Starting phenix.real_space_refine on Fri Sep 11 21:27:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d8n_27252/09_2026/8d8n_27252.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d8n_27252/09_2026/8d8n_27252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d8n_27252/09_2026/8d8n_27252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d8n_27252/09_2026/8d8n_27252.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d8n_27252/09_2026/8d8n_27252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d8n_27252/09_2026/8d8n_27252.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8d8n_27252/09_2026/8d8n_27252.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d8n_27252/09_2026/8d8n_27252.cif" } resolution = 3.6 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= -0.001 sd= 0.034 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 56 5.49 5 S 33 5.16 5 C 6943 2.51 5 N 1978 2.21 5 O 2261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11275 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 10082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1256, 10082 Classifications: {'peptide': 1256} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 57, 'TRANS': 1198} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 734 Classifications: {'RNAv2': 35} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 11, 'rna3p_pur': 4, 'rna3p_pyr': 10} Link IDs: {'rna2p': 21, 'rna3p': 13} Chain: "D" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 455 Classifications: {'RNAv2': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 13, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, '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 668 SG CYS B 83 34.918 38.620 15.837 1.00144.18 S ATOM 939 SG CYS B 116 34.715 35.721 17.170 1.00147.58 S ATOM 3436 SG CYS B 486 27.334 55.044 47.908 1.00128.06 S ATOM 3504 SG CYS B 496 24.506 55.520 44.527 1.00118.68 S ATOM 3518 SG CYS B 498 27.634 56.725 45.105 1.00111.43 S ATOM 5546 SG CYS B 750 20.418 60.286 76.922 1.00144.62 S ATOM 7491 SG CYS B1018 22.015 49.825 113.127 1.00164.52 S ATOM 7738 SG CYS B1406 19.065 50.188 111.390 1.00169.95 S ATOM 7789 SG CYS B1414 21.102 52.908 112.245 1.00150.23 S ATOM 7806 SG CYS B1417 23.491 51.123 110.375 1.00144.38 S Time building chain proxies: 2.63, per 1000 atoms: 0.23 Number of scatterers: 11275 At special positions: 0 Unit cell: (78.324, 91.164, 159.216, 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 33 16.00 P 56 15.00 O 2261 8.00 N 1978 7.00 C 6943 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: 1.01 Conformation dependent library (CDL) restraints added in 495.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1801 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 116 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 83 " pdb=" ZN B1802 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 486 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 498 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 496 " pdb=" ZN B1803 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 750 " pdb=" ZN B1804 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1018 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1417 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1406 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1414 " Number of angles added : 6 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2296 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 16 sheets defined 30.8% alpha, 19.2% beta 8 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 27 through 31 Processing helix chain 'B' and resid 54 through 73 removed outlier: 3.753A pdb=" N VAL B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 129 removed outlier: 3.768A pdb=" N ILE B 126 " --> pdb=" O CYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 removed outlier: 3.838A pdb=" N ILE B 167 " --> pdb=" O ARG B 163 " (cutoff:3.500A) 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 219 removed outlier: 3.894A pdb=" N LEU B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 282 removed outlier: 4.130A pdb=" N ARG B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 270 " --> pdb=" O ASP B 266 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 278 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 removed outlier: 4.169A pdb=" N ILE B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 309 Processing helix chain 'B' and resid 334 through 345 removed outlier: 4.144A pdb=" N LYS B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 370 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 575 Processing helix chain 'B' and resid 589 through 593 removed outlier: 3.743A pdb=" N THR B 592 " --> pdb=" O LEU B 589 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY B 593 " --> pdb=" O ASP B 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 589 through 593' Processing helix chain 'B' and resid 612 through 619 removed outlier: 3.599A pdb=" N GLU B 619 " --> pdb=" O GLU B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 623 removed outlier: 3.616A pdb=" N ARG B 623 " --> pdb=" O ARG B 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 620 through 623' Processing helix chain 'B' and resid 627 through 632 removed outlier: 4.126A pdb=" N GLU B 631 " --> pdb=" O LYS B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.811A pdb=" N LEU B 637 " --> pdb=" O GLU B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 659 Processing helix chain 'B' and resid 660 through 662 No H-bonds generated for 'chain 'B' and resid 660 through 662' Processing helix chain 'B' and resid 681 through 686 removed outlier: 3.940A pdb=" N ALA B 685 " --> pdb=" O ASP B 681 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 686 " --> pdb=" O THR B 682 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 681 through 686' Processing helix chain 'B' and resid 718 through 735 removed outlier: 3.584A pdb=" N HIS B 722 " --> pdb=" O LYS B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 753 removed outlier: 3.759A pdb=" N ILE B 751 " --> pdb=" O CYS B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 843 removed outlier: 3.516A pdb=" N LEU B 831 " --> pdb=" O GLY B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 877 Processing helix chain 'B' and resid 910 through 914 removed outlier: 3.654A pdb=" N GLN B 913 " --> pdb=" O SER B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 980 removed outlier: 3.967A pdb=" N GLY B 979 " --> pdb=" O LYS B 976 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN B 980 " --> pdb=" O LEU B 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 976 through 980' Processing helix chain 'B' and resid 999 through 