Starting phenix.real_space_refine on Mon Dec 30 00:15:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d8n_27252/12_2024/8d8n_27252.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d8n_27252/12_2024/8d8n_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d8n_27252/12_2024/8d8n_27252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d8n_27252/12_2024/8d8n_27252.map" model { file = "/net/cci-nas-00/data/ceres_data/8d8n_27252/12_2024/8d8n_27252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d8n_27252/12_2024/8d8n_27252.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'TYR:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 734 Classifications: {'RNA': 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: {'RNA': 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: 6.70, per 1000 atoms: 0.59 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: 2.87 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 3.77 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: 4.66 Time building geometry restraints manager: 3.33 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: 15466 2.07 - 4.14: 428 4.14 - 6.21: 42 6.21 - 8.28: 12 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 - 35.65: 6767 35.65 - 71.29: 241 71.29 - 106.94: 34 106.94 - 142.59: 1 142.59 - 178.23: 3 Dihedral angle restraints: 7046 sinusoidal: 3461 harmonic: 3585 Sorted by residual: dihedral pdb=" O4' C C 22 " pdb=" C1' C C 22 " pdb=" N1 C C 22 " pdb=" C2 C C 22 " ideal model delta sinusoidal sigma weight residual 200.00 53.09 146.91 1 1.50e+01 4.44e-03 7.84e+01 dihedral pdb=" CA GLY B1439 " pdb=" C GLY B1439 " pdb=" N PRO B1440 " pdb=" CA PRO B1440 " ideal model delta harmonic sigma weight residual -180.00 -139.09 -40.91 0 5.00e+00 4.00e-02 6.70e+01 dihedral pdb=" O4' U C 27 " pdb=" C1' U C 27 " pdb=" N1 U C 27 " pdb=" C2 U C 27 " ideal model delta sinusoidal sigma weight residual 232.00 53.77 178.23 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 7043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1451 0.061 - 0.121: 266 0.121 - 0.182: 22 0.182 - 0.243: 1 0.243 - 0.303: 3 Chirality restraints: 1743 Sorted by residual: chirality pdb=" CA PRO B 911 " pdb=" N PRO B 911 " pdb=" C PRO B 911 " pdb=" CB PRO B 911 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA PRO B 906 " pdb=" N PRO B 906 " pdb=" C PRO B 906 " pdb=" CB PRO B 906 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C1' A C 13 " pdb=" O4' A C 13 " pdb=" C2' A C 13 " pdb=" N9 A C 13 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.26 2.00e-01 2.50e+01 1.65e+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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.250 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 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 0.074 11637 Z= 0.508 Angle : 0.841 10.354 15953 Z= 0.482 Chirality : 0.047 0.303 1743 Planarity : 0.005 0.058 1855 Dihedral : 18.210 178.235 4750 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.002 TRP B 21 HIS 0.008 0.001 HIS B 561 PHE 0.021 0.002 PHE B 52 TYR 0.018 0.002 TYR B 616 ARG 0.006 0.001 ARG B 140 *********************** 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 : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 LEU cc_start: 0.8689 (tp) cc_final: 0.8414 (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: 0.8129 (tt) REVERT: B 178 PHE cc_start: 0.7726 (t80) cc_final: 0.7389 (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: 0.8204 (mp10) REVERT: B 362 TYR cc_start: 0.7946 (t80) cc_final: 0.7651 (t80) REVERT: B 562 LYS cc_start: 0.8940 (tppt) cc_final: 0.8708 (tttp) REVERT: B 618 LYS cc_start: 0.9101 (tppt) cc_final: 0.8654 (ttpt) REVERT: B 627 LYS cc_start: 0.9147 (ttpt) cc_final: 0.8856 (tptt) REVERT: B 652 CYS cc_start: 0.8255 (m) cc_final: 0.7587 (t) REVERT: B 1028 LEU cc_start: 0.7714 (pt) cc_final: 0.7507 (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: 0.5945 (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: 0.2585 time to fit residues: 61.5625 Evaluate side-chains 81 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 109 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN B 155 HIS B 281 GLN ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 ASN B 771 ASN B 980 ASN B1483 HIS B1485 ASN B1544 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11637 Z= 0.202 Angle : 0.623 9.195 15953 Z= 0.324 Chirality : 0.043 0.240 1743 Planarity : 0.005 0.049 1855 Dihedral : 18.304 178.175 2224 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.03 % Favored : 93.65 % Rotamer: Outliers : 2.50 % Allowed : 11.93 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.22), residues: 1244 helix: 0.02 (0.28), residues: 336 sheet: -1.51 (0.34), residues: 186 loop : -2.50 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 585 HIS 0.007 0.001 HIS B 104 PHE 0.017 0.002 PHE B1520 TYR 0.024 0.001 TYR B 194 ARG 0.004 0.000 ARG B1505 *********************** 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 122 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 LEU cc_start: 0.8054 (tp) cc_final: 0.7738 (tp) REVERT: B 166 ASP cc_start: 0.8389 (m-30) cc_final: 0.8035 (t0) REVERT: B 178 PHE cc_start: 0.7787 (t80) cc_final: 0.7398 (t80) REVERT: B 213 LYS cc_start: 0.8294 (mtmt) cc_final: 0.7828 (pttp) REVERT: B 343 GLN cc_start: 0.8750 (tp40) cc_final: 0.8186 (mp10) REVERT: B 362 TYR cc_start: 0.8080 (t80) cc_final: 0.7780 (t80) REVERT: B 608 ASP cc_start: 0.7366 (t0) cc_final: 0.7011 (t70) REVERT: B 618 LYS cc_start: 0.9033 (tppt) cc_final: 0.8669 (ttpt) REVERT: B 632 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.6926 (ptm) REVERT: B 652 CYS cc_start: 0.8412 (m) cc_final: 0.7665 (t) REVERT: B 1028 LEU cc_start: 0.7855 (pt) cc_final: 0.7357 (pp) REVERT: B 1474 GLU cc_start: 0.7613 (pm20) cc_final: 0.7391 (mp0) REVERT: B 1571 LYS cc_start: 0.7989 (mtmm) cc_final: 0.7592 (mttt) REVERT: B 1600 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8063 (tt0) REVERT: B 1640 GLU cc_start: 0.8118 (pm20) cