Starting phenix.real_space_refine on Sat Jul 4 01:19:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d9g_27261/07_2026/8d9g_27261.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d9g_27261/07_2026/8d9g_27261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d9g_27261/07_2026/8d9g_27261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d9g_27261/07_2026/8d9g_27261.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d9g_27261/07_2026/8d9g_27261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d9g_27261/07_2026/8d9g_27261.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8d9g_27261/07_2026/8d9g_27261.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d9g_27261/07_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-dev-6108/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: {'RNA': 36} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 10, 'rna3p_pur': 5, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 15} Chain: "D" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 498 Classifications: {'RNA': 23} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 13, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 19} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6184 SG CYS B 83 55.509 70.014 21.893 1.00 70.17 S ATOM 6455 SG CYS B 116 56.901 72.883 21.151 1.00 87.17 S ATOM 6501 SG CYS B 122 54.473 74.020 23.376 1.00 69.96 S ATOM 6525 SG CYS B 125 58.265 71.375 24.386 1.00 57.55 S ATOM 9248 SG CYS B 486 47.866 48.591 48.967 1.00 45.05 S ATOM 9316 SG CYS B 496 48.333 49.220 45.654 1.00 40.89 S ATOM 9330 SG CYS B 498 44.875 48.538 47.463 1.00 42.52 S ATOM 9352 SG CYS B 501 48.213 52.200 48.185 1.00 37.30 S ATOM 11336 SG CYS B 747 48.333 32.100 75.440 1.00 55.21 S ATOM 13333 SG CYS B1013 59.273 32.549 110.818 1.00 65.16 S ATOM 13543 SG CYS B1401 59.920 30.605 107.976 1.00 68.33 S ATOM 13594 SG CYS B1409 56.903 30.269 109.626 1.00 59.43 S ATOM 13611 SG CYS B1412 57.239 33.708 108.067 1.00 55.42 S Time building chain proxies: 3.73, per 1000 atoms: 0.22 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: 1.84 Conformation dependent library (CDL) restraints added in 728.8 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: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 15 through 33 Processing helix chain 'A' and resid 39 through 59 removed outlier: 4.292A pdb=" N LYS A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 81 removed outlier: 3.700A pdb=" N THR A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.701A pdb=" N LYS A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 136 Processing helix chain 'A' and resid 141 through 155 removed outlier: 3.514A pdb=" N LEU A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 Processing helix chain 'A' and resid 180 through 190 removed outlier: 4.539A pdb=" N ASP A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ASN A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 208 through 223 Processing helix chain 'A' and resid 230 through 247 removed outlier: 4.337A pdb=" N ASP A 234 " --> pdb=" O HIS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 297 removed outlier: 3.559A pdb=" N ASP A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 339 through 357 removed outlier: 3.965A pdb=" N HIS A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 450 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 454 through 469 Processing helix chain 'A' and resid 470 through 474 Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 509 through 514 removed outlier: 3.966A pdb=" N ASN A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 552 removed outlier: 3.701A pdb=" N ASN A 552 " --> pdb=" O GLU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 572 Processing helix chain 'A' and resid 606 through 614 Processing helix chain 'A' and resid 644 through 653 Processing helix chain 'A' and resid 665 through 679 removed outlier: 3.645A pdb=" N THR A 669 " --> pdb=" O ARG A 665 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN A 679 " --> pdb=" O TRP A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 691 removed outlier: 4.190A pdb=" N TRP A 687 " --> pdb=" O LYS A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.761A pdb=" N PHE A 703 " --> pdb=" O HIS A 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 26 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 54 through 72 Processing helix chain 'B' and resid 122 through 128 Processing helix chain 'B' and resid 164 through 167 No H-bonds generated for 'chain 'B' and resid 164 through 167' Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.596A pdb=" N ALA B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 282 removed outlier: 3.554A pdb=" N ASN B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 removed outlier: 4.093A pdb=" N ILE B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 302 removed outlier: 4.502A pdb=" N GLY B 302 " --> pdb=" O ARG B 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 299 through 302' Processing helix chain 'B' and resid 303 through 308 Processing helix chain 'B' and resid 333 through 345 Processing helix chain 'B' and resid 349 through 369 Processing helix chain 'B' and resid 429 through 433 Processing helix chain 'B' and resid 466 through 483 Processing helix chain 'B' and resid 498 through 505 Processing helix chain 'B' and resid 564 through 574 Processing helix chain 'B' and resid 612 through 620 Processing helix chain 'B' and resid 621 through 623 No H-bonds generated for 'chain 'B' and resid 621 through 623' Processing helix chain 'B' and resid 625 through 631 Processing helix chain 'B' and resid 633 through 637 Processing helix chain 'B' and resid 649 through 652 Processing helix chain 'B' and resid 653 through 659 Processing helix chain 'B' and resid 682 through 688 Processing helix chain 'B' and resid 718 through 735 Processing helix chain 'B' and resid 749 through 754 Processing helix chain 'B' and resid 771 through 775 Processing helix chain 'B' and resid 826 through 842 Processing helix chain 'B' and resid 850 through 854 Processing helix chain 'B' and resid 868 through 878 removed outlier: 3.801A pdb=" N THR B 878 " --> pdb=" O MET B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1011 removed outlier: 3.702A pdb=" N LEU B 998 " --> pdb=" O PRO B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1389 through 1394 Processing helix chain 'B' and resid 1395 through 1399 Processing helix chain 'B' and resid 1409 through 1415 Processing helix chain 'B' and resid 1481 through 1488 removed outlier: 3.722A pdb=" N ILE B1485 " --> pdb=" O GLY B1481 " (cutoff:3.500A) Processing helix chain 'B' and resid 1488 through 1496 Processing helix chain 'B' and resid 1523 through 1535 Processing helix chain 'B' and resid 1547 through 1551 Processing helix chain 'B' and resid 1578 through 1598 removed outlier: 3.770A pdb=" N GLY B1598 " --> pdb=" O ILE B1594 " (cutoff:3.500A) Processing helix chain 'B' and resid 1610 through 1613 removed outlier: 3.727A pdb=" N VAL B1613 " --> pdb=" O GLN B1610 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1610 through 1613' Processing helix chain 'B' and resid 1614 through 1624 Processing helix chain 'B' and resid 1668 through 1678 Processing sheet with id=AA1, first strand: chain 'A' and resid 425 through 431 removed outlier: 6.629A pdb=" N VAL A 401 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A 487 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 403 " --> pdb=" O VAL A 487 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 