1016 removed outlier: 4.057A pdb=" N LEU B1003 " --> pdb=" O PRO B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1394 through 1399 removed outlier: 3.591A pdb=" N LYS B1398 " --> pdb=" O THR B1394 " (cutoff:3.500A) Processing helix chain 'B' and resid 1400 through 1404 Processing helix chain 'B' and resid 1414 through 1421 Processing helix chain 'B' and resid 1463 through 1468 removed outlier: 4.242A pdb=" N SER B1467 " --> pdb=" O ARG B1463 " (cutoff:3.500A) Processing helix chain 'B' and resid 1489 through 1492 Processing helix chain 'B' and resid 1493 through 1501 removed outlier: 3.694A pdb=" N GLU B1499 " --> pdb=" O LEU B1495 " (cutoff:3.500A) Processing helix chain 'B' and resid 1528 through 1540 removed outlier: 4.090A pdb=" N LEU B1532 " --> pdb=" O ARG B1528 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY B1533 " --> pdb=" O GLU B1529 " (cutoff:3.500A) Processing helix chain 'B' and resid 1586 through 1603 removed outlier: 3.672A pdb=" N GLY B1603 " --> pdb=" O ILE B1599 " (cutoff:3.500A) Processing helix chain 'B' and resid 1619 through 1629 removed outlier: 3.674A pdb=" N LEU B1629 " --> pdb=" O LEU B1625 " (cutoff:3.500A) Processing helix chain 'B' and resid 1673 through 1682 Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 3 removed outlier: 5.127A pdb=" N ARG B 203 " --> pdb=" O ASN B 150 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASN B 150 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N THR B 205 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N PHE B 148 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N SER B 51 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ARG B 14 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N TRP B 39 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 16 " --> pdb=" O TRP B 39 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N TRP B 41 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TRP B 190 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N GLU B 17 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 13.476A pdb=" N ARG B 188 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP B 185 " --> pdb=" O ARG B 175 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 175 " --> pdb=" O ASP B 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 3 removed outlier: 4.015A pdb=" N VAL B 5 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 329 Processing sheet with id=AA5, first strand: chain 'B' and resid 507 through 508 Processing sheet with id=AA6, first strand: chain 'B' and resid 507 through 508 removed outlier: 4.086A pdb=" N VAL B 414 " --> pdb=" O LYS B 603 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 603 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARG B 416 " --> pdb=" O ASP B 601 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASP B 601 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LYS B 418 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU B 599 " --> pdb=" O LYS B 418 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 521 through 528 removed outlier: 3.896A pdb=" N ALA B 527 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER B 539 " --> pdb=" O ALA B 527 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 698 through 699 removed outlier: 6.247A pdb=" N PHE B 715 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU B 769 " --> pdb=" O PHE B 715 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 698 through 699 removed outlier: 6.247A pdb=" N PHE B 715 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU B 769 " --> pdb=" O PHE B 715 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLN B 668 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE B 863 " --> pdb=" O GLN B 668 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR B 670 " --> pdb=" O ILE B 861 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ILE B 861 " --> pdb=" O THR B 670 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU B 672 " --> pdb=" O ALA B 859 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 782 through 785 Processing sheet with id=AB2, first strand: chain 'B' and resid 920 through 921 Processing sheet with id=AB3, first strand: chain 'B' and resid 924 through 927 Processing sheet with id=AB4, first strand: chain 'B' and resid 1429 through 1430 removed outlier: 3.604A pdb=" N ASN B1526 " --> pdb=" O LEU B 950 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU B 950 " --> pdb=" O ASN B1526 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER B1566 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LYS B 957 " --> pdb=" O ILE B1564 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE B1564 " --> pdb=" O LYS B 957 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLU B 959 " --> pdb=" O ILE B1562 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ILE B1562 " --> pdb=" O GLU B 959 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1435 through 1436 removed outlier: 3.604A pdb=" N ASN B1526 " --> pdb=" O LEU B 950 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU B 950 " --> pdb=" O ASN B1526 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER B1566 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LYS B 957 " --> pdb=" O ILE B1564 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE B1564 " --> pdb=" O LYS B 957 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLU B 959 " --> pdb=" O ILE B1562 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ILE B1562 " --> pdb=" O GLU B 959 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B1569 " --> pdb=" O LYS B1580 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS B1580 " --> pdb=" O THR B1569 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 985 through 986 removed outlier: 6.698A pdb=" N LYS B 985 " --> pdb=" O THR B1508 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N GLU B1510 " --> pdb=" O LYS B 985 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1029 through 1030 removed outlier: 3.610A pdb=" N LYS B1389 " --> pdb=" O TRP B1030 " (cutoff:3.500A) 325 hydrogen bonds defined for protein. 