 2.29e-02 1.18e+01 pdb=" N1 C C 38 " -0.048 2.00e-02 2.50e+03 pdb=" C2 C C 38 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C C 38 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C C 38 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C C 38 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C C 38 " 0.015 2.00e-02 2.50e+03 pdb=" C5 C C 38 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C C 38 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 28 " 0.033 2.00e-02 2.50e+03 1.73e-02 8.26e+00 pdb=" N9 A C 28 " -0.045 2.00e-02 2.50e+03 pdb=" C8 A C 28 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A C 28 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A C 28 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A C 28 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A C 28 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A C 28 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A C 28 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A C 28 " -0.008 2.00e-02 2.50e+03 pdb=" C4 A C 28 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 40 " 0.033 2.00e-02 2.50e+03 1.63e-02 7.94e+00 pdb=" N9 G C 40 " -0.044 2.00e-02 2.50e+03 pdb=" C8 G C 40 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G C 40 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G C 40 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G C 40 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G C 40 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G C 40 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G C 40 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G C 40 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G C 40 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G C 40 " -0.006 2.00e-02 2.50e+03 ... (remaining 2881 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 241 2.61 - 3.18: 15249 3.18 - 3.75: 27244 3.75 - 4.33: 40035 4.33 - 4.90: 63007 Nonbonded interactions: 145776 Sorted by model distance: nonbonded pdb=" O ASP B 796 " pdb=" O2' C D 26 " model vdw 2.036 3.040 nonbonded pdb=" O PHE A 122 " pdb=" OG SER A 126 " model vdw 2.100 3.040 nonbonded pdb=" OD2 ASP B 681 " pdb=" OG SER B 684 " model vdw 2.115 3.040 nonbonded pdb=" O GLU B1455 " pdb=" O2' C C 42 " model vdw 2.131 3.040 nonbonded pdb=" NH1 ARG B 299 " pdb=" OE2 GLU B 355 " model vdw 2.160 3.120 ... (remaining 145771 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.680 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:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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= 0.492 Angle : 1.050 41.917 24103 Z= 0.495 Chirality : 0.070 0.364 2620 Planarity : 0.005 0.043 2884 Dihedral : 18.772 88.534 6845 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/Z covalent geometry : bond 0.01039 / 0.45 (17652) covalent geometry : angle 0.92799 / 0.49 (24085) hydrogen bonds : bond 0.15603 / 10.34 ( 671) hydrogen bonds : angle 6.78837 / 4.90 ( 1938) metal coordination : bond 0.19822 / 9.64 ( 14) metal coordination : angle 17.98042 / 10.26 ( 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 : 0.637 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: 0.6271 time to fit residues: 287.0411 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 : 0.655 ------------------------------------------------------------------------------- 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... A 109 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 450 HIS B 614 ASN B 896 ASN ** B 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 ASN B1005 HIS ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1571 ASN ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1684 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.171179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.121517 restraints weight = 20174.955| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.19 r_work: 0.3408 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17666 Z= 0.173 Angle : 0.981 21.999 24103 Z= 0.426 Chirality : 0.096 1.320 2620 Planarity : 0.004 0.045 2884 Dihedral : 13.121 161.883 2890 Min Nonbonded Distance : 1.567 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.40 % Favored : 95.55 % Rotamer: Outliers : 3.47 % Allowed : 21.92 % Favored : 74.61 % 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: -0.63 (0.18), residues: 1953 helix: 0.65 (0.19), residues: 713 sheet: -0.46 (0.30), residues: 242 loop : -1.19 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 59 TYR 0.017 0.001 TYR B 13 PHE 0.017 0.002 PHE A 348 TRP 0.012 0.001 TRP B 607 HIS 0.006 0.001 HIS B 903 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (17652) covalent geometry : angle 0.96755 / 0.43 (24085) hydrogen bonds : bond 0.04545 / 3.03 ( 671) hydrogen bonds : angle 4.77045 / 3.46 ( 1938) metal coordination : bond 0.01639 / 1.01 ( 14) metal coordination : angle 6.00582 / 3.47 ( 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 259 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 199 time to evaluate : 0.638 Fit side-chains REVERT: A 88 THR cc_start: 0.7032 (p) cc_final: 0.6712 (t) REVERT: A 180 MET cc_start: 0.8721 (mmm) cc_final: 0.8520 (mmm) REVERT: A 216 MET cc_start: 0.7032 (tpt) cc_final: 0.6731 (tpt) REVERT: A 254 PHE cc_start: 0.8439 (m-10) cc_final: 0.8211 (m-10) REVERT: A 587 GLU cc_start: 0.7020 (pt0) cc_final: 0.6775 (pm20) REVERT: A 686 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7031 (mt-10) REVERT: A 690 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7452 (pp20) REVERT: B 68 GLU cc_start: 0.8283 (tt0) cc_final: 0.7890 (mt-10) REVERT: B 118 LYS cc_start: 0.7917 (mtmt) cc_final: 0.7700 (mttm) REVERT: B 162 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8301 (tp) REVERT: B 235 ILE cc_start: 0.8445 (pt) cc_final: 