540 removed outlier: 7.080A pdb=" N VAL A 537 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU A 583 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 539 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU A 580 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY A 625 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 582 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR A 660 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 146 through 148 removed outlier: 6.529A pdb=" N SER B 51 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG B 14 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N TRP B 39 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL B 16 " --> pdb=" O TRP B 39 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N TRP B 41 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP B 190 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N GLU B 17 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 13.336A pdb=" N ARG B 188 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP B 185 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 162 through 163 removed outlier: 3.915A pdb=" N LEU B 162 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER B 51 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AA6, first strand: chain 'B' and resid 105 through 106 removed outlier: 6.034A pdb=" N THR B 105 " --> pdb=" O VAL B 400 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 374 through 375 Processing sheet with id=AA8, first strand: chain 'B' and resid 507 through 509 removed outlier: 6.533A pdb=" N GLU B 410 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU B 606 " --> pdb=" O GLU B 410 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 412 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE B 604 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 414 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE B 602 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 507 through 509 removed outlier: 6.533A pdb=" N GLU B 410 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU B 606 " --> pdb=" O GLU B 410 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 412 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE B 604 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 414 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE B 602 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 426 through 427 removed outlier: 4.182A pdb=" N ASN B 454 " --> pdb=" O VAL B 427 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 464 through 465 Processing sheet with id=AB3, first strand: chain 'B' and resid 521 through 528 removed outlier: 10.144A pdb=" N GLU B 521 " --> pdb=" O ASP B 542 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N ASP B 542 " --> pdb=" O GLU B 521 " (cutoff:3.500A) removed outlier: 11.103A pdb=" N ARG B 523 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 9.851A pdb=" N LEU B 540 " --> pdb=" O ARG B 523 " (cutoff:3.500A) removed outlier: 10.435A pdb=" N ARG B 525 " --> pdb=" O GLY B 538 " (cutoff:3.500A) removed outlier: 9.557A pdb=" N GLY B 538 " --> pdb=" O ARG B 525 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA B 527 " --> pdb=" O GLU B 536 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 698 through 699 removed outlier: 5.791A pdb=" N PHE B 715 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 698 through 699 removed outlier: 5.791A pdb=" N PHE B 715 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLN B 668 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ILE B 863 " --> pdb=" O GLN B 668 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR B 670 " --> pdb=" O ILE B 861 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE B 861 " --> pdb=" O THR B 670 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU B 672 " --> pdb=" O ALA B 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 680 through 681 removed outlier: 3.626A pdb=" N ILE B 695 " --> pdb=" O ASP B 681 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AB8, first strand: chain 'B' and resid 782 through 787 removed outlier: 6.020A pdb=" N ALA B 798 " --> pdb=" O ALA B 786 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 915 through 916 Processing sheet with id=AC1, first strand: chain 'B' and resid 919 through 922 Processing sheet with id=AC2, first strand: chain 'B' and resid 986 through 987 removed outlier: 6.614A pdb=" N LEU B 991 " --> pdb=" O TYR B1431 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ALA B1429 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ASP B1516 " --> pdb=" O ALA B1429 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N TYR B1431 " --> pdb=" O SER B1514 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER B1514 " --> pdb=" O TYR B1431 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN B1433 " --> pdb=" O VAL B1512 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B1512 " --> pdb=" O THR B 955 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR B 955 " --> pdb=" O VAL B1512 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N SER B1514 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU B 953 " --> pdb=" O SER B1514 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASP B1516 " --> pdb=" O CYS B 951 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N CYS B 951 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ARG B1518 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE B 949 " --> pdb=" O ARG B1518 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLU B1520 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY B 947 " --> pdb=" O GLU B1520 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N SER B 946 " --> pdb=" O THR B1564 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR B1564 " --> pdb=" O SER B 946 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS B 948 " --> pdb=" O LEU B1562 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU B1562 " --> pdb=" O LYS B 948 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASN B 950 " --> pdb=" O ASP B1560 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1424 through 1426 removed outlier: 6.862A pdb=" N VAL B1512 " --> pdb=" O THR B 955 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR B 955 " --> pdb=" O VAL B1512 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N SER B1514 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU B 953 " --> pdb=" O SER B1514 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASP B1516 " --> pdb=" O CYS B 951 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N CYS B 951 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ARG B1518 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE B 949 " --> pdb=" O ARG B1518 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLU B1520 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY B 947 " --> pdb=" O GLU B1520 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N SER B 946 " --> pdb=" O THR B1564 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR B1564 " --> pdb=" O SER B 946 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS B 948 " --> pdb=" O LEU B1562 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU B1562 " --> pdb=" O LYS B 948 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASN B 950 " --> pdb=" O ASP B1560 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 980 through 982 removed outlier: 6.197A pdb=" N LYS B 980 " --> pdb=" O THR B1503 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N