894 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2829 1.33 - 1.45: 2504 1.45 - 1.57: 6148 1.57 - 1.69: 111 1.69 - 1.81: 45 Bond restraints: 11637 Sorted by residual: bond pdb=" CA TYR B 197 " pdb=" CB TYR B 197 " ideal model delta sigma weight residual 1.531 1.457 0.074 3.12e-02 1.03e+03 5.56e+00 bond pdb=" CA PHE B 423 " pdb=" CB PHE B 423 " ideal model delta sigma weight residual 1.534 1.500 0.035 1.60e-02 3.91e+03 4.75e+00 bond pdb=" CB TRP B 820 " pdb=" CG TRP B 820 " ideal model delta sigma weight residual 1.498 1.438 0.060 3.10e-02 1.04e+03 3.77e+00 bond pdb=" C GLY B 807 " pdb=" N SER B 808 " ideal model delta sigma weight residual 1.327 1.300 0.026 1.71e-02 3.42e+03 2.36e+00 bond pdb=" N1 C C 31 " pdb=" C2 C C 31 " ideal model delta sigma weight residual 1.397 1.367 0.030 2.00e-02 2.50e+03 2.31e+00 ... (remaining 11632 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 15265 2.07 - 4.14: 582 4.14 - 6.21: 86 6.21 - 8.28: 15 8.28 - 10.35: 5 Bond angle restraints: 15953 Sorted by residual: angle pdb=" N PRO B 911 " pdb=" CA PRO B 911 " pdb=" CB PRO B 911 " ideal model delta sigma weight residual 103.25 112.54 -9.29 1.05e+00 9.07e-01 7.82e+01 angle pdb=" N PRO B 898 " pdb=" CA PRO B 898 " pdb=" CB PRO B 898 " ideal model delta sigma weight residual 103.25 111.26 -8.01 1.05e+00 9.07e-01 5.81e+01 angle pdb=" N PRO B 906 " pdb=" CA PRO B 906 " pdb=" CB PRO B 906 " ideal model delta sigma weight residual 103.25 109.92 -6.67 1.05e+00 9.07e-01 4.04e+01 angle pdb=" C SER B 910 " pdb=" N PRO B 911 " pdb=" CA PRO B 911 " ideal model delta sigma weight residual 119.84 127.28 -7.44 1.25e+00 6.40e-01 3.54e+01 angle pdb=" N ILE B 447 " pdb=" CA ILE B 447 " pdb=" C ILE B 447 " ideal model delta sigma weight residual 111.91 107.64 4.27 8.90e-01 1.26e+00 2.30e+01 ... (remaining 15948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 5826 17.74 - 35.48: 738 35.48 - 53.23: 162 53.23 - 70.97: 100 70.97 - 88.71: 30 Dihedral angle restraints: 6856 sinusoidal: 3271 harmonic: 3585 Sorted by residual: dihedral pdb=" C4' G C 20 " pdb=" C3' G C 20 " pdb=" C2' G C 20 " pdb=" C1' G C 20 " ideal model delta sinusoidal sigma weight residual 36.35 -43.49 79.84 1 3.10e+00 1.04e-01 8.23e+02 dihedral pdb=" C4' A C 33 " pdb=" C3' A C 33 " pdb=" C2' A C 33 " pdb=" C1' A C 33 " ideal model delta sinusoidal sigma weight residual 36.35 -40.03 76.37 1 3.10e+00 1.04e-01 7.64e+02 dihedral pdb=" C4' U C 21 " pdb=" C3' U C 21 " pdb=" C2' U C 21 " pdb=" C1' U C 21 " ideal model delta sinusoidal sigma weight residual 36.35 -39.00 75.35 1 3.10e+00 1.04e-01 7.46e+02 ... (remaining 6853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1466 0.076 - 0.151: 170 0.151 - 0.226: 47 0.226 - 0.302: 55 0.302 - 0.377: 5 Chirality restraints: 1743 Sorted by residual: chirality pdb=" C2' G C 20 " pdb=" C3' G C 20 " pdb=" O2' G C 20 " pdb=" C1' G C 20 " both_signs ideal model delta sigma weight residual False -2.79 -2.41 -0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" C3' U C 21 " pdb=" C4' U C 21 " pdb=" O3' U C 21 " pdb=" C2' U C 21 " both_signs ideal model delta sigma weight residual False -2.50 -2.84 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" C3' G C 40 " pdb=" C4' G C 40 " pdb=" O3' G C 40 " pdb=" C2' G C 40 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 1740 not shown) Planarity restraints: 1855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 99 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C PHE B 99 " 0.060 2.00e-02 2.50e+03 pdb=" O PHE B 99 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU B 100 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G D 36 " 0.011 2.00e-02 2.50e+03 1.51e-02 6.80e+00 pdb=" N9 G D 36 " -0.005 2.00e-02 2.50e+03 pdb=" C8 G D 36 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G D 36 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G D 36 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G D 36 " -0.027 2.00e-02 2.50e+03 pdb=" O6 G D 36 " 0.028 2.00e-02 2.50e+03 pdb=" N1 G D 36 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G D 36 " -0.027 2.00e-02 2.50e+03 pdb=" N2 G D 36 " 0.015 2.00e-02 2.50e+03 pdb=" N3 G D 36 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G D 36 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 13 " -0.032 2.00e-02 2.50e+03 1.49e-02 6.08e+00 pdb=" N9 A C 13 " 0.035 2.00e-02 2.50e+03 pdb=" C8 A C 13 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A C 13 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A C 13 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A C 13 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A C 13 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A C 13 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A C 13 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A C 13 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A C 13 " 0.004 2.00e-02 2.50e+03 ... (remaining 1852 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 89 2.44 - 3.06: 7882 3.06 - 3.67: 16286 3.67 - 4.29: 22723 4.29 - 4.90: 36637 Nonbonded interactions: 83617 Sorted by model distance: nonbonded pdb=" O CYS B 745 " pdb="ZN ZN B1803 " model vdw 1.828 2.230 nonbonded pdb=" O ILE B 115 " pdb="ZN ZN B1801 " model vdw 1.944 2.230 nonbonded pdb=" N4 C C 29 " pdb=" N6 A D 37 " model vdw 2.078 2.560 nonbonded pdb=" O2' U C 16 " pdb=" O4' A C 17 " model vdw 2.093 3.040 nonbonded pdb=" NE ARG B 101 " pdb=" O5' U C 21 " model vdw 2.116 3.120 ... (remaining 83612 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 group one per residue 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.590 Find NCS groups from input model: 0.050 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 0.008 0.141 11647 Z= 0.367 Angle : 1.071 55.277 15959 Z= 0.510 Chirality : 0.074 0.377 1743 Planarity : 0.005 0.058 1855 Dihedral : 18.167 88.710 4560 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.17 % Favored : 88.50 % Rotamer: Outliers : 0.28 % Allowed : 8.05 % Favored : 91.67 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.25 % 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: -4.01 (0.19), residues: 1244 helix: -1.90 (0.23), residues: 315 sheet: -2.52 (0.32), residues: 180 loop : -3.20 (0.19), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 140 TYR 0.018 0.002 TYR B 616 PHE 0.021 0.002 PHE B 52 TRP 0.010 0.002 TRP B 21 HIS 0.008 0.001 HIS B 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00787 / 0.36 (11637) covalent geometry : angle 0.93971 / 0.50 (15953) hydrogen bonds : bond 0.20375 / 13.42 ( 318) hydrogen bonds : angle 8.40446 / 5.69 ( 926) metal coordination : bond 0.06410 / 3.72 ( 10) metal coordination : angle 26.48146 / 12.