0.8098 (pt) REVERT: B 339 LYS cc_start: 0.8006 (mtmt) cc_final: 0.7753 (mtpp) REVERT: B 460 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: B 499 LYS cc_start: 0.8461 (mmtm) cc_final: 0.7730 (mtmt) REVERT: B 639 ASP cc_start: 0.8160 (m-30) cc_final: 0.7929 (m-30) REVERT: B 981 ASN cc_start: 0.6910 (OUTLIER) cc_final: 0.6194 (p0) REVERT: B 1516 ASP cc_start: 0.8435 (m-30) cc_final: 0.8107 (m-30) REVERT: B 1597 SER cc_start: 0.8512 (t) cc_final: 0.8150 (t) REVERT: B 1618 ASP cc_start: 0.7810 (t0) cc_final: 0.7315 (t70) REVERT: B 1639 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7225 (pmm-80) REVERT: B 1660 LYS cc_start: 0.6331 (tptt) cc_final: 0.6087 (tmtm) outliers start: 60 outliers final: 24 residues processed: 245 average time/residue: 0.6269 time to fit residues: 171.3524 Evaluate side-chains 199 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 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 29 SER Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1453 VAL 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: 3.9990 chunk 123 optimal weight: 4.9990 chunk 35 optimal weight: 0.0040 chunk 85 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 ASN A 183 HIS A 476 ASN A 551 GLN A 553 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN B 155 HIS ** B 919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1603 GLN B1630 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.163043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.111609 restraints weight = 20334.048| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.22 r_work: 0.3286 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17666 Z= 0.204 Angle : 0.873 20.188 24103 Z= 0.395 Chirality : 0.082 1.281 2620 Planarity : 0.004 0.047 2884 Dihedral : 13.269 158.349 2857 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.76 % Favored : 95.19 % Rotamer: Outliers : 3.64 % Allowed : 22.44 % Favored : 73.92 % 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: -0.08 (0.19), residues: 1953 helix: 1.16 (0.19), residues: 723 sheet: -0.11 (0.32), residues: 248 loop : -0.96 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 471 TYR 0.019 0.002 TYR A 704 PHE 0.016 0.002 PHE A 594 TRP 0.016 0.001 TRP A 675 HIS 0.005 0.001 HIS B 784 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (17652) covalent geometry : angle 0.85955 / 0.39 (24085) hydrogen bonds : bond 0.04339 / 2.90 ( 671) hydrogen bonds : angle 4.47796 / 3.25 ( 1938) metal coordination : bond 0.00940 / 0.61 ( 14) metal coordination : angle 5.60189 / 3.14 ( 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: 63 poor density : 187 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 88 THR cc_start: 0.7234 (p) cc_final: 0.6930 (t) REVERT: A 180 MET cc_start: 0.8782 (mmm) cc_final: 0.8295 (mmm) REVERT: A 189 LYS cc_start: 0.8435 (tmtt) cc_final: 0.8180 (tmmm) REVERT: A 675 TRP cc_start: 0.7610 (t60) cc_final: 0.7342 (t60) REVERT: A 686 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7183 (mt-10) REVERT: A 690 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7318 (pp20) REVERT: A 697 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6900 (pmtt) REVERT: B 31 MET cc_start: 0.9226 (mmm) cc_final: 0.8975 (mmm) REVERT: B 118 LYS cc_start: 0.8100 (mtmt) cc_final: 0.7591 (tptt) REVERT: B 193 ASP cc_start: 0.8348 (t0) cc_final: 0.8090 (t0) REVERT: B 213 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8591 (tttt) REVERT: B 235 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8299 (pp) REVERT: B 309 ASP cc_start: 0.7737 (m-30) cc_final: 0.7493 (m-30) REVERT: B 339 LYS cc_start: 0.8174 (mtmt) cc_final: 0.7869 (tttm) REVERT: B 368 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: B 437 LYS cc_start: 0.7657 (mppt) cc_final: 0.7173 (mmmt) REVERT: B 499 LYS cc_start: 0.8532 (mmtm) cc_final: 0.8105 (mmmt) REVERT: B 504 MET cc_start: 0.9259 (mmm) cc_final: 0.8975 (mmm) REVERT: B 625 LYS cc_start: 0.8363 (mtmm) cc_final: 0.7781 (mttm) REVERT: B 639 ASP cc_start: 0.8537 (m-30) cc_final: 0.7775 (t70) REVERT: B 756 GLU cc_start: 0.7934 (mp0) cc_final: 0.7710 (mm-30) REVERT: B 837 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8441 (tt) REVERT: B 981 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7413 (p0) REVERT: B 1396 LYS cc_start: 0.7981 (tppt) cc_final: 0.7405 (ttpp) REVERT: B 1455 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6870 (mm-30) REVERT: B 1458 ARG cc_start: 0.8462 (mtp180) cc_final: 0.7942 (mtp180) REVERT: B 1469 GLU cc_start: 0.7879 (pm20) cc_final: 0.7668 (pm20) REVERT: B 1502 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.7635 (t) REVERT: B 1524 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8060 (mt-10) REVERT: B 1569 SER cc_start: 0.6711 (OUTLIER) cc_final: 0.6133 (p) REVERT: B 1610 GLN cc_start: 0.8282 (mm-40) cc_final: 0.8028 (mm-40) REVERT: B 1618 ASP cc_start: 0.7979 (t0) cc_final: 0.7356 (t70) outliers start: 63 outliers final: 18 residues processed: 231 average time/residue: 0.6087 time to fit residues: 157.0685 Evaluate side-chains 183 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 551 GLN Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 690 GLU 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 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 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 1419 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 140 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 0.1980 chunk 131 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 19 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 190 optimal weight: 40.0000 chunk 109 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN A 592 ASN A 602 ASN B 155 HIS 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** ** 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 = 0.4011 r_free = 0.4011 target = 0.166555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.116098 restraints weight = 20361.939| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.23 r_work: 0.3346 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17666 Z= 0.126 Angle : 0.740 11.396 24103 Z= 0.339 Chirality : 0.067 0.769 2620 Planarity : 0.004 0.048 2884 Dihedral : 13.132 165.926 2846 Min Nonbonded Distance : 1.612 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.15 % Favored : 95.80 % Rotamer: Outliers : 3.01 % Allowed : 22.67 % Favored : 74.32 % 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: 0.25 (0.19), residues: 1953 helix: 1.52 (0.20), residues: 722 sheet: 0.19 (0.32), residues: 236 loop : -0.86 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 140 TYR 0.018 0.001 TYR A 607 PHE 0.024 0.001 PHE B 453 TRP 0.011 0.001 TRP B 607 HIS 0.004 0.001 HIS B 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (17652) covalent geometry : angle 0.73252 / 0.34 (24085) hydrogen bonds : bond 0.03549 / 2.37 ( 671) hydrogen bonds : angle 4.21241 / 3.06 ( 1938) metal coordination : bond 0.00623 / 0.39 ( 14) metal coordination : angle 3.81651 / 2.18 ( 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 235 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 88 THR cc_start: 0.7052 (p) cc_final: 0.6781 (t) REVERT: A 180 MET cc_start: 0.8750 (mmm) cc_final: 0.8259 (mmm) REVERT: A 189 LYS cc_start: 0.8357 (tmtt) cc_final: 0.8079 (tmmm) REVERT: A 216 MET cc_start: 0.7226 (tpt) cc_final: 0.6867 (tpt) REVERT: A 331 MET cc_start: 0.4695 (tpt) cc_final: 0.3635 (mmt) REVERT: A 594 PHE cc_start: 0.7150 (OUTLIER) cc_final: 0.6945 (t80) REVERT: A 597 MET cc_start: 0.2746 (mpt) cc_final: 0.2096 (ptp) REVERT: A 630 ASP cc_start: 0.7444 (t0) cc_final: 0.7100 (t0) REVERT: A 639 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6824 (ptm) REVERT: A 686 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7163 (mt-10) REVERT: B 11 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8695 (pt0) REVERT: B 31 MET cc_start: 0.9211 (mmm) cc_final: 0.8866 (mmm) REVERT: B 93 LYS cc_start: 0.8703 (mptp) cc_final: 0.8003 (ttpp) REVERT: B 118 LYS cc_start: 0.7980 (mtmt) cc_final: 0.7711 (mtpt) REVERT: B 207 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7871 (mpt-90) REVERT: B 235 ILE cc_start: 0.8764 (pt) cc_final: 0.8393 (pp) REVERT: B 309 ASP cc_start: 0.7621 (m-30) cc_final: 0.7402 (m-30) REVERT: B 339 LYS cc_start: 0.8030 (mtmt) cc_final: 0.7720 (mttm) REVERT: B 460 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8416 (mm-30) REVERT: B 499 LYS cc_start: 0.8479 (mmtm) cc_final: 0.8044 (mmmt) REVERT: B 625 LYS cc_start: 0.8219 (mtmm) cc_final: 0.7601 (mttm) REVERT: B 639 ASP cc_start: 0.8519 (m-30) cc_final: 0.7701 (t70) REVERT: B 740 GLU cc_start: 0.6939 (tp30) cc_final: 0.6678 (tp30) REVERT: B 745 CYS cc_start: 0.6033 (p) cc_final: 0.5299 (p) REVERT: B 756 GLU cc_start: 0.7851 (mp0) cc_final: 0.7579 (mm-30) REVERT: B 981 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.7503 (p0) REVERT: B 1396 LYS cc_start: 0.7869 (tppt) cc_final: 0.7332 (ttpp) REVERT: B 1455 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6940 (mm-30) REVERT: B 1458 ARG cc_start: 0.8404 (mtp180) cc_final: 0.8003 (mtp180) REVERT: B 1502 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.7687 (t) REVERT: B 1569 SER cc_start: 0.6721 (OUTLIER) cc_final: 0.6142 (p) REVERT: B 1610 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7955 (mm-40) REVERT: B 1639 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7220 (pmm-80) outliers start: 52 outliers final: 21 residues processed: 221 average time/residue: 0.6366 time to fit residues: 156.5432 Evaluate side-chains 194 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 225 TYR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 22 ASP 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 460 GLU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 981 ASN 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 1507 MET Chi-restraints excluded: chain B residue 1569 SER 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: 0.8980 chunk 127 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 181 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN A 553 ASN A 585 HIS B 155 HIS B 429 GLN ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1591 GLN ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1684 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.159944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111463 restraints weight = 20197.362| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.13 r_work: 0.3237 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 17666 Z= 0.242 Angle : 0.855 16.984 24103 Z= 0.391 Chirality : 0.081 1.101 2620 Planarity : 0.005 0.055 2884 Dihedral : 13.346 177.528 2844 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.11 % Allowed : 22.09 % Favored : 73.80 % 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: 0.04 (0.19), residues: 1953 helix: 1.26 (0.19), residues: 723 sheet: -0.00 (0.32), residues: 259 loop : -0.90 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 140 TYR 0.023 0.002 TYR A 704 PHE 0.018 0.002 PHE B 187 TRP 0.018 0.002 TRP A 675 HIS 0.005 0.001 HIS A 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.24 (17652) covalent geometry : angle 0.84388 / 0.39 (24085) hydrogen bonds : bond 0.04377 / 2.95 ( 671) hydrogen bonds : angle 4.46840 / 3.24 ( 1938) metal coordination : bond 0.00958 / 0.64 ( 14) metal coordination : angle 5.18981 / 2.93 ( 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 250 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 179 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 THR cc_start: 0.7117 (p) cc_final: 0.6836 (t) REVERT: A 180 MET cc_start: 0.8765 (mmm) cc_final: 0.8357 (mmm) REVERT: A 189 LYS cc_start: 0.8362 (tmtt) cc_final: 0.8028 (pttp) REVERT: A 216 MET cc_start: 0.7220 (tpt) cc_final: 0.6761 (tpt) REVERT: A 331 MET cc_start: 0.4747 (tpt) cc_final: 0.4090 (tpt) REVERT: A 578 ARG cc_start: 0.6774 (ttm-80) cc_final: 0.6516 (ttt-90) REVERT: A 597 MET cc_start: 0.2917 (mpt) cc_final: 0.2052 (ptp) REVERT: A 630 ASP cc_start: 0.7879 (t0) cc_final: 0.7222 (t0) REVERT: A 686 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7368 (mt-10) REVERT: B 11 GLU cc_start: 0.9337 (OUTLIER) cc_final: 0.9006 (pt0) REVERT: B 31 MET cc_start: 0.9316 (mmm) cc_final: 0.8935 (mmm) REVERT: B 118 LYS cc_start: 0.8011 (mtmt) cc_final: 0.7644 (tptt) REVERT: B 127 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8138 (mp) REVERT: B 235 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8425 (pp) REVERT: B 309 ASP cc_start: 0.7631 (m-30) cc_final: 0.7334 (m-30) REVERT: B 339 LYS cc_start: 0.8176 (mtmt) cc_final: 0.7878 (mttm) REVERT: B 340 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: B 368 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7114 (mm-30) REVERT: B 437 LYS cc_start: 0.7634 (mppt) cc_final: 0.7363 (mptt) REVERT: B 499 LYS cc_start: 0.8535 (mmtm) cc_final: 0.8142 (mmmt) REVERT: B 612 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7365 (mtpp) REVERT: B 625 LYS cc_start: 0.8438 (mtmm) cc_final: 0.7840 (mttm) REVERT: B 639 ASP cc_start: 0.8598 (m-30) cc_final: 0.7858 (t70) REVERT: B 649 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: B 712 GLU cc_start: 0.8088 (pm20) cc_final: 0.7814 (pm20) REVERT: B 740 GLU cc_start: 0.7016 (tp30) cc_final: 0.6730 (tp30) REVERT: B 745 CYS cc_start: 0.6503 (p) cc_final: 0.6168 (p) REVERT: B 756 GLU cc_start: 0.8076 (mp0) cc_final: 0.7790 (mm-30) REVERT: B 927 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7656 (tmtt) REVERT: B 973 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7834 (mt0) REVERT: B 1396 LYS cc_start: 0.7977 (tppt) cc_final: 0.7443 (ttpp) REVERT: B 1455 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7089 (mm-30) REVERT: B 1458 ARG cc_start: 0.8573 (mtp180) cc_final: 0.8216 (mtp180) REVERT: B 1483 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6432 (mtt180) REVERT: B 1499 GLU cc_start: 0.8417 (pm20) cc_final: 0.8163 (pm20) REVERT: B 1502 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.7871 (t) REVERT: B 1569 SER cc_start: 0.6769 (OUTLIER) cc_final: 0.6175 (p) REVERT: B 1619 LYS cc_start: 0.7483 (mtpp) cc_final: 0.7257 (mttp) REVERT: B 1670 LYS cc_start: 0.8468 (mttp) cc_final: 0.7707 (mppt) outliers start: 71 outliers final: 27 residues processed: 227 average time/residue: 0.6424 time to fit residues: 162.7004 Evaluate side-chains 202 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 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 665 ARG Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 80 VAL 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 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 612 LYS Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 973 GLN Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1419 ASP 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 1504 THR Chi-restraints excluded: chain B residue 1558 LYS Chi-restraints excluded: chain B residue 1569 SER Chi-restraints excluded: chain B residue 1629 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 89 optimal weight: 0.5980 chunk 194 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 199 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 171 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN A 480 ASN B 155 HIS ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 ASN B 973 GLN B 981 ASN ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1487 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.162259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.111156 restraints weight = 20133.998| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.21 r_work: 0.3282 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17666 Z= 0.160 Angle : 0.761 12.686 24103 Z= 0.348 Chirality : 0.070 0.833 2620 Planarity : 0.004 0.047 2884 Dihedral : 13.263 173.818 2842 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.24 % Allowed : 23.60 % Favored : 73.16 % 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: 0.26 (0.19), residues: 1953 helix: 1.47 (0.19), residues: 722 sheet: 0.39 (0.33), residues: 243 loop : -0.88 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 140 TYR 0.019 0.001 TYR A 607 PHE 0.023 0.001 PHE B 453 TRP 0.021 0.001 TRP A 675 HIS 0.004 0.001 HIS B 784 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (17652) covalent geometry : angle 0.75176 / 0.35 (24085) hydrogen bonds : bond 0.03784 / 2.54 ( 671) hydrogen bonds : angle 4.27835 / 3.10 ( 1938) metal coordination : bond 0.00724 / 0.47 ( 14) metal coordination : angle 4.30732 / 2.46 ( 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 235 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 88 THR cc_start: 0.7110 (p) cc_final: 0.6830 (t) REVERT: A 180 MET cc_start: 0.8728 (mmm) cc_final: 0.8312 (mmm) REVERT: A 189 LYS cc_start: 0.8262 (tmtt) cc_final: 0.8048 (tmmm) REVERT: A 597 MET cc_start: 0.2609 (OUTLIER) cc_final: 0.1809 (ptp) REVERT: A 630 ASP cc_start: 0.7479 (t0) cc_final: 0.6994 (t0) REVERT: A 639 MET cc_start: 0.7027 (OUTLIER) cc_final: 0.6816 (ptm) REVERT: A 686 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7274 (mt-10) REVERT: A 690 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7170 (pp20) REVERT: B 11 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8875 (pt0) REVERT: B 26 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8111 (mmtt) REVERT: B 31 MET cc_start: 0.9233 (mmm) cc_final: 