GLU B1505 " --> pdb=" O LYS B 980 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N TYR B 982 " --> pdb=" O GLU B1505 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 4.20 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3379 1.32 - 1.45: 4563 1.45 - 1.57: 9514 1.57 - 1.69: 116 1.69 - 1.82: 80 Bond restraints: 17652 Sorted by residual: bond pdb=" CA ASN B 73 " pdb=" C ASN B 73 " ideal model delta sigma weight residual 1.523 1.494 0.030 1.56e-02 4.11e+03 3.62e+00 bond pdb=" C PHE A 714 " pdb=" N PRO A 715 " ideal model delta sigma weight residual 1.335 1.319 0.016 8.70e-03 1.32e+04 3.29e+00 bond pdb=" CD1 TYR B 365 " pdb=" CE1 TYR B 365 " ideal model delta sigma weight residual 1.382 1.331 0.051 3.00e-02 1.11e+03 2.90e+00 bond pdb=" CD1 TYR B 558 " pdb=" CE1 TYR B 558 " ideal model delta sigma weight residual 1.382 1.331 0.051 3.00e-02 1.11e+03 2.86e+00 bond pdb=" CB LEU A 598 " pdb=" CG LEU A 598 " ideal model delta sigma weight residual 1.530 1.563 -0.033 2.00e-02 2.50e+03 2.77e+00 ... (remaining 17647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 23455 2.26 - 4.52: 575 4.52 - 6.78: 46 6.78 - 9.03: 7 9.03 - 11.29: 2 Bond angle restraints: 24085 Sorted by residual: angle pdb=" C PRO A 335 " pdb=" N LYS A 336 " pdb=" CA LYS A 336 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" O4' G C 40 " pdb=" C1' G C 40 " pdb=" N9 G C 40 " ideal model delta sigma weight residual 108.20 114.22 -6.02 1.50e+00 4.44e-01 1.61e+01 angle pdb=" O4' A C 28 " pdb=" C1' A C 28 " pdb=" N9 A C 28 " ideal model delta sigma weight residual 108.20 114.05 -5.85 1.50e+00 4.44e-01 1.52e+01 angle pdb=" N GLU B1436 " pdb=" CA GLU B1436 " pdb=" CB GLU B1436 " ideal model delta sigma weight residual 114.17 109.80 4.37 1.14e+00 7.69e-01 1.47e+01 angle pdb=" N GLN B 34 " pdb=" CA GLN B 34 " pdb=" C GLN B 34 " ideal model delta sigma weight residual 111.75 116.56 -4.81 1.28e+00 6.10e-01 1.41e+01 ... (remaining 24080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 10096 35.32 - 70.64: 360 70.64 - 105.95: 27 105.95 - 141.27: 1 141.27 - 176.59: 5 Dihedral angle restraints: 10489 sinusoidal: 4820 harmonic: 5669 Sorted by residual: dihedral pdb=" O4' C C 22 " pdb=" C1' C C 22 " pdb=" N1 C C 22 " pdb=" C2 C C 22 " ideal model delta sinusoidal sigma weight residual 200.00 23.97 176.03 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C D 21 " pdb=" C1' C D 21 " pdb=" N1 C D 21 " pdb=" C2 C D 21 " ideal model delta sinusoidal sigma weight residual -160.00 -11.80 -148.20 1 1.50e+01 4.44e-03 7.89e+01 dihedral pdb=" O4' U C 15 " pdb=" C1' U C 15 " pdb=" N1 U C 15 " pdb=" C2 U C 15 " ideal model delta sinusoidal sigma weight residual 232.00 55.41 176.59 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 10486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2062 0.061 - 0.121: 491 0.121 - 0.182: 59 0.182 - 0.243: 6 0.243 - 0.303: 2 Chirality restraints: 2620 Sorted by residual: chirality pdb=" C1' A C 28 " pdb=" O4' A C 28 " pdb=" C2' A C 28 " pdb=" N9 A C 28 " both_signs ideal model delta sigma weight residual False 2.44 2.13 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C1' G C 40 " pdb=" O4' G C 40 " pdb=" C2' G C 40 " pdb=" N9 G C 40 " both_signs ideal model delta sigma weight residual False 2.44 2.15 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1' C D 38 " pdb=" O4' C D 38 " pdb=" C2' C D 38 " pdb=" N1 C D 38 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2617 not shown) Planarity restraints: 2884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C C 38 " 0.045 2.00e-02 2.50e+03 2.29e-02 1.18e+01 pdb=" N1 C C 38 " -0.048 2.00e-02 2.50e+03 pdb=" C2 C C 38 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C C 38 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C C 38 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C C 38 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C C 38 " 0.015 2.00e-02 2.50e+03 pdb=" C5 C C 38 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C C 38 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 28 " 0.033 2.00e-02 2.50e+03 1.73e-02 8.26e+00 pdb=" N9 A C 28 " -0.045 2.00e-02 2.50e+03 pdb=" C8 A C 28 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A C 28 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A C 28 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A C 28 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A C 28 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A C 28 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A C 28 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A C 28 " -0.008 2.00e-02 2.50e+03 pdb=" C4 A C 28 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 40 " 0.033 2.00e-02 2.50e+03 1.63e-02 7.94e+00 pdb=" N9 G C 40 " -0.044 2.00e-02 2.50e+03 pdb=" C8 G C 40 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G C 40 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G C 40 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G C 40 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G C 40 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G C 40 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G C 40 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G C 40 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G C 40 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G C 40 " -0.006 2.00e-02 2.50e+03 ... (remaining 2881 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 241 2.61 - 3.18: 15249 3.18 - 3.75: 27244 3.75 - 4.33: 40035 4.33 - 4.90: 63007 Nonbonded interactions: 145776 Sorted by model distance: nonbonded pdb=" O ASP B 796 " pdb=" O2' C D 26 " model vdw 2.036 3.040 nonbonded pdb=" O PHE A 122 " pdb=" OG SER A 126 " model vdw 2.100 3.040 nonbonded pdb=" OD2 ASP B 681 " pdb=" OG SER B 684 " model vdw 2.115 3.040 nonbonded pdb=" O GLU B1455 " pdb=" O2' C C 42 " model vdw 2.131 3.040 nonbonded pdb=" NH1 ARG B 299 " pdb=" OE2 GLU B 355 " model vdw 2.160 3.120 ... (remaining 145771 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.220 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:8.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.720 ------------------------------------------------------------------------------- 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= 0.493 Angle : 0.987 41.917 24103 Z= 0.484 Chirality : 0.053 0.303 2620 Planarity : 0.005 0.043 2884 Dihedral : 17.821 176.590 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 0.01035 / 0.45 (17652) covalent geometry : angle 0.85590 / 0.48 (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 : 0.689 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: 0.5843 time to fit residues: 267.2536 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 : 0.562 ------------------------------------------------------------------------------- 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 133 ASN A 183 HIS A 476 ASN A 541 ASN A 551 GLN A 552 ASN A 553 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS B 155 HIS B 345 ASN B 360 ASN B 614 ASN B 896 ASN ** B 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 ASN B1005 HIS ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1542 HIS B1571 ASN ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.167476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.115812 restraints weight = 20128.467| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.21 r_work: 0.3337 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17666 Z= 0.143 Angle : 0.642 13.118 24103 Z= 0.329 Chirality : 0.043 0.342 2620 