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 164 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 LEU cc_start: 0.8689 (tp) cc_final: 0.8413 (tp) REVERT: B 166 ASP cc_start: 0.8419 (m-30) cc_final: 0.8144 (t0) REVERT: B 172 ILE cc_start: 0.8441 (mt) cc_final: 0.8128 (tt) REVERT: B 178 PHE cc_start: 0.7726 (t80) cc_final: 0.7388 (t80) REVERT: B 213 LYS cc_start: 0.8429 (mtmt) cc_final: 0.7880 (pttp) REVERT: B 343 GLN cc_start: 0.8875 (tp40) cc_final: 0.8299 (mp10) REVERT: B 362 TYR cc_start: 0.7946 (t80) cc_final: 0.7649 (t80) REVERT: B 562 LYS cc_start: 0.8940 (tppt) cc_final: 0.8707 (tttp) REVERT: B 618 LYS cc_start: 0.9101 (tppt) cc_final: 0.8652 (ttpt) REVERT: B 627 LYS cc_start: 0.9147 (ttpt) cc_final: 0.8853 (tptt) REVERT: B 652 CYS cc_start: 0.8255 (m) cc_final: 0.7580 (t) REVERT: B 1028 LEU cc_start: 0.7714 (pt) cc_final: 0.7509 (pp) REVERT: B 1500 THR cc_start: 0.9426 (t) cc_final: 0.9130 (p) REVERT: B 1578 LYS cc_start: 0.6302 (mmtt) cc_final: 0.5944 (mmtt) REVERT: B 1600 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8391 (tt0) outliers start: 3 outliers final: 3 residues processed: 167 average time/residue: 0.1101 time to fit residues: 26.3085 Evaluate side-chains 85 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 1629 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.0270 chunk 55 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 GLN B 150 ASN B 155 HIS B 281 GLN B 691 ASN B 771 ASN B 784 HIS B 980 ASN B1418 HIS B1483 HIS ** B1485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1544 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.121699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.091332 restraints weight = 20775.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.094882 restraints weight = 10434.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.097204 restraints weight = 7001.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.098691 restraints weight = 5524.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.099576 restraints weight = 4776.525| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11647 Z= 0.167 Angle : 1.108 20.773 15959 Z= 0.470 Chirality : 0.099 1.060 1743 Planarity : 0.005 0.049 1855 Dihedral : 14.282 151.885 2034 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.43 % Favored : 93.25 % Rotamer: Outliers : 1.76 % Allowed : 12.49 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.25 % 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: -2.37 (0.22), residues: 1244 helix: 0.01 (0.29), residues: 324 sheet: -1.59 (0.34), residues: 187 loop : -2.43 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 471 TYR 0.011 0.001 TYR B 803 PHE 0.017 0.002 PHE B1520 TRP 0.012 0.001 TRP B 585 HIS 0.007 0.001 HIS B 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (11637) covalent geometry : angle 1.10456 / 0.47 (15953) hydrogen bonds : bond 0.06418 / 3.76 ( 318) hydrogen bonds : angle 5.50003 / 3.74 ( 926) metal coordination : bond 0.00556 / 0.32 ( 10) metal coordination : angle 4.86141 / 2.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: B 164 LEU cc_start: 0.7999 (tp) cc_final: 0.7724 (tp) REVERT: B 166 ASP cc_start: 0.8385 (m-30) cc_final: 0.8055 (t0) REVERT: B 178 PHE cc_start: 0.7636 (t80) cc_final: 0.7350 (t80) REVERT: B 213 LYS cc_start: 0.8169 (mtmt) cc_final: 0.7662 (pttp) REVERT: B 343 GLN cc_start: 0.8738 (tp40) cc_final: 0.8427 (mp10) REVERT: B 608 ASP cc_start: 0.6971 (t0) cc_final: 0.6708 (t70) REVERT: B 618 LYS cc_start: 0.9091 (tppt) cc_final: 0.8769 (ttpt) REVERT: B 639 ASP cc_start: 0.7973 (p0) cc_final: 0.7619 (t70) REVERT: B 652 CYS cc_start: 0.7873 (m) cc_final: 0.7372 (t) REVERT: B 874 MET cc_start: 0.5175 (mtp) cc_final: 0.4952 (mtp) REVERT: B 1028 LEU cc_start: 0.8234 (pt) cc_final: 0.7732 (pp) REVERT: B 1571 LYS cc_start: 0.8204 (mtmm) cc_final: 0.7947 (mttt) outliers start: 19 outliers final: 11 residues processed: 110 average time/residue: 0.1060 time to fit residues: 17.2103 Evaluate side-chains 79 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 1441 GLU Chi-restraints excluded: chain B residue 1453 SER Chi-restraints excluded: chain B residue 1467 SER Chi-restraints excluded: chain B residue 1579 ILE Chi-restraints excluded: chain B residue 1586 ASP Chi-restraints excluded: chain B residue 1589 GLU Chi-restraints excluded: chain B residue 1629 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 86 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 89 optimal weight: 0.0980 chunk 21 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 0.1980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 HIS B 112 ASN ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 ASN ** B1485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1575 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.114744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.084195 restraints weight = 20759.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.087586 restraints weight = 10422.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.089846 restraints weight = 6997.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.091274 restraints weight = 5510.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.092167 restraints weight = 4763.079| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11647 Z= 0.193 Angle : 0.866 15.741 15959 Z= 0.390 Chirality : 0.073 0.805 1743 Planarity : 0.005 0.051 1855 Dihedral : 14.325 168.820 2033 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.32 % Favored : 92.36 % Rotamer: Outliers : 3.15 % Allowed : 13.04 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.17 % 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: -1.77 (0.23), residues: 1244 helix: 0.69 (0.29), residues: 322 sheet: -1.25 (0.36), residues: 198 loop : -2.13 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 130 TYR 0.017 0.002 TYR B 558 PHE 0.021 0.002 PHE B1520 TRP 0.022 0.002 TRP B1030 HIS 0.005 0.001 HIS B 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (11637) covalent geometry : angle 0.86403 / 0.39 (15953) hydrogen bonds : bond 0.06579 / 3.88 ( 318) hydrogen bonds : angle 4.94175 / 3.36 ( 926) metal coordination : bond 0.00543 / 0.32 ( 10) metal coordination : angle 3.28203 / 1.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 77 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 166 ASP cc_start: 0.8317 (m-30) cc_final: 0.7957 (t0) REVERT: B 178 PHE cc_start: 0.7871 (t80) cc_final: 0.7400 (t80) REVERT: B 213 LYS cc_start: 0.8408 (mtmt) cc_final: 0.7991 (pttp) REVERT: B 343 GLN cc_start: 0.8718 (tp40) cc_final: 0.8210 (mp10) REVERT: B 652 CYS cc_start: 0.8179 (m) cc_final: 0.7786 (t) REVERT: B 742 HIS cc_start: 0.5898 (OUTLIER) cc_final: 0.5561 (t-170) REVERT: B 1027 THR cc_start: 0.8794 (m) cc_final: 0.8573 (t) REVERT: B 1028 LEU cc_start: 0.8452 (pt) cc_final: 0.8215 (pp) REVERT: B 1401 LYS cc_start: 0.8193 (tptt) cc_final: 0.7761 (mtpp) outliers start: 34 outliers final: 22 residues processed: 109 average time/residue: 0.0951 time to fit residues: 15.7490 Evaluate side-chains 84 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 779 GLU Chi-restraints excluded: chain B residue 1393 LYS Chi-restraints excluded: chain B residue 1395 LEU Chi-restraints excluded: chain B residue 1441 GLU Chi-restraints excluded: chain B residue 1467 SER Chi-restraints excluded: chain B residue 1500 THR Chi-restraints excluded: chain B residue 1522 VAL Chi-restraints excluded: chain B residue 1586 ASP Chi-restraints excluded: chain B residue 1629 LEU Chi-restraints excluded: chain B residue 1647 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 73 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 116 optimal weight: 0.4980 chunk 71 optimal weight: 0.6980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 ASN B 991 ASN ** B1485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.114665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.084168 restraints weight = 20681.