0.8847 (mmm) REVERT: B 93 LYS cc_start: 0.8798 (mptp) cc_final: 0.8091 (ttpp) REVERT: B 118 LYS cc_start: 0.7963 (mtmt) cc_final: 0.7601 (tppt) REVERT: B 127 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8137 (mp) REVERT: B 235 ILE cc_start: 0.8804 (pt) cc_final: 0.8409 (pp) REVERT: B 309 ASP cc_start: 0.7671 (m-30) cc_final: 0.7364 (m-30) REVERT: B 339 LYS cc_start: 0.8092 (mtmt) cc_final: 0.7790 (mttm) REVERT: B 340 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7116 (tt0) REVERT: B 375 ARG cc_start: 0.7762 (ttm110) cc_final: 0.7456 (mtm-85) REVERT: B 404 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7675 (tp30) REVERT: B 437 LYS cc_start: 0.7510 (mppt) cc_final: 0.7243 (mptt) REVERT: B 625 LYS cc_start: 0.8239 (mtmm) cc_final: 0.7643 (mttm) REVERT: B 639 ASP cc_start: 0.8534 (m-30) cc_final: 0.7772 (t70) REVERT: B 649 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: B 712 GLU cc_start: 0.8022 (pm20) cc_final: 0.7756 (pm20) REVERT: B 740 GLU cc_start: 0.7074 (tp30) cc_final: 0.6752 (tp30) REVERT: B 743 GLU cc_start: 0.5234 (OUTLIER) cc_final: 0.4178 (tm-30) REVERT: B 756 GLU cc_start: 0.8021 (mp0) cc_final: 0.7703 (mm-30) REVERT: B 1396 LYS cc_start: 0.7906 (tppt) cc_final: 0.7394 (ttpp) REVERT: B 1447 ARG cc_start: 0.8076 (ttp-170) cc_final: 0.7862 (ptt-90) REVERT: B 1455 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6948 (mm-30) REVERT: B 1458 ARG cc_start: 0.8517 (mtp180) cc_final: 0.8013 (mtp180) REVERT: B 1483 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6516 (mtt180) REVERT: B 1499 GLU cc_start: 0.8394 (pm20) cc_final: 0.8126 (pm20) REVERT: B 1502 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.7931 (t) REVERT: B 1583 ARG cc_start: 0.7851 (mpt180) cc_final: 0.7382 (mmt180) REVERT: B 1619 LYS cc_start: 0.7357 (mtpp) cc_final: 0.7150 (mttp) REVERT: B 1670 LYS cc_start: 0.8412 (mttp) cc_final: 0.7657 (mppt) outliers start: 56 outliers final: 21 residues processed: 217 average time/residue: 0.7216 time to fit residues: 173.7538 Evaluate side-chains 199 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 476 ASN Chi-restraints excluded: chain A residue 491 PHE 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 690 GLU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 26 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 270 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 340 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 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 927 LYS Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1419 ASP 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 1629 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 123 optimal weight: 3.9990 chunk 133 optimal weight: 0.2980 chunk 112 optimal weight: 1.9990 chunk 32 optimal weight: 30.0000 chunk 173 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 62 optimal weight: 0.0070 chunk 166 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 0.0170 chunk 91 optimal weight: 1.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 ASN B 155 HIS ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 981 ASN ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.166256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.115626 restraints weight = 19858.891| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.23 r_work: 0.3321 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17666 Z= 0.117 Angle : 0.708 10.770 24103 Z= 0.326 Chirality : 0.063 0.745 2620 Planarity : 0.004 0.042 2884 Dihedral : 13.054 174.326 2842 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.43 % Allowed : 24.58 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z 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: 0.51 (0.19), residues: 1953 helix: 1.68 (0.20), residues: 724 sheet: 0.53 (0.33), residues: 237 loop : -0.72 (0.19), residues: 992 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 0.011 0.001 PHE A 703 TRP 0.025 0.001 TRP A 675 HIS 0.004 0.001 HIS B1616 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (17652) covalent geometry : angle 0.70209 / 0.33 (24085) hydrogen bonds : bond 0.03443 / 2.28 ( 671) hydrogen bonds : angle 4.08035 / 2.95 ( 1938) metal coordination : bond 0.00534 / 0.31 ( 14) metal coordination : angle 3.42106 / 1.97 ( 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: 42 poor density : 184 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 88 THR cc_start: 0.7228 (p) cc_final: 0.7008 (t) REVERT: A 180 MET cc_start: 0.8683 (mmm) cc_final: 0.8279 (mmm) REVERT: A 189 LYS cc_start: 0.7978 (tmtt) cc_final: 0.7762 (tmmm) REVERT: A 216 MET cc_start: 0.7507 (tpt) cc_final: 0.7158 (tpt) REVERT: A 590 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6515 (ttm) REVERT: A 597 MET cc_start: 0.2673 (OUTLIER) cc_final: 0.1612 (ptm) REVERT: A 630 ASP cc_start: 0.7169 (t0) cc_final: 0.6799 (t0) REVERT: A 683 LYS cc_start: 0.6638 (mmtt) cc_final: 0.6177 (mmtt) REVERT: A 686 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7199 (mt-10) REVERT: B 11 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8450 (pt0) REVERT: B 31 MET cc_start: 0.9223 (mmm) cc_final: 0.8834 (mmm) REVERT: B 68 GLU cc_start: 0.8378 (tt0) cc_final: 0.8026 (mt-10) REVERT: B 93 LYS cc_start: 0.8817 (mptp) cc_final: 0.8066 (ttpp) REVERT: B 118 LYS cc_start: 0.7972 (mtmt) cc_final: 0.7592 (tptt) REVERT: B 127 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8082 (mp) REVERT: B 235 ILE cc_start: 0.8760 (pt) cc_final: 0.8496 (pt) REVERT: B 309 ASP cc_start: 0.7670 (m-30) cc_final: 0.7398 (m-30) REVERT: B 339 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7704 (mttm) REVERT: B 375 ARG cc_start: 0.7803 (ttm110) cc_final: 0.7535 (mtm-85) REVERT: B 404 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7672 (tp30) REVERT: B 437 LYS