Planarity : 0.004 0.045 2884 Dihedral : 13.119 177.506 2890 Min Nonbonded Distance : 1.540 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.94 % Favored : 95.95 % Rotamer: Outliers : 3.24 % Allowed : 21.75 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.18), residues: 1953 helix: 0.69 (0.19), residues: 716 sheet: -0.46 (0.30), residues: 240 loop : -1.13 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 841 TYR 0.019 0.001 TYR B 13 PHE 0.019 0.002 PHE B 453 TRP 0.013 0.001 TRP B 607 HIS 0.006 0.001 HIS B 903 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (17652) covalent geometry : angle 0.62488 / 0.33 (24085) hydrogen bonds : bond 0.04118 / 2.75 ( 671) hydrogen bonds : angle 4.60602 / 3.32 ( 1938) metal coordination : bond 0.01261 / 0.80 ( 14) metal coordination : angle 5.40006 / 3.08 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 209 time to evaluate : 0.520 Fit side-chains REVERT: A 88 THR cc_start: 0.7017 (p) cc_final: 0.6709 (t) REVERT: A 180 MET cc_start: 0.8769 (mmm) cc_final: 0.8365 (mmm) REVERT: A 216 MET cc_start: 0.7085 (tpt) cc_final: 0.6812 (tpt) REVERT: A 346 LYS cc_start: 0.6382 (tmmt) cc_final: 0.6130 (ttpt) REVERT: A 518 TYR cc_start: 0.7248 (m-80) cc_final: 0.6870 (m-80) REVERT: A 574 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.6654 (mpp-170) REVERT: A 587 GLU cc_start: 0.7014 (pt0) cc_final: 0.6763 (pm20) REVERT: A 686 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7103 (mt-10) REVERT: A 690 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7415 (pp20) REVERT: B 68 GLU cc_start: 0.8231 (tt0) cc_final: 0.7873 (mt-10) REVERT: B 93 LYS cc_start: 0.8589 (mmmt) cc_final: 0.8054 (ttpp) REVERT: B 118 LYS cc_start: 0.7927 (mtmt) cc_final: 0.7661 (mttm) REVERT: B 235 ILE cc_start: 0.8553 (pt) cc_final: 0.8207 (pt) REVERT: B 306 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7336 (mm) REVERT: B 339 LYS cc_start: 0.7980 (mtmt) cc_final: 0.7622 (mttm) REVERT: B 368 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6740 (mp0) REVERT: B 460 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: B 639 ASP cc_start: 0.8192 (m-30) cc_final: 0.7965 (m-30) REVERT: B 788 ASP cc_start: 0.8338 (t70) cc_final: 0.8127 (t0) REVERT: B 981 ASN cc_start: 0.7128 (OUTLIER) cc_final: 0.6388 (p0) REVERT: B 1469 GLU cc_start: 0.7738 (pm20) cc_final: 0.7456 (pm20) REVERT: B 1597 SER cc_start: 0.8661 (t) cc_final: 0.8378 (t) REVERT: B 1618 ASP cc_start: 0.7810 (t0) cc_final: 0.7319 (t70) REVERT: B 1639 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7243 (pmm-80) outliers start: 56 outliers final: 19 residues processed: 250 average time/residue: 0.5640 time to fit residues: 157.2518 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 : 0.405 ------------------------------------------------------------------------------- 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 401 VAL Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 574 ARG Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1639 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 83 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN A 553 ASN A 585 HIS ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN B 155 HIS B 450 HIS ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1603 GLN B1630 ASN ** B1666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.157964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.106718 restraints weight = 20416.844| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.31 r_work: 0.3189 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17666 Z= 0.211 Angle : 0.665 16.488 24103 Z= 0.338 Chirality : 0.045 0.321 2620 Planarity : 0.005 0.048 2884 Dihedral : 12.478 178.904 2851 Min Nonbonded Distance : 1.620 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.07 % Favored : 94.88 % Rotamer: Outliers : 3.88 % Allowed : 22.38 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.19), residues: 1953 helix: 1.11 (0.19), residues: 723 sheet: -0.24 (0.31), residues: 254 loop : -0.94 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 16 TYR 0.023 0.002 TYR A 704 PHE 0.019 0.002 PHE A 594 TRP 0.016 0.002 TRP A 675 HIS 0.008 0.001 HIS B 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (17652) covalent geometry : angle 0.64391 / 0.34 (24085) hydrogen bonds : bond 0.04563 / 3.05 ( 671) hydrogen bonds : angle 4.52710 / 3.28 ( 1938) metal coordination : bond 0.01016 / 0.69 ( 14) metal coordination : angle 6.17706 / 3.44 ( 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 257 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 190 time to evaluate : 0.544 Fit side-chains REVERT: A 88 THR cc_start: 0.7133 (p) cc_final: 0.6826 (t) REVERT: A 180 MET cc_start: 0.8774 (mmm) cc_final: 0.8401 (mmm) REVERT: A 231 ARG cc_start: 0.7827 (ptm160) cc_final: 0.6914 (ptp90) REVERT: A 331 MET cc_start: 0.4936 (tpp) cc_final: 0.3946 (tpt) REVERT: A 686 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7199 (mt-10) REVERT: B 31 MET cc_start: 0.9190 (mmm) cc_final: 0.8917 (mmm) REVERT: B 93 LYS cc_start: 0.8641 (mmmt) cc_final: 0.8104 (ttpp) REVERT: B 118 LYS cc_start: 0.8077 (mtmt) cc_final: 0.7818 (mtpt) REVERT: B 235 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8381 (pp) REVERT: B 309 ASP cc_start: 0.7674 (m-30) cc_final: 0.7417 (m-30) REVERT: B 339 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7921 (mttm) REVERT: B 499 LYS cc_start: 0.8527 (mmtm) cc_final: 0.8105 (mmmt) REVERT: B 524 TYR cc_start: 0.9068 (m-80) cc_final: 0.8829 (m-80) REVERT: B 625 LYS cc_start: 0.8395 (mtmm) cc_final: 0.7815 (mttm) REVERT: B 639 ASP cc_start: 0.8661 (m-30) cc_final: 0.7832 (t70) REVERT: B 649 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: B 756 GLU cc_start: 0.8019 (mp0) cc_final: 0.7792 (mm-30) REVERT: B 837 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8432 (tt) REVERT: B 981 ASN cc_start: 0.8064 (OUTLIER) cc_final: 0.7755 (p0) REVERT: B 1396 LYS cc_start: 0.7918 (tppt) cc_final: 0.7329 (ttpp) REVERT: B 1502 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.7800 (t) REVERT: B 1569 SER cc_start: 0.6761 (OUTLIER) cc_final: 0.6179 (p) REVERT: B 1610 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8030 (mm-40) REVERT: B 1612 HIS cc_start: 0.8289 (p-80) cc_final: 0.7598 (p-80) REVERT: B 1618 ASP cc_start: 0.7904 (t0) cc_final: 0.7287 (t70) REVERT: B 1670 LYS cc_start: 0.8419 (mttp) cc_final: 0.7670 (mppt) outliers start: 67 outliers final: 21 residues processed: 238 average time/residue: 0.6255 time to fit residues: 165.8735 Evaluate side-chains 192 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1024 SER Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 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: 2.9990 chunk 80 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 127 optimal weight: 0.8980 chunk 190 optimal weight: 50.0000 chunk 109 optimal weight: 0.4980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN A 551 GLN A 592 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.156801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.106366 restraints weight = 20436.644| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.34 r_work: 0.3174 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17666 Z= 0.211 Angle : 0.630 12.384 24103 Z= 0.323 Chirality : 0.044 0.336 2620 Planarity : 0.004 0.052 2884 Dihedral : 12.419 177.937 2846 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.51 % Favored : 95.44 % Rotamer: Outliers : 4.11 % Allowed : 22.33 % Favored : 73.57 % 