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.087562 restraints weight = 10320.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.089823 restraints weight = 6906.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.091231 restraints weight = 5432.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.092040 restraints weight = 4700.686| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11647 Z= 0.160 Angle : 0.804 15.636 15959 Z= 0.360 Chirality : 0.070 0.760 1743 Planarity : 0.004 0.050 1855 Dihedral : 13.947 175.817 2033 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.35 % Favored : 93.33 % Rotamer: Outliers : 3.15 % Allowed : 15.17 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.17 % 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: -1.55 (0.23), residues: 1244 helix: 0.97 (0.30), residues: 325 sheet: -1.11 (0.36), residues: 192 loop : -2.05 (0.21), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 130 TYR 0.011 0.001 TYR B 194 PHE 0.020 0.001 PHE B1520 TRP 0.008 0.001 TRP B1616 HIS 0.003 0.001 HIS B 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (11637) covalent geometry : angle 0.80344 / 0.36 (15953) hydrogen bonds : bond 0.06055 / 3.44 ( 318) hydrogen bonds : angle 4.73492 / 3.21 ( 926) metal coordination : bond 0.00394 / 0.24 ( 10) metal coordination : angle 2.27875 / 1.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 67 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: B 166 ASP cc_start: 0.8343 (m-30) cc_final: 0.7945 (t0) REVERT: B 178 PHE cc_start: 0.8009 (t80) cc_final: 0.7602 (t80) REVERT: B 343 GLN cc_start: 0.8719 (tp40) cc_final: 0.8212 (mp10) REVERT: B 618 LYS cc_start: 0.9053 (tppt) cc_final: 0.8663 (ttpt) REVERT: B 652 CYS cc_start: 0.8091 (m) cc_final: 0.7736 (t) REVERT: B 972 GLU cc_start: 0.8571 (tp30) cc_final: 0.8309 (tp30) REVERT: B 1027 THR cc_start: 0.8863 (m) cc_final: 0.8612 (t) REVERT: B 1028 LEU cc_start: 0.8394 (pt) cc_final: 0.7938 (pp) REVERT: B 1401 LYS cc_start: 0.8185 (tptt) cc_final: 0.7855 (mttp) REVERT: B 1422 THR cc_start: 0.8332 (t) cc_final: 0.8111 (m) REVERT: B 1607 ILE cc_start: 0.1978 (OUTLIER) cc_final: 0.1647 (mt) outliers start: 34 outliers final: 23 residues processed: 98 average time/residue: 0.0957 time to fit residues: 14.3478 Evaluate side-chains 86 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 83 CYS Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain B residue 779 GLU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 1006 MET Chi-restraints excluded: chain B residue 1393 LYS Chi-restraints excluded: chain B residue 1441 GLU Chi-restraints excluded: chain B residue 1467 SER Chi-restraints excluded: chain B residue 1522 VAL Chi-restraints excluded: chain B residue 1586 ASP Chi-restraints excluded: chain B residue 1607 ILE Chi-restraints excluded: chain B residue 1629 LEU Chi-restraints excluded: chain B residue 1647 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 97 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.115644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.084792 restraints weight = 20736.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.088226 restraints weight = 10338.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.090520 restraints weight = 6926.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.091967 restraints weight = 5455.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.092891 restraints weight = 4711.727| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11647 Z= 0.136 Angle : 0.753 11.767 15959 Z= 0.337 Chirality : 0.064 0.599 1743 Planarity : 0.004 0.048 1855 Dihedral : 13.713 170.262 2033 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.03 % Favored : 93.65 % Rotamer: Outliers : 3.15 % Allowed : 16.28 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.17 % 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: -1.27 (0.23), residues: 1244 helix: 1.26 (0.30), residues: 328 sheet: -0.81 (0.36), residues: 186 loop : -1.96 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 471 TYR 0.010 0.001 TYR B 194 PHE 0.018 0.001 PHE B1520 TRP 0.006 0.001 TRP B 607 HIS 0.003 0.001 HIS B1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (11637) covalent geometry : angle 0.75162 / 0.34 (15953) hydrogen bonds : bond 0.05595 / 3.16 ( 318) hydrogen bonds : angle 4.46171 / 3.02 ( 926) metal coordination : bond 0.00298 / 0.18 ( 10) metal coordination : angle 2.83270 / 1.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 ARG cc_start: 0.7389 (ttp-110) cc_final: 0.7154 (ttp80) REVERT: B 67 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7333 (mt-10) REVERT: B 166 ASP cc_start: 0.8275 (m-30) cc_final: 0.7919 (t0) REVERT: B 178 PHE cc_start: 0.7836 (t80) cc_final: 0.7405 (t80) REVERT: B 343 GLN cc_start: 0.8704 (tp40) cc_final: 0.8204 (mp10) REVERT: B 618 LYS cc_start: 0.9049 (tppt) cc_final: 0.8623 (ttpt) REVERT: B 631 GLU cc_start: 0.8411 (pt0) cc_final: 0.7854 (pm20) REVERT: B 639 ASP cc_start: 0.8057 (p0) cc_final: 0.7384 (t70) REVERT: B 652 CYS cc_start: 0.8030 (m) cc_final: 0.7703 (t) REVERT: B 864 ASP cc_start: 0.8230 (t70) cc_final: 0.7292 (p0) REVERT: B 972 GLU cc_start: 0.8526 (tp30) cc_final: 0.8242 (tp30) REVERT: B 1028 LEU cc_start: 0.8455 (pt) cc_final: 0.8065 (pp) outliers start: 34 outliers final: 25 residues processed: 106 average time/residue: 0.0947 time to fit residues: 15.3679 Evaluate side-chains 91 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 779 GLU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 1006 MET Chi-restraints excluded: chain B residue 1395 LEU Chi-restraints excluded: chain B residue 1441 GLU Chi-restraints excluded: chain B residue 1461 SER Chi-restraints excluded: chain B residue 1467 SER Chi-restraints excluded: chain B residue 1495 LEU Chi-restraints excluded: chain B residue 1522 VAL Chi-restraints excluded: chain B residue 1572 ILE Chi-restraints excluded: chain B residue 1586 ASP Chi-restraints excluded: chain B residue 1647 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.112633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.081995 restraints weight = 20804.