cc_start: 0.7410 (mppt) cc_final: 0.7155 (mptt) REVERT: B 460 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8317 (mm-30) REVERT: B 625 LYS cc_start: 0.8122 (mtmm) cc_final: 0.7598 (mttm) REVERT: B 639 ASP cc_start: 0.8466 (m-30) cc_final: 0.7657 (t70) REVERT: B 740 GLU cc_start: 0.7080 (tp30) cc_final: 0.6837 (tp30) REVERT: B 745 CYS cc_start: 0.6499 (p) cc_final: 0.5847 (p) REVERT: B 756 GLU cc_start: 0.7896 (mp0) cc_final: 0.7579 (mm-30) REVERT: B 954 GLU cc_start: 0.8133 (tt0) cc_final: 0.7829 (tm-30) REVERT: B 1396 LYS cc_start: 0.7809 (tppt) cc_final: 0.7277 (ttpp) REVERT: B 1455 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6913 (mm-30) REVERT: B 1458 ARG cc_start: 0.8540 (mtp180) cc_final: 0.8088 (mtp180) REVERT: B 1499 GLU cc_start: 0.8410 (pm20) cc_final: 0.8129 (pm20) REVERT: B 1502 VAL cc_start: 0.8336 (OUTLIER) cc_final: 0.7869 (t) REVERT: B 1583 ARG cc_start: 0.7778 (mpt180) cc_final: 0.7324 (mmt180) REVERT: B 1619 LYS cc_start: 0.7310 (mtpp) cc_final: 0.7074 (mttp) REVERT: B 1670 LYS cc_start: 0.8379 (mttp) cc_final: 0.7616 (mppt) outliers start: 42 outliers final: 20 residues processed: 213 average time/residue: 0.6702 time to fit residues: 159.6862 Evaluate side-chains 198 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 337 SER Chi-restraints excluded: chain A residue 476 ASN 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 711 SER Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 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: 0.0470 chunk 32 optimal weight: 0.0770 chunk 141 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 181 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 198 optimal weight: 9.9990 overall best weight: 0.5836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN A 230 HIS A 476 ASN A 575 ASN B 155 HIS ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 981 ASN ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.166258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114468 restraints weight = 20000.587| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.28 r_work: 0.3306 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4833 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= 0.117 Angle : 0.702 10.305 24103 Z= 0.323 Chirality : 0.062 0.726 2620 Planarity : 0.004 0.043 2884 Dihedral : 12.942 174.622 2842 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.14 % Allowed : 25.45 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z 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: 0.62 (0.19), residues: 1953 helix: 1.78 (0.20), residues: 724 sheet: 0.49 (0.33), residues: 244 loop : -0.64 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 733 TYR 0.016 0.001 TYR A 607 PHE 0.022 0.001 PHE A 184 TRP 0.031 0.001 TRP A 675 HIS 0.003 0.001 HIS B1616 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (17652) covalent geometry : angle 0.69564 / 0.32 (24085) hydrogen bonds : bond 0.03396 / 2.26 ( 671) hydrogen bonds : angle 3.99861 / 2.90 ( 1938) metal coordination : bond 0.00531 / 0.32 ( 14) metal coordination : angle 3.47107 / 1.99 ( 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: 37 poor density : 185 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 88 THR cc_start: 0.7278 (p) cc_final: 0.7023 (t) REVERT: A 180 MET cc_start: 0.8673 (mmm) cc_final: 0.8385 (mmm) REVERT: A 534 ASP cc_start: 0.6778 (t0) cc_final: 0.6539 (m-30) REVERT: A 574 ARG cc_start: 0.6822 (tpp-160) cc_final: 0.6471 (mpp-170) REVERT: A 590 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6389 (ttm) REVERT: A 597 MET cc_start: 0.2255 (OUTLIER) cc_final: 0.1100 (ptm) REVERT: A 630 ASP cc_start: 0.7112 (t0) cc_final: 0.6788 (t0) REVERT: A 683 LYS cc_start: 0.6563 (mmtt) cc_final: 0.6108 (mmtt) REVERT: A 686 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7267 (mt-10) REVERT: B 11 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8631 (pt0) REVERT: B 31 MET cc_start: 0.9193 (mmm) cc_final: 0.8810 (mmm) REVERT: B 68 GLU cc_start: 0.8409 (tt0) cc_final: 0.8059 (mt-10) REVERT: B 93 LYS cc_start: 0.8789 (mptp) cc_final: 0.8029 (ttpp) REVERT: B 118 LYS cc_start: 0.7995 (mtmt) cc_final: 0.7602 (tptt) REVERT: B 207 ARG cc_start: 0.8136 (ttm-80) cc_final: 0.7861 (mpt-90) REVERT: B 235 ILE cc_start: 0.8758 (pt) cc_final: 0.8480 (pt) REVERT: B 309 ASP cc_start: 0.7687 (m-30) cc_final: 0.7383 (m-30) REVERT: B 339 LYS cc_start: 0.8027 (mtmt) cc_final: 0.7693 (mttm) REVERT: B 375 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7562 (mtm-85) REVERT: B 404 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7672 (tp30) REVERT: B 437 LYS cc_start: 0.7283 (mppt) cc_final: 0.7038 (mptt) REVERT: B 460 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8118 (mm-30) REVERT: B 499 LYS cc_start: 0.8439 (mmtm) cc_final: 0.7940 (mmmt) REVERT: B 625 LYS cc_start: 0.8067 (mtmm) cc_final: 0.7493 (mttm) REVERT: B 639 ASP cc_start: 0.8471 (m-30) cc_final: 0.7651 (t70) REVERT: B 740 GLU cc_start: 0.7070 (tp30) cc_final: 0.6810 (tp30) REVERT: B 756 GLU cc_start: 0.7899 (mp0) cc_final: 0.7583 (mm-30) REVERT: B 954 GLU cc_start: 0.8121 (tt0) cc_final: 0.7816 (tm-30) REVERT: B 1396 LYS cc_start: 0.7801 (tppt) cc_final: 0.7263 (ttpp) REVERT: B 1455 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6731 (mm-30) REVERT: B 1458 ARG cc_start: 0.8413 (mtp180) cc_final: 0.7953 (mtp180) REVERT: B 1499 GLU cc_start: 0.8486 (pm20) cc_final: 0.8106 (pm20) REVERT: B 1502 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.7867 (t) REVERT: B 1569 SER cc_start: 0.6687 (OUTLIER) cc_final: 0.6045 (p) REVERT: B 1583 ARG cc_start: 0.7785 (mpt180) cc_final: 0.7319 (mmt180) REVERT: B 1619 LYS cc_start: 0.7390 (mtpp) cc_final: 0.7162 (mttp) REVERT: B 1639 ARG cc_start: 0.7936 (mtp180) cc_final: 0.7580 (pmm-80) REVERT: B 1670 LYS cc_start: 0.8377 (mttp) cc_final: 0.7559 (mppt) outliers start: 37 outliers final: 18 residues processed: 212 average time/residue: 0.6680 time to fit residues: 158.5959 Evaluate side-chains 191 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 337 SER 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 11 GLU Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1569 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 145 optimal weight: 0.0370 chunk 105 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 181 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 overall best weight: 1.