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: -0.00 (0.19), residues: 1953 helix: 1.21 (0.19), residues: 721 sheet: -0.12 (0.31), residues: 259 loop : -0.88 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 140 TYR 0.020 0.002 TYR A 607 PHE 0.029 0.002 PHE B 453 TRP 0.016 0.002 TRP B 607 HIS 0.006 0.001 HIS B 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (17652) covalent geometry : angle 0.61418 / 0.32 (24085) hydrogen bonds : bond 0.04209 / 2.83 ( 671) hydrogen bonds : angle 4.46131 / 3.23 ( 1938) metal coordination : bond 0.00892 / 0.60 ( 14) metal coordination : angle 5.16018 / 2.91 ( 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 254 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 183 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 88 THR cc_start: 0.7136 (p) cc_final: 0.6862 (t) REVERT: A 180 MET cc_start: 0.8765 (mmm) cc_final: 0.8283 (mmm) REVERT: A 231 ARG cc_start: 0.7840 (ptm160) cc_final: 0.6940 (ptp90) REVERT: A 630 ASP cc_start: 0.7696 (t0) cc_final: 0.7263 (t0) REVERT: A 686 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7278 (mt-10) REVERT: A 690 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7177 (pp20) REVERT: B 90 ASP cc_start: 0.8101 (p0) cc_final: 0.7879 (p0) REVERT: B 93 LYS cc_start: 0.8677 (mmmt) cc_final: 0.7779 (ttpp) REVERT: B 118 LYS cc_start: 0.7964 (mtmt) cc_final: 0.7654 (tptt) REVERT: B 184 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8062 (pmtt) REVERT: B 235 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8394 (pp) REVERT: B 309 ASP cc_start: 0.7608 (m-30) cc_final: 0.7337 (m-30) REVERT: B 339 LYS cc_start: 0.8085 (mtmt) cc_final: 0.7844 (mttp) REVERT: B 340 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7262 (tt0) REVERT: B 368 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7129 (mm-30) REVERT: B 460 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8608 (mm-30) REVERT: B 499 LYS cc_start: 0.8519 (mmtm) cc_final: 0.8093 (mmmt) REVERT: B 528 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8328 (mtmt) REVERT: B 625 LYS cc_start: 0.8406 (mtmm) cc_final: 0.7834 (mttm) REVERT: B 639 ASP cc_start: 0.8642 (m-30) cc_final: 0.7881 (t70) REVERT: B 649 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: B 740 GLU cc_start: 0.7017 (tp30) cc_final: 0.6752 (tp30) REVERT: B 745 CYS cc_start: 0.6481 (p) cc_final: 0.6076 (p) REVERT: B 756 GLU cc_start: 0.8123 (mp0) cc_final: 0.7839 (mm-30) REVERT: B 837 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8401 (tt) REVERT: B 927 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7584 (tmtt) REVERT: B 1396 LYS cc_start: 0.7923 (tppt) cc_final: 0.7405 (ttpp) REVERT: B 1499 GLU cc_start: 0.8428 (pm20) cc_final: 0.8207 (pm20) REVERT: B 1502 VAL cc_start: 0.8460 (OUTLIER) cc_final: 0.7894 (t) REVERT: B 1670 LYS cc_start: 0.8471 (mttp) cc_final: 0.7708 (mppt) outliers start: 71 outliers final: 26 residues processed: 236 average time/residue: 0.5926 time to fit residues: 156.1031 Evaluate side-chains 201 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 591 SER 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 80 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 698 LYS Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain B residue 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 1002 LEU Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 1 optimal weight: 0.4980 chunk 127 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 181 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN A 602 ASN B 155 HIS B 691 ASN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.156799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.105242 restraints weight = 20172.951| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.28 r_work: 0.3176 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17666 Z= 0.188 Angle : 0.608 11.589 24103 Z= 0.312 Chirality : 0.043 0.329 2620 Planarity : 0.004 0.049 2884 Dihedral : 12.370 178.003 2844 Min Nonbonded Distance : 1.610 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.76 % Favored : 95.19 % Rotamer: Outliers : 3.70 % Allowed : 23.77 % Favored : 72.53 % 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: 0.09 (0.19), residues: 1953 helix: 1.27 (0.19), residues: 723 sheet: -0.03 (0.32), residues: 259 loop : -0.83 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 574 TYR 0.018 0.002 TYR A 704 PHE 0.014 0.002 PHE B 187 TRP 0.018 0.001 TRP A 675 HIS 0.005 0.001 HIS B 784 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (17652) covalent geometry : angle 0.59299 / 0.31 (24085) hydrogen bonds : bond 0.04071 / 2.74 ( 671) hydrogen bonds : angle 4.39643 / 3.18 ( 1938) metal coordination : bond 0.00854 / 0.57 ( 14) metal coordination : angle 4.91601 / 2.79 ( 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 234 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 170 time to evaluate : 0.636 Fit side-chains REVERT: A 88 THR cc_start: 0.7138 (p) cc_final: 0.6836 (t) REVERT: A 180 MET cc_start: 0.8750 (mmm) cc_final: 0.8260 (mmm) REVERT: A 216 MET cc_start: 0.7244 (tpt) cc_final: 0.6890 (tpt) REVERT: A 231 ARG cc_start: 0.7858 (ptm160) cc_final: 0.6948 (ptp90) REVERT: A 630 ASP cc_start: 0.7681 (t0) cc_final: 0.7256 (t0) REVERT: A 686 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7314 (mt-10) REVERT: A 690 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7189 (pp20) REVERT: B 29 SER cc_start: 0.7930 (OUTLIER) cc_final: 0.7707 (m) REVERT: B 90 ASP cc_start: 0.8070 (p0) cc_final: 0.7787 (p0) REVERT: B 93 LYS cc_start: 0.8694 (mmmt) cc_final: 0.7785 (ttpp) REVERT: B 118 LYS cc_start: 0.8020 (mtmt) cc_final: 0.7624 (tppt) REVERT: B 184 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8088 (pmtt) REVERT: B 235 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8388 (pp) REVERT: B 309 ASP cc_start: 0.7635 (m-30) cc_final: 0.7342 (m-30) REVERT: B 339 LYS cc_start: 0.8063 (mtmt) cc_final: 0.7760 (mttp) REVERT: B 340 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7258 (tt0) REVERT: B 368 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7161 (mm-30) REVERT: B 499 LYS cc_start: 0.8503 (mmtm) cc_final: 0.8072 (mmmt) REVERT: B 504 MET cc_start: 0.9160 (mmm) cc_final: 0.8863 (mmm) REVERT: B 528 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8296 (mtmt) REVERT: B 612 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7278 (mtpp) REVERT: B 625 LYS cc_start: 0.8302 (mtmm) cc_final: 0.7715 (mttm) REVERT: B 639 ASP cc_start: 0.8555 (m-30) cc_final: 0.7789 (t0) REVERT: B 649 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: B 733 ARG cc_start: 0.8479 (mmm160) cc_final: 0.8247 (tpt170) REVERT: B 745 CYS cc_start: 0.6765 (p) cc_final: 0.6397 (p) REVERT: B 756 GLU cc_start: 0.8102 (mp0) cc_final: 0.7777 (mm-30) REVERT: B 837 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8419 (tt) REVERT: B 973 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: B 1396 LYS cc_start: 0.7905 (tppt) cc_final: 0.7403 (ttpp) REVERT: B 1483 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6500 (mtt180) REVERT: B 1499 GLU cc_start: 0.8382 (pm20) cc_final: 0.8068 (pm20) REVERT: B 1502 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.8005 (t) REVERT: B 1583 ARG cc_start: 0.7822 (mpt180) cc_final: 0.7338 (mmt180) REVERT: B 1660 LYS cc_start: 0.6773 (ptpt) cc_final: 0.6549 (pttt) REVERT: B 1670 LYS cc_start: 0.8455 (mttp) cc_final: 0.7698 (mppt) outliers start: 64 outliers final: 29 residues processed: 218 average time/residue: 0.6127 time to fit residues: 148.7281 