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.085334 restraints weight = 10385.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.087535 restraints weight = 7001.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.088975 restraints weight = 5538.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.089828 restraints weight = 4793.459| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11647 Z= 0.181 Angle : 0.796 10.886 15959 Z= 0.359 Chirality : 0.066 0.703 1743 Planarity : 0.004 0.050 1855 Dihedral : 13.805 169.585 2031 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.83 % Favored : 92.85 % Rotamer: Outliers : 3.42 % Allowed : 16.74 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.17 % 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: -1.27 (0.23), residues: 1244 helix: 1.29 (0.30), residues: 319 sheet: -0.91 (0.35), residues: 186 loop : -1.90 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 32 TYR 0.012 0.001 TYR B 558 PHE 0.020 0.001 PHE B1520 TRP 0.008 0.001 TRP B1601 HIS 0.003 0.001 HIS B1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (11637) covalent geometry : angle 0.79480 / 0.36 (15953) hydrogen bonds : bond 0.06065 / 3.48 ( 318) hydrogen bonds : angle 4.54162 / 3.07 ( 926) metal coordination : bond 0.00548 / 0.32 ( 10) metal coordination : angle 2.56870 / 1.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 68 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 TRP cc_start: 0.7317 (t-100) cc_final: 0.6602 (t-100) REVERT: B 67 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7392 (mt-10) REVERT: B 166 ASP cc_start: 0.8277 (m-30) cc_final: 0.7922 (t0) REVERT: B 178 PHE cc_start: 0.7765 (t80) cc_final: 0.7337 (t80) REVERT: B 343 GLN cc_start: 0.8725 (tp40) cc_final: 0.8343 (tm-30) REVERT: B 608 ASP cc_start: 0.7904 (t0) cc_final: 0.7642 (t0) REVERT: B 618 LYS cc_start: 0.8979 (tppt) cc_final: 0.8579 (ttpt) REVERT: B 631 GLU cc_start: 0.8386 (pt0) cc_final: 0.7936 (pm20) REVERT: B 652 CYS cc_start: 0.8177 (m) cc_final: 0.7838 (t) REVERT: B 864 ASP cc_start: 0.8303 (t70) cc_final: 0.7293 (p0) REVERT: B 865 ASP cc_start: 0.8549 (p0) cc_final: 0.7724 (p0) REVERT: B 972 GLU cc_start: 0.8538 (tp30) cc_final: 0.8203 (tp30) REVERT: B 1028 LEU cc_start: 0.8481 (pt) cc_final: 0.8153 (pp) REVERT: B 1538 SER cc_start: 0.9415 (t) cc_final: 0.8988 (p) REVERT: B 1672 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7889 (tt) outliers start: 37 outliers final: 26 residues processed: 101 average time/residue: 0.0946 time to fit residues: 14.7216 Evaluate side-chains 93 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 83 CYS Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 779 GLU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 1006 MET Chi-restraints excluded: chain B residue 1393 LYS Chi-restraints excluded: chain B residue 1395 LEU Chi-restraints excluded: chain B residue 1441 GLU Chi-restraints excluded: chain B residue 1461 SER Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1522 VAL Chi-restraints excluded: chain B residue 1572 ILE Chi-restraints excluded: chain B residue 1586 ASP Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1672 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 123 optimal weight: 0.0470 chunk 13 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 561 HIS ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 HIS B 919 ASN ** B1485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.112175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.081569 restraints weight = 20869.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.084917 restraints weight = 10448.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.087138 restraints weight = 7045.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.088536 restraints weight = 5566.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.089371 restraints weight = 4829.094| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11647 Z= 0.185 Angle : 0.788 11.248 15959 Z= 0.356 Chirality : 0.066 0.700 1743 Planarity : 0.004 0.051 1855 Dihedral : 13.820 169.834 2031 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.23 % Favored : 92.44 % Rotamer: Outliers : 3.15 % Allowed : 17.67 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.17 % 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: -1.25 (0.23), residues: 1244 helix: 1.34 (0.30), residues: 319 sheet: -0.97 (0.35), residues: 184 loop : -1.88 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 471 TYR 0.012 0.001 TYR B 558 PHE 0.018 0.001 PHE B1520 TRP 0.010 0.001 TRP B1601 HIS 0.003 0.001 HIS B 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (11637) covalent geometry : angle 0.78619 / 0.36 (15953) hydrogen bonds : bond 0.06043 / 3.45 ( 318) hydrogen bonds : angle 4.56749 / 3.08 ( 926) metal coordination : bond 0.00516 / 0.30 ( 10) metal coordination : angle 2.72252 / 1.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 66 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: B 39 TRP cc_start: 0.7540 (t-100) cc_final: 0.6925 (t-100) REVERT: B 67 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7368 (mt-10) REVERT: B 166 ASP cc_start: 0.8246 (m-30) cc_final: 0.7867 (t0) REVERT: B 178 PHE cc_start: 0.7825 (t80) cc_final: 0.7383 (t80) REVERT: B 343 GLN cc_start: 0.8712 (tp40) cc_final: 0.8361 (tm-30) REVERT: B 618 LYS cc_start: 0.8967 (tppt) cc_final: 0.8522 (ttpt) REVERT: B 631 GLU cc_start: 0.8361 (pt0) cc_final: 0.7908 (pm20) REVERT: B 639 ASP cc_start: 0.8029 (p0) cc_final: 0.7342 (t70) REVERT: B 652 CYS cc_start: 0.8006 (m) cc_final: 0.7761 (t) REVERT: B 688 GLU cc_start: 0.8238 (tp30) cc_final: 0.7481 (tm-30) REVERT: B 864 ASP cc_start: 0.8351 (t70) cc_final: 0.7851 (p0) REVERT: B 865 ASP cc_start: 0.8713 (p0) cc_final: 0.8095 (p0) REVERT: B 972 GLU cc_start: 0.8500 (tp30) cc_final: 0.8164 (tp30) REVERT: B 1028 LEU cc_start: 0.8407 (pt) cc_final: 0.8146 (pp) REVERT: B 1538 SER cc_start: 0.9422 (t) cc_final: 0.8995 (p) REVERT: B 1672 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7947 (tt) outliers start: 34 outliers final: 27 residues processed: 98 average time/residue: 0.0838 time to fit residues: 13.1480 Evaluate side-chains 90 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 83 CYS Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain B residue 779 GLU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 1006 MET Chi-restraints excluded: chain B residue 1395 LEU Chi-restraints excluded: chain B residue 1441 GLU Chi-restraints excluded: chain B residue 1461 SER Chi-restraints excluded: chain B residue 1489 ILE Chi-restraints excluded: chain B residue 1495 LEU Chi-restraints excluded: chain B residue 1520 PHE Chi-restraints excluded: chain B residue 1522 VAL Chi-restraints excluded: chain B residue 1572 ILE Chi-restraints excluded: chain B residue 1586 ASP Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1672 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 127 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 561 HIS ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 HIS B1483 HIS ** B1485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.111361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.080822 restraints weight = 20747.