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN A 230 HIS A 575 ASN A 585 HIS B 155 HIS ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 981 ASN ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.163476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.111597 restraints weight = 19993.260| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.24 r_work: 0.3264 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17666 Z= 0.145 Angle : 0.738 10.731 24103 Z= 0.339 Chirality : 0.067 0.787 2620 Planarity : 0.004 0.043 2884 Dihedral : 12.961 175.396 2840 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.14 % Allowed : 25.91 % Favored : 71.95 % 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: 0.61 (0.19), residues: 1953 helix: 1.73 (0.20), residues: 722 sheet: 0.58 (0.33), residues: 248 loop : -0.64 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 471 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 A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (17652) covalent geometry : angle 0.73008 / 0.34 (24085) hydrogen bonds : bond 0.03602 / 2.41 ( 671) hydrogen bonds : angle 4.10215 / 2.96 ( 1938) metal coordination : bond 0.00661 / 0.41 ( 14) metal coordination : angle 4.05875 / 2.32 ( 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 218 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 181 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 88 THR cc_start: 0.7180 (p) cc_final: 0.6901 (t) REVERT: A 180 MET cc_start: 0.8666 (mmm) cc_final: 0.8283 (mmm) REVERT: A 574 ARG cc_start: 0.6794 (tpp-160) cc_final: 0.6306 (mpp-170) REVERT: A 575 ASN cc_start: 0.7792 (m-40) cc_final: 0.7017 (t0) REVERT: A 578 ARG cc_start: 0.6668 (ttm-80) cc_final: 0.6384 (ttt-90) REVERT: A 583 LEU cc_start: 0.6294 (mp) cc_final: 0.5727 (mt) REVERT: A 590 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.6528 (ttm) REVERT: A 630 ASP cc_start: 0.7300 (t0) cc_final: 0.6947 (t0) REVERT: A 686 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7157 (mt-10) REVERT: B 11 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8683 (pt0) REVERT: B 31 MET cc_start: 0.9241 (mmm) cc_final: 0.8850 (mmm) REVERT: B 68 GLU cc_start: 0.8469 (tt0) cc_final: 0.8129 (mt-10) REVERT: B 93 LYS cc_start: 0.8797 (mptp) cc_final: 0.8036 (ttpp) REVERT: B 118 LYS cc_start: 0.7990 (mtmt) cc_final: 0.7614 (tptt) REVERT: B 127 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8149 (mp) REVERT: B 235 ILE cc_start: 0.8788 (pt) cc_final: 0.8403 (pp) REVERT: B 309 ASP cc_start: 0.7694 (m-30) cc_final: 0.7344 (m-30) REVERT: B 339 LYS cc_start: 0.8039 (mtmt) cc_final: 0.7679 (mttp) REVERT: B 375 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7509 (mtm-85) REVERT: B 404 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7629 (tp30) REVERT: B 437 LYS cc_start: 0.7293 (mppt) cc_final: 0.7039 (mptt) REVERT: B 460 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8241 (mm-30) REVERT: B 499 LYS cc_start: 0.8471 (mmtm) cc_final: 0.7913 (mmpt) REVERT: B 625 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7498 (mttm) REVERT: B 639 ASP cc_start: 0.8504 (m-30) cc_final: 0.7736 (t0) REVERT: B 740 GLU cc_start: 0.7090 (tp30) cc_final: 0.6824 (tp30) REVERT: B 756 GLU cc_start: 0.7917 (mp0) cc_final: 0.7610 (mm-30) REVERT: B 909 ASP cc_start: 0.5273 (OUTLIER) cc_final: 0.5049 (p0) REVERT: B 954 GLU cc_start: 0.8150 (tt0) cc_final: 0.7840 (tm-30) REVERT: B 1396 LYS cc_start: 0.7808 (tppt) cc_final: 0.7289 (ttpp) REVERT: B 1455 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6681 (mm-30) REVERT: B 1458 ARG cc_start: 0.8511 (mtp180) cc_final: 0.7991 (mtp180) REVERT: B 1499 GLU cc_start: 0.8585 (pm20) cc_final: 0.8205 (pm20) REVERT: B 1502 VAL cc_start: 0.8333 (OUTLIER) cc_final: 0.7946 (t) REVERT: B 1569 SER cc_start: 0.6717 (OUTLIER) cc_final: 0.6074 (p) REVERT: B 1583 ARG cc_start: 0.7825 (mpt180) cc_final: 0.7346 (mmt180) REVERT: B 1619 LYS cc_start: 0.7413 (mtpp) cc_final: 0.7163 (mttp) REVERT: B 1639 ARG cc_start: 0.8012 (mtp180) cc_final: 0.7523 (pmm-80) REVERT: B 1670 LYS cc_start: 0.8364 (mttp) cc_final: 0.7560 (mppt) outliers start: 37 outliers final: 19 residues processed: 206 average time/residue: 0.6800 time to fit residues: 156.9842 Evaluate side-chains 195 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 337 SER 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 711 SER Chi-restraints excluded: chain B residue 11 GLU 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 374 THR Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1569 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 63 optimal weight: 0.8980 chunk 59 optimal weight: 0.0070 chunk 192 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 166 optimal weight: 0.0980 chunk 47 optimal weight: 0.1980 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN A 230 HIS B 155 HIS ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN B 981 ASN ** B1443 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 = 0.3979 r_free = 0.3979 target = 0.164894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.113409 restraints weight = 19815.955| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.24 r_work: 0.3290 