Evaluate side-chains 201 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 639 MET Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 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 528 LYS Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 698 LYS Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 861 ILE 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 1451 LEU Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1483 ARG Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1629 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 89 optimal weight: 0.7980 chunk 194 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 199 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 171 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN A 480 ASN B 155 HIS ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1487 GLN ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.157224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.104366 restraints weight = 19988.531| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.38 r_work: 0.3138 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4526 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= 0.148 Angle : 0.572 9.846 24103 Z= 0.294 Chirality : 0.042 0.324 2620 Planarity : 0.004 0.048 2884 Dihedral : 12.282 176.910 2844 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.47 % Allowed : 23.71 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.19), residues: 1953 helix: 1.34 (0.19), residues: 731 sheet: 0.34 (0.33), residues: 243 loop : -0.85 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 140 TYR 0.018 0.001 TYR A 607 PHE 0.014 0.001 PHE B 800 TRP 0.023 0.001 TRP A 675 HIS 0.005 0.001 HIS B 784 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (17652) covalent geometry : angle 0.55974 / 0.29 (24085) hydrogen bonds : bond 0.03772 / 2.52 ( 671) hydrogen bonds : angle 4.24321 / 3.06 ( 1938) metal coordination : bond 0.00726 / 0.47 ( 14) metal coordination : angle 4.28703 / 2.45 ( 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 234 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 174 time to evaluate : 0.646 Fit side-chains REVERT: A 88 THR cc_start: 0.7121 (p) cc_final: 0.6917 (t) REVERT: A 180 MET cc_start: 0.8726 (mmm) cc_final: 0.8234 (mmm) REVERT: A 216 MET cc_start: 0.7208 (tpt) cc_final: 0.6944 (tpt) REVERT: A 225 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.7235 (m-80) REVERT: A 231 ARG cc_start: 0.7795 (ptm160) cc_final: 0.6860 (ptp90) REVERT: A 241 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: A 597 MET cc_start: 0.2788 (OUTLIER) cc_final: 0.2155 (ptp) REVERT: A 630 ASP cc_start: 0.7558 (t0) cc_final: 0.6980 (t0) REVERT: A 686 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7263 (mt-10) REVERT: A 690 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7082 (pp20) REVERT: A 697 LYS cc_start: 0.7106 (pmtt) cc_final: 0.6454 (tppt) REVERT: B 29 SER cc_start: 0.7883 (OUTLIER) cc_final: 0.7661 (m) REVERT: B 90 ASP cc_start: 0.8028 (p0) cc_final: 0.7754 (p0) REVERT: B 93 LYS cc_start: 0.8694 (mmmt) cc_final: 0.7927 (ttpp) REVERT: B 118 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7666 (tptt) REVERT: B 127 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8092 (mp) REVERT: B 184 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8061 (pmtt) REVERT: B 193 ASP cc_start: 0.8183 (t0) cc_final: 0.7948 (t0) REVERT: B 235 ILE cc_start: 0.8798 (pt) cc_final: 0.8429 (pp) REVERT: B 309 ASP cc_start: 0.7670 (m-30) cc_final: 0.7356 (m-30) REVERT: B 339 LYS cc_start: 0.8017 (mtmt) cc_final: 0.7718 (mttp) REVERT: B 340 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7296 (tt0) REVERT: B 368 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.7077 (mm-30) REVERT: B 404 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7776 (tp30) REVERT: B 499 LYS cc_start: 0.8489 (mmtm) cc_final: 0.8032 (mmmt) REVERT: B 504 MET cc_start: 0.9156 (mmm) cc_final: 0.8844 (mmm) REVERT: B 528 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8258 (mtmt) REVERT: B 625 LYS cc_start: 0.8245 (mtmm) cc_final: 0.7642 (mttm) REVERT: B 639 ASP cc_start: 0.8533 (m-30) cc_final: 0.7731 (t0) REVERT: B 649 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: B 745 CYS cc_start: 0.7010 (p) cc_final: 0.6472 (p) REVERT: B 756 GLU cc_start: 0.8076 (mp0) cc_final: 0.7742 (mm-30) REVERT: B 927 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7534 (tmtt) REVERT: B 1396 LYS cc_start: 0.7875 (tppt) cc_final: 0.7362 (ttpp) REVERT: B 1447 ARG cc_start: 0.8247 (ptp90) cc_final: 0.8004 (ptt-90) REVERT: B 1483 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6440 (mtt180) REVERT: B 1499 GLU cc_start: 0.8452 (pm20) cc_final: 0.8202 (pm20) REVERT: B 1502 VAL cc_start: 0.8343 (OUTLIER) cc_final: 0.7880 (t) REVERT: B 1583 ARG cc_start: 0.7832 (mpt180) cc_final: 0.7353 (mmt180) REVERT: B 1670 LYS cc_start: 0.8444 (mttp) cc_final: 0.7682 (mppt) outliers start: 60 outliers final: 21 residues processed: 218 average time/residue: 0.6286 time to fit residues: 152.9300 Evaluate side-chains 194 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 241 GLU Chi-restraints excluded: chain A residue 401 VAL 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 632 VAL Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 698 LYS Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 927 LYS Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 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: 0.9990 chunk 112 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 173 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN A 575 ASN B 155 HIS ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1591 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.156195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.103086 restraints weight = 20001.029| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.45 r_work: 0.3117 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17666 Z= 0.177 Angle : 0.592 10.660 24103 Z= 0.304 Chirality : 0.043 0.324 2620 Planarity : 0.004 0.048 2884 Dihedral : 12.283 177.294 2844 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.47 % Allowed : 24.06 % Favored : 72.47 % 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: 1.41 (0.19), residues: 722 sheet: 0.34 (0.33), residues: 243 loop : -0.82 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 733 TYR 0.019 0.002 TYR A 607 PHE 0.020 0.002 PHE A 184 TRP 0.027 0.001 TRP A 675 HIS 0.004 0.001 HIS B 784 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (17652) covalent geometry : angle 0.57832 / 0.30 (24085) hydrogen bonds : bond 0.03977 / 2.68 ( 671) hydrogen bonds : angle 4.31077 / 3.11 ( 1938) metal coordination : bond 0.00760 / 0.50 ( 14) metal coordination : angle 4.70689 / 2.68 ( 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 228 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 168 time to evaluate : 0.618 Fit side-chains REVERT: A 88 THR cc_start: 0.7077 (p) cc_final: 0.6829 (t) REVERT: A 180 MET cc_start: 0.8728 (mmm) cc_final: 0.8259 (mmm) REVERT: A 216 MET cc_start: 0.7168 (tpt) cc_final: 0.6926 (tpt) REVERT: A 225 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.7197 (m-80) REVERT: A 231 ARG cc_start: 0.7826 (ptm160) cc_final: 0.6895 (ptp90) REVERT: A 241 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: A 583 LEU cc_start: 0.6464 (mp) cc_final: 0.6244 (mp) REVERT: A 630 ASP cc_start: 0.7680 (t0) cc_final: 0.7088 (t0) REVERT: A 686 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7209 (mt-10) REVERT: A 690 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7033 (pp20) REVERT: A 697 LYS cc_start: 0.7223 (pmtt) cc_final: 0.6496 (tppt) REVERT: B 29 SER cc_start: 0.7905 (OUTLIER) cc_final: 0.7683 (m) REVERT: B 90 ASP cc_start: 0.8035 (p0) cc_final: 0.7813 (p0) REVERT: B 93 LYS cc_start: 0.8721 (mmmt) cc_final: 0.7982 (ttpp) REVERT: B 118 LYS cc_start: 0.7968 (mtmt) cc_final: 0.7509 (tptt) REVERT: B 127 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8070 (mp) REVERT: B 184 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8130 (pmtt) REVERT: B 193 ASP cc_start: 0.8215 (t0) cc_final: 0.7955 (t0) REVERT: B 207 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7910 (mtt90) REVERT: B 235 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8445 (pp) REVERT: B 309 ASP cc_start: 0.7724 (m-30) cc_final: 0.7396 (m-30) REVERT: B 339 LYS cc_start: 0.8050 (mtmt) cc_final: 0.7744 (mttp) REVERT: B 340 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7316 (tt0) REVERT: B 404 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7754 (tp30) REVERT: B 499 LYS cc_start: 0.8498 (mmtm) cc_final: 0.8043 (mmmt) REVERT: B 504 MET cc_start: 0.9166 (mmm) cc_final: 0.8889 (mmm) REVERT: B 528 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8289 (mtmt) REVERT: B 625 LYS cc_start: 0.8273 (mtmm) cc_final: 0.7664 (mttm) REVERT: B 639 ASP cc_start: 0.8537 (m-30) cc_final: 0.7747 (t0) REVERT: B 649 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: B 743 GLU cc_start: 0.5319 (OUTLIER) cc_final: 0.4100 (tm-30) REVERT: B 745 CYS cc_start: 0.7121 (p) cc_final: 0.6659 (p) REVERT: B 756 GLU cc_start: 0.8115 (mp0) cc_final: 0.7781 (mm-30) REVERT: B 973 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: B 1396 LYS cc_start: 0.7884 (tppt) cc_final: 0.7369 (ttpp) REVERT: B 1483 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6428 (mtt180) REVERT: B 1499 GLU cc_start: 0.8594 (pm20) cc_final: 0.8317 (pm20) REVERT: B 1502 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.7921 (t) REVERT: B 1583 ARG cc_start: 0.7826 (mpt180) cc_final: 0.7334 (mmt180) REVERT: B 1660 LYS cc_start: 0.6571 (ptpp) cc_final: 0.6315 (ptpt) REVERT: B 1670 LYS cc_start: 0.8470 (mttp) cc_final: 0.7714 (mppt) outliers start: 60 outliers final: 25 residues processed: 213 average time/residue: 0.6347 time to fit residues: 149.5872 Evaluate side-chains 198 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 241 GLU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 698 LYS Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 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 973 GLN Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1483 ARG Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1629 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 53 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 198 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 ASN A 476 ASN A 575 ASN B 155 HIS B 981 ASN ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1591 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.158054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105170 restraints weight = 20076.952| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.46 r_work: 0.3135 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17666 Z= 0.125 Angle : 0.555 9.260 24103 Z= 0.286 Chirality : 0.041 0.318 2620 Planarity : 0.004 0.047 2884 Dihedral : 12.201 176.033 2844 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.83 % Allowed : 24.99 % Favored : 72.18 % 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: 0.42 (0.19), residues: 1953 helix: 1.60 (0.19), residues: 721 sheet: 0.42 (0.33), residues: 243 loop : -0.76 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 733 TYR 0.019 0.001 TYR A 607 PHE 0.023 0.001 PHE B 453 TRP 0.031 0.001 TRP A 675 HIS 0.004 0.001 HIS B 784 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (17652) covalent geometry : angle 0.54401 / 0.29 (24085) hydrogen bonds : bond 0.03575 / 2.40 ( 671) hydrogen bonds : angle 4.15603 / 2.99 ( 1938) metal coordination : bond 0.00625 / 0.39 ( 14) metal coordination : angle 4.00636 / 2.32 ( 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 227 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 178 time to evaluate : 0.636 Fit side-chains REVERT: A 88 THR cc_start: 0.7232 (p) cc_final: 0.7024 (t) REVERT: A 166 ASP cc_start: 0.7738 (m-30) cc_final: 0.7035 (m-30) REVERT: A 180 MET cc_start: 0.8704 (mmm) cc_final: 0.8316 (mmm) REVERT: A 225 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7141 (m-80) REVERT: A 231 ARG cc_start: 0.7782 (ptm160) cc_final: 0.6857 (ptp90) REVERT: A 574 ARG cc_start: 0.6735 (tpp-160) cc_final: 0.6283 (mpp-170) REVERT: A 583 LEU cc_start: 0.6438 (mp) cc_final: 0.6194 (mp) REVERT: A 590 MET cc_start: 0.6801 (OUTLIER) cc_final: 0.6329 (ttm) REVERT: A 597 MET cc_start: 0.3061 (OUTLIER) cc_final: 0.2818 (mtt) REVERT: A 630 ASP cc_start: 0.7321 (t0) cc_final: 0.6832 (t0) REVERT: A 683 LYS cc_start: 0.6716 (mmtt) cc_final: 0.6239 (mmtm) REVERT: A 686 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7192 (mt-10) REVERT: A 697 LYS cc_start: 0.7304 (pmtt) cc_final: 0.6530 (tppt) REVERT: B 68 GLU cc_start: 0.8311 (tt0) cc_final: 0.7955 (mt-10) REVERT: B 83 CYS cc_start: 0.6848 (OUTLIER) cc_final: 0.6152 (p) REVERT: B 90 ASP cc_start: 0.7983 (p0) cc_final: 0.7713 (p0) REVERT: B 93 LYS cc_start: 0.8701 (mmmt) cc_final: 0.7907 (ttpp) REVERT: B 118 LYS cc_start: 0.8032 (mtmt) cc_final: 0.7631 (tptt) REVERT: B 127 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8085 (mp) REVERT: B 184 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.7979 (pmtt) REVERT: B 193 ASP cc_start: 0.8121 (t0) cc_final: 0.7892 (t0) REVERT: B 207 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7875 (mtt90) REVERT: B 235 ILE cc_start: 0.8800 (pt) cc_final: 0.8426 (pp) REVERT: B 293 ASP cc_start: 0.8222 (m-30) cc_final: 0.7971 (m-30) REVERT: B 309 ASP cc_start: 0.7752 (m-30) cc_final: 0.7386 (m-30) REVERT: B 339 LYS cc_start: 0.7972 (mtmt) cc_final: 0.7666 (mttp) REVERT: B 404 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7787 (tp30) REVERT: B 499 LYS cc_start: 0.8448 (mmtm) cc_final: 0.7982 (mmmt) REVERT: B 528 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8215 (mtmt) REVERT: B 625 LYS cc_start: 0.8107 (mtmm) cc_final: 0.7417 (mttm) REVERT: B 639 ASP cc_start: 0.8525 (m-30) cc_final: 0.7694 (t0) REVERT: B 649 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: B 745 CYS cc_start: 0.7113 (p) cc_final: 0.6598 (p) REVERT: B 756 GLU cc_start: 0.8015 (mp0) cc_final: 0.7661 (mm-30) REVERT: B 954 GLU cc_start: 0.8239 (tt0) cc_final: 0.7886 (tm-30) REVERT: B 973 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: B 1396 LYS cc_start: 0.7771 (tppt) cc_final: 0.7296 (ttpp) REVERT: B 1447 ARG cc_start: 0.8237 (ptp90) cc_final: 0.8023 (ptt-90) REVERT: B 1499 GLU cc_start: 0.8617 (pm20) cc_final: 0.8343 (pm20) REVERT: B 1502 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.7857 (t) REVERT: B 1583 ARG cc_start: 0.7790 (mpt180) cc_final: 0.7291 (mmt180) REVERT: B 1670 LYS cc_start: 0.8432 (mttp) cc_final: 0.7669 (mppt) outliers start: 49 outliers final: 22 residues processed: 217 average time/residue: 0.6542 time to fit residues: 158.1526 Evaluate side-chains 203 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 584 CYS 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 22 ASP Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 83 