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.084142 restraints weight = 10427.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.086337 restraints weight = 7040.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.087699 restraints weight = 5573.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.088607 restraints weight = 4840.658| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11647 Z= 0.196 Angle : 0.805 11.258 15959 Z= 0.364 Chirality : 0.067 0.738 1743 Planarity : 0.005 0.053 1855 Dihedral : 13.845 170.569 2027 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.32 % Favored : 92.36 % Rotamer: Outliers : 3.33 % Allowed : 17.95 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.17 % 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: -1.27 (0.23), residues: 1244 helix: 1.30 (0.30), residues: 319 sheet: -1.05 (0.35), residues: 184 loop : -1.86 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 464 TYR 0.013 0.001 TYR B 558 PHE 0.018 0.001 PHE B1520 TRP 0.008 0.001 TRP B1601 HIS 0.009 0.001 HIS B 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (11637) covalent geometry : angle 0.80310 / 0.36 (15953) hydrogen bonds : bond 0.06142 / 3.52 ( 318) hydrogen bonds : angle 4.59215 / 3.10 ( 926) metal coordination : bond 0.00595 / 0.34 ( 10) metal coordination : angle 2.60501 / 1.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 61 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: B 39 TRP cc_start: 0.7497 (t-100) cc_final: 0.6811 (t-100) REVERT: B 67 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7363 (mt-10) REVERT: B 148 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.5909 (m-10) REVERT: B 166 ASP cc_start: 0.8260 (m-30) cc_final: 0.7882 (t0) REVERT: B 178 PHE cc_start: 0.7855 (t80) cc_final: 0.7398 (t80) REVERT: B 343 GLN cc_start: 0.8731 (tp40) cc_final: 0.8377 (tm-30) REVERT: B 618 LYS cc_start: 0.8984 (tppt) cc_final: 0.8556 (ttpt) REVERT: B 631 GLU cc_start: 0.8377 (pt0) cc_final: 0.7909 (pm20) REVERT: B 639 ASP cc_start: 0.8042 (p0) cc_final: 0.7356 (t70) REVERT: B 652 CYS cc_start: 0.8002 (m) cc_final: 0.7765 (t) REVERT: B 688 GLU cc_start: 0.8260 (tp30) cc_final: 0.7517 (tm-30) REVERT: B 972 GLU cc_start: 0.8491 (tp30) cc_final: 0.8164 (tp30) REVERT: B 1028 LEU cc_start: 0.8447 (pt) cc_final: 0.8194 (pp) REVERT: B 1538 SER cc_start: 0.9420 (t) cc_final: 0.9001 (p) REVERT: B 1672 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7991 (tt) outliers start: 36 outliers final: 31 residues processed: 93 average time/residue: 0.0783 time to fit residues: 11.7760 Evaluate side-chains 93 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 83 CYS Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain B residue 779 GLU Chi-restraints excluded: chain B residue 876 ASN Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 1006 MET Chi-restraints excluded: chain B residue 1395 LEU Chi-restraints excluded: chain B residue 1441 GLU Chi-restraints excluded: chain B residue 1461 SER Chi-restraints excluded: chain B residue 1467 SER Chi-restraints excluded: chain B residue 1489 ILE Chi-restraints excluded: chain B residue 1495 LEU Chi-restraints excluded: chain B residue 1520 PHE Chi-restraints excluded: chain B residue 1522 VAL Chi-restraints excluded: chain B residue 1572 ILE Chi-restraints excluded: chain B residue 1586 ASP Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1672 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 123 optimal weight: 0.0670 chunk 129 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 150 ASN B 561 HIS ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 HIS ** B1485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.112450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.081895 restraints weight = 20617.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.085277 restraints weight = 10351.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.087494 restraints weight = 6967.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.088907 restraints weight = 5502.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.089784 restraints weight = 4773.016| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11647 Z= 0.158 Angle : 0.774 11.157 15959 Z= 0.351 Chirality : 0.065 0.679 1743 Planarity : 0.004 0.053 1855 Dihedral : 13.808 171.916 2027 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.07 % Favored : 92.60 % Rotamer: Outliers : 3.33 % Allowed : 18.87 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.17 % 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: -1.20 (0.23), residues: 1244 helix: 1.39 (0.30), residues: 320 sheet: -1.11 (0.35), residues: 183 loop : -1.80 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 471 TYR 0.011 0.001 TYR B 558 PHE 0.018 0.001 PHE B1520 TRP 0.006 0.001 TRP B 664 HIS 0.005 0.001 HIS B1483 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (11637) covalent geometry : angle 0.77255 / 0.35 (15953) hydrogen bonds : bond 0.05780 / 3.26 ( 318) hydrogen bonds : angle 4.48286 / 3.03 ( 926) metal coordination : bond 0.00416 / 0.24 ( 10) metal coordination : angle 2.38321 / 1.