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17666 Z= 0.125 Angle : 0.713 10.653 24103 Z= 0.327 Chirality : 0.064 0.729 2620 Planarity : 0.004 0.046 2884 Dihedral : 12.904 174.541 2840 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.85 % Allowed : 26.32 % Favored : 71.83 % 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: 0.65 (0.19), residues: 1953 helix: 1.79 (0.20), residues: 722 sheet: 0.52 (0.32), residues: 249 loop : -0.62 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 140 TYR 0.018 0.001 TYR A 607 PHE 0.018 0.001 PHE A 184 TRP 0.041 0.001 TRP A 675 HIS 0.004 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (17652) covalent geometry : angle 0.70555 / 0.33 (24085) hydrogen bonds : bond 0.03435 / 2.29 ( 671) hydrogen bonds : angle 4.05329 / 2.93 ( 1938) metal coordination : bond 0.00586 / 0.35 ( 14) metal coordination : angle 3.74451 / 2.16 ( 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 211 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 0.682 Fit side-chains REVERT: A 61 ASP cc_start: 0.7640 (m-30) cc_final: 0.7060 (t0) REVERT: A 88 THR cc_start: 0.7266 (p) cc_final: 0.7020 (t) REVERT: A 180 MET cc_start: 0.8655 (mmm) cc_final: 0.8265 (mmm) REVERT: A 216 MET cc_start: 0.7297 (tpt) cc_final: 0.7048 (tmt) REVERT: A 225 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.7292 (m-80) REVERT: A 574 ARG cc_start: 0.6864 (tpp-160) cc_final: 0.6414 (mpp-170) REVERT: A 575 ASN cc_start: 0.7836 (m-40) cc_final: 0.7078 (t0) REVERT: A 583 LEU cc_start: 0.6296 (mp) cc_final: 0.5730 (mt) REVERT: A 590 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6477 (ttm) REVERT: A 630 ASP cc_start: 0.7217 (t0) cc_final: 0.6912 (t0) REVERT: A 686 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7192 (mt-10) REVERT: B 11 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8681 (pt0) REVERT: B 31 MET cc_start: 0.9215 (mmm) cc_final: 0.8823 (mmm) REVERT: B 68 GLU cc_start: 0.8457 (tt0) cc_final: 0.8086 (mt-10) REVERT: B 93 LYS cc_start: 0.8802 (mptp) cc_final: 0.8061 (ttpp) REVERT: B 118 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7598 (tptt) REVERT: B 127 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8090 (mp) REVERT: B 235 ILE cc_start: 0.8773 (pt) cc_final: 0.8498 (pt) REVERT: B 309 ASP cc_start: 0.7657 (m-30) cc_final: 0.7333 (m-30) REVERT: B 339 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7612 (mttp) REVERT: B 375 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7430 (mtm-85) REVERT: B 404 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7705 (tp30) REVERT: B 437 LYS cc_start: 0.7264 (mppt) cc_final: 0.7019 (mptt) REVERT: B 460 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8242 (mm-30) REVERT: B 499 LYS cc_start: 0.8456 (mmtm) cc_final: 0.7948 (mmmt) REVERT: B 625 LYS cc_start: 0.8045 (mtmm) cc_final: 0.7452 (mttm) REVERT: B 639 ASP cc_start: 0.8490 (m-30) cc_final: 0.7686 (t0) REVERT: B 740 GLU cc_start: 0.7096 (tp30) cc_final: 0.6829 (tp30) REVERT: B 756 GLU cc_start: 0.7870 (mp0) cc_final: 0.7565 (mm-30) REVERT: B 909 ASP cc_start: 0.5379 (OUTLIER) cc_final: 0.5155 (p0) REVERT: B 954 GLU cc_start: 0.8151 (tt0) cc_final: 0.7847 (tm-30) REVERT: B 1396 LYS cc_start: 0.7794 (tppt) cc_final: 0.7284 (ttpp) REVERT: B 1455 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6634 (mm-30) REVERT: B 1458 ARG cc_start: 0.8487 (mtp180) cc_final: 0.7980 (mtp180) REVERT: B 1499 GLU cc_start: 0.8566 (pm20) cc_final: 0.8203 (pm20) REVERT: B 1502 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.7952 (t) REVERT: B 1569 SER cc_start: 0.6806 (OUTLIER) cc_final: 0.6152 (p) REVERT: B 1583 ARG cc_start: 0.7756 (mpt180) cc_final: 0.7275 (mmt180) REVERT: B 1619 LYS cc_start: 0.7398 (mtpp) cc_final: 0.7150 (mttp) REVERT: B 1639 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7523 (pmm-80) REVERT: B 1670 LYS cc_start: 0.8367 (mttp) cc_final: 0.7547 (mppt) outliers start: 32 outliers final: 20 residues processed: 201 average time/residue: 0.6640 time to fit residues: 149.7795 Evaluate side-chains 200 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 337 SER 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 A residue 711 SER Chi-restraints excluded: chain B residue 11 GLU 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 374 THR Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1569 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 81 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 47 optimal weight: 0.0370 chunk 105 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN A 230 HIS B 981 ASN ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.160865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.108004 restraints weight = 20050.152| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.26 r_work: 0.3239 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17666 Z= 0.187 Angle : 0.790 13.417 24103 Z= 0.361 Chirality : 0.073 0.969 2620 Planarity : 0.004 0.044 2884 Dihedral : 13.081 174.697 2840 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.14 % Allowed : 26.49 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z 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: 1.59 (0.20), residues: 722 sheet: 0.52 (0.32), residues: 248 loop : -0.71 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 471 TYR 0.020 0.002 TYR A 704 PHE 0.018 0.002 PHE A 254 TRP 0.045 0.002 TRP A 675 HIS 0.006 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (17652) covalent geometry : angle 0.77976 / 0.36 (24085) hydrogen bonds : bond 0.03925 / 2.64 ( 671) hydrogen bonds : angle 4.26530 / 3.08 ( 1938) metal coordination : bond 0.00755 / 0.49 ( 14) metal coordination : angle 4.70049 / 2.69 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7480.46 seconds wall clock time: 128 minutes 8.48 seconds (7688.48 seconds total)