CYS Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 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 1453 VAL Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1569 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 145 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 113 optimal weight: 0.3980 chunk 110 optimal weight: 0.2980 chunk 48 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN A 575 ASN B 155 HIS B 914 ASN B 981 ASN ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1591 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.158613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.106461 restraints weight = 20087.870| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.41 r_work: 0.3164 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17666 Z= 0.116 Angle : 0.553 9.334 24103 Z= 0.285 Chirality : 0.041 0.314 2620 Planarity : 0.004 0.049 2884 Dihedral : 12.131 175.332 2842 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.43 % Allowed : 25.62 % 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: 0.49 (0.19), residues: 1953 helix: 1.64 (0.19), residues: 724 sheet: 0.37 (0.33), residues: 245 loop : -0.69 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 140 TYR 0.019 0.001 TYR A 607 PHE 0.025 0.001 PHE A 254 TRP 0.036 0.001 TRP A 675 HIS 0.004 0.001 HIS B1616 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (17652) covalent geometry : angle 0.54273 / 0.28 (24085) hydrogen bonds : bond 0.03472 / 2.32 ( 671) hydrogen bonds : angle 4.11493 / 2.95 ( 1938) metal coordination : bond 0.00594 / 0.35 ( 14) metal coordination : angle 3.89237 / 2.24 ( 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 219 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.471 Fit side-chains REVERT: A 166 ASP cc_start: 0.7739 (m-30) cc_final: 0.7045 (m-30) REVERT: A 180 MET cc_start: 0.8664 (mmm) cc_final: 0.8400 (mmm) REVERT: A 225 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.7099 (m-80) REVERT: A 231 ARG cc_start: 0.7809 (ptm160) cc_final: 0.6893 (ptp90) REVERT: A 574 ARG cc_start: 0.6818 (tpp-160) cc_final: 0.6413 (mpp-170) REVERT: A 578 ARG cc_start: 0.6684 (ttm-80) cc_final: 0.6370 (ttt-90) REVERT: A 583 LEU cc_start: 0.6509 (mp) cc_final: 0.6251 (mp) REVERT: A 590 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.6330 (ttm) REVERT: A 597 MET cc_start: 0.2894 (OUTLIER) cc_final: 0.2668 (mtt) REVERT: A 630 ASP cc_start: 0.7318 (t0) cc_final: 0.6862 (t0) REVERT: A 683 LYS cc_start: 0.6738 (mmtt) cc_final: 0.6276 (mmtm) REVERT: A 686 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7228 (mt-10) REVERT: A 697 LYS cc_start: 0.7443 (pmtt) cc_final: 0.6680 (tppt) REVERT: B 68 GLU cc_start: 0.8319 (tt0) cc_final: 0.7963 (mt-10) REVERT: B 90 ASP cc_start: 0.7983 (p0) cc_final: 0.7756 (p0) REVERT: B 93 LYS cc_start: 0.8708 (mmmt) cc_final: 0.7972 (ttpp) REVERT: B 118 LYS cc_start: 0.8035 (mtmt) cc_final: 0.7646 (tptt) REVERT: B 127 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8107 (mp) REVERT: B 207 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7911 (mtt90) REVERT: B 213 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8540 (tttt) REVERT: B 235 ILE cc_start: 0.8800 (pt) cc_final: 0.8427 (pp) REVERT: B 293 ASP cc_start: 0.8177 (m-30) cc_final: 0.7935 (m-30) REVERT: B 309 ASP cc_start: 0.7758 (m-30) cc_final: 0.7384 (m-30) REVERT: B 339 LYS cc_start: 0.7986 (mtmt) cc_final: 0.7685 (mttp) REVERT: B 404 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7740 (tp30) REVERT: B 499 LYS cc_start: 0.8468 (mmtm) cc_final: 0.8010 (mmmt) REVERT: B 528 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8222 (mtmt) REVERT: B 625 LYS cc_start: 0.8176 (mtmm) cc_final: 0.7503 (mttm) REVERT: B 639 ASP cc_start: 0.8534 (m-30) cc_final: 0.7721 (t0) REVERT: B 649 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: B 756 GLU cc_start: 0.8004 (mp0) cc_final: 0.7658 (mm-30) REVERT: B 927 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7524 (tmtt) REVERT: B 954 GLU cc_start: 0.8232 (tt0) cc_final: 0.7892 (tm-30) REVERT: B 973 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: B 1396 LYS cc_start: 0.7784 (tppt) cc_final: 0.7315 (ttpp) REVERT: B 1447 ARG cc_start: 0.8264 (ptp90) cc_final: 0.8024 (ptt-90) REVERT: B 1499 GLU cc_start: 0.8607 (pm20) cc_final: 0.8344 (pm20) REVERT: B 1502 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.7921 (t) REVERT: B 1583 ARG cc_start: 0.7786 (mpt180) cc_final: 0.7304 (mmt180) REVERT: B 1660 LYS cc_start: 0.6735 (ptpp) cc_final: 0.6447 (pttt) REVERT: B 1670 LYS cc_start: 0.8437 (mttp) cc_final: 0.7676 (mppt) outliers start: 42 outliers final: 19 residues processed: 210 average time/residue: 0.6420 time to fit residues: 149.5252 Evaluate side-chains 197 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 597 MET Chi-restraints excluded: chain A residue 632 VAL 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 207 ARG Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 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 1453 VAL Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1569 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.6319 > 50: distance: 16 - 130: 24.007 distance: 82 - 88: 18.461 distance: 88 - 89: 9.811 distance: 89 - 90: 3.595 distance: 89 - 92: 11.582 distance: 90 - 91: 17.110 distance: 90 - 94: 24.519 distance: 92 - 93: 23.894 distance: 94 - 95: 6.618 distance: 95 - 96: 5.795 distance: 95 - 98: 14.861 distance: 96 - 97: 32.589 distance: 96 - 103: 29.984 distance: 98 - 99: 22.989 distance: 99 - 100: 30.100 distance: 100 - 101: 18.198 distance: 101 - 102: 27.187 distance: 103 - 104: 11.861 distance: 104 - 105: 14.480 distance: 104 - 107: 12.340 distance: 105 - 106: 5.892 distance: 107 - 108: 11.545 distance: 108 - 109: 11.449 distance: 108 - 110: 16.039 distance: 111 - 112: 8.325 distance: 112 - 113: 32.276 distance: 112 - 115: 26.053 distance: 113 - 114: 33.539 distance: 113 - 120: 35.287 distance: 115 - 116: 20.342 distance: 116 - 117: 5.858 distance: 117 - 118: 16.352 distance: 117 - 119: 10.541 distance: 120 - 121: 23.722 distance: 120 - 126: 24.627 distance: 121 - 122: 8.508 distance: 121 - 124: 13.956 distance: 122 - 123: 23.883 distance: 122 - 127: 18.191 distance: 124 - 125: 6.521 distance: 125 - 126: 12.828 distance: 127 - 128: 22.789 distance: 128 - 129: 15.261 distance: 128 - 131: 16.977 distance: 129 - 130: 36.876 distance: 129 - 135: 5.577 distance: 131 - 132: 5.990 distance: 132 - 133: 14.494 distance: 132 - 134: 44.589 distance: 135 - 136: 7.676 distance: 136 - 137: 4.199 distance: 136 - 139: 3.924 distance: 137 - 138: 18.182 distance: 137 - 142: 32.471 distance: 139 - 140: 26.967 distance: 139 - 141: 29.040 distance: 142 - 143: 19.501 distance: 143 - 144: 7.865 distance: 143 - 146: 10.386 distance: 144 - 145: 10.993 distance: 144 - 153: 15.266 distance: 146 - 147: 9.808 distance: 147 - 148: 6.780 distance: 148 - 149: 10.756 distance: 149 - 150: 6.343 distance: 150 - 151: 6.412 distance: 150 - 152: 10.660 distance: 153 - 154: 11.330 distance: 154 - 155: 6.544 distance: 154 - 157: 21.055 distance: 155 - 156: 10.077 distance: 155 - 165: 22.584 distance: 157 - 158: 13.794 distance: 158 - 159: 13.081 distance: 158 - 160: 22.338 distance: 159 - 161: 15.595 distance: 160 - 162: 5.266 distance: 161 - 163: 21.634 distance: 162 - 163: 19.910 distance: 163 - 164: 13.483 distance: 165 - 166: 5.484 distance: 165 - 171: 27.349 distance: 166 - 167: 17.175 distance: 167 - 168: 29.200 distance: 167 - 172: 10.498 distance: 169 - 170: 42.627 distance: 170 - 171: 32.572