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 59 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: B 39 TRP cc_start: 0.7433 (t-100) cc_final: 0.6804 (t-100) REVERT: B 67 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7356 (mt-10) REVERT: B 148 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.5757 (m-10) REVERT: B 166 ASP cc_start: 0.8211 (m-30) cc_final: 0.7874 (t0) REVERT: B 178 PHE cc_start: 0.7826 (t80) cc_final: 0.7387 (t80) REVERT: B 232 ILE cc_start: 0.8870 (mt) cc_final: 0.8293 (tt) REVERT: B 343 GLN cc_start: 0.8722 (tp40) cc_final: 0.8384 (tm-30) REVERT: B 618 LYS cc_start: 0.8966 (tppt) cc_final: 0.8535 (ttpt) REVERT: B 631 GLU cc_start: 0.8406 (pt0) cc_final: 0.7894 (pm20) REVERT: B 639 ASP cc_start: 0.7972 (p0) cc_final: 0.7348 (t70) REVERT: B 652 CYS cc_start: 0.8017 (m) cc_final: 0.7777 (t) REVERT: B 688 GLU cc_start: 0.8251 (tp30) cc_final: 0.7495 (tm-30) REVERT: B 972 GLU cc_start: 0.8403 (tp30) cc_final: 0.8126 (tp30) REVERT: B 1538 SER cc_start: 0.9429 (t) cc_final: 0.9003 (p) REVERT: B 1672 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7939 (tt) outliers start: 36 outliers final: 29 residues processed: 89 average time/residue: 0.0800 time to fit residues: 11.4823 Evaluate side-chains 90 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 59 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 83 CYS Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain B residue 779 GLU Chi-restraints excluded: chain B residue 876 ASN Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 1006 MET Chi-restraints excluded: chain B residue 1393 LYS Chi-restraints excluded: chain B residue 1395 LEU Chi-restraints excluded: chain B residue 1441 GLU Chi-restraints excluded: chain B residue 1461 SER Chi-restraints excluded: chain B residue 1467 SER Chi-restraints excluded: chain B residue 1489 ILE Chi-restraints excluded: chain B residue 1520 PHE Chi-restraints excluded: chain B residue 1522 VAL Chi-restraints excluded: chain B residue 1572 ILE Chi-restraints excluded: chain B residue 1586 ASP Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1672 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 0.0030 chunk 85 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 561 HIS ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 HIS ** B1485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.114458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.083771 restraints weight = 20698.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.087232 restraints weight = 10271.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.089535 restraints weight = 6848.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.090972 restraints weight = 5378.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.091899 restraints weight = 4643.469| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11647 Z= 0.125 Angle : 0.739 11.158 15959 Z= 0.335 Chirality : 0.061 0.584 1743 Planarity : 0.004 0.053 1855 Dihedral : 13.735 173.883 2027 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.87 % Favored : 93.81 % Rotamer: Outliers : 3.15 % Allowed : 19.06 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.17 % 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: -1.05 (0.23), residues: 1244 helix: 1.52 (0.31), residues: 321 sheet: -0.95 (0.35), residues: 181 loop : -1.74 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 471 TYR 0.008 0.001 TYR B 803 PHE 0.017 0.001 PHE B1520 TRP 0.006 0.001 TRP B 664 HIS 0.004 0.001 HIS B 742 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (11637) covalent geometry : angle 0.73744 / 0.33 (15953) hydrogen bonds : bond 0.05401 / 2.98 ( 318) hydrogen bonds : angle 4.32879 / 2.92 ( 926) metal coordination : bond 0.00226 / 0.13 ( 10) metal coordination : angle 2.48743 / 1.10 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 62 time to evaluate : 0.436 Fit side-chains REVERT: B 39 TRP cc_start: 0.7387 (t-100) cc_final: 0.6846 (t-100) REVERT: B 67 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7345 (mt-10) REVERT: B 166 ASP cc_start: 0.8195 (m-30) cc_final: 0.7913 (t0) REVERT: B 178 PHE cc_start: 0.7773 (t80) cc_final: 0.7265 (t80) REVERT: B 232 ILE cc_start: 0.8795 (mt) cc_final: 0.8232 (tt) REVERT: B 343 GLN cc_start: 0.8680 (tp40) cc_final: 0.8370 (tm-30) REVERT: B 618 LYS cc_start: 0.8955 (tppt) cc_final: 0.8507 (ttpt) REVERT: B 631 GLU cc_start: 0.8387 (pt0) cc_final: 0.7867 (pm20) REVERT: B 639 ASP cc_start: 0.7935 (p0) cc_final: 0.7340 (t70) REVERT: B 688 GLU cc_start: 0.8182 (tp30) cc_final: 0.7246 (pp20) REVERT: B 972 GLU cc_start: 0.8367 (tp30) cc_final: 0.8116 (tp30) REVERT: B 1538 SER cc_start: 0.9411 (t) cc_final: 0.8954 (p) outliers start: 34 outliers final: 30 residues processed: 91 average time/residue: 0.0818 time to fit residues: 12.2056 Evaluate side-chains 90 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 561 HIS Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain B residue 779 GLU Chi-restraints excluded: chain B residue 876 ASN Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 1006 MET Chi-restraints excluded: chain B residue 1393 LYS Chi-restraints excluded: chain B residue 1395 LEU Chi-restraints excluded: chain B residue 1441 GLU Chi-restraints excluded: chain B residue 1461 SER Chi-restraints excluded: chain B residue 1467 SER Chi-restraints excluded: chain B residue 1489 ILE Chi-restraints excluded: chain B residue 1495 LEU Chi-restraints excluded: chain B residue 1520 PHE Chi-restraints excluded: chain B residue 1522 VAL Chi-restraints excluded: chain B residue 1572 ILE Chi-restraints excluded: chain B residue 1599 ILE Chi-restraints excluded: chain B residue 1647 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 68 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 128 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 561 HIS ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 HIS ** B1485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.112809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.082327 restraints weight = 20741.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.085688 restraints weight = 10360.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.087933 restraints weight = 6970.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.089334 restraints weight = 5502.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.090225 restraints weight = 4767.730| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11647 Z= 0.163 Angle : 0.762 11.269 15959 Z= 0.344 Chirality : 0.063 0.627 1743 Planarity : 0.004 0.055 1855 Dihedral : 13.750 173.492 2027 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.23 % Favored : 92.44 % Rotamer: Outliers : 2.87 % Allowed : 19.06 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.17 % 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: -1.10 (0.23), residues: 1244 helix: 1.46 (0.30), residues: 321 sheet: -1.03 (0.35), residues: 183 loop : -1.74 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 471 TYR 0.011 0.001 TYR B 558 PHE 0.018 0.001 PHE B1520 TRP 0.007 0.001 TRP B1030 HIS 0.004 0.001 HIS B1483 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (11637) covalent geometry : angle 0.76025 / 0.34 (15953) hydrogen bonds : bond 0.05687 / 3.21 ( 318) hydrogen bonds : angle 4.38662 / 2.97 ( 926) metal coordination : bond 0.00443 / 0.26 ( 10) metal coordination : angle 2.47812 / 1.10 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1773.86 seconds wall clock time: 31 minutes 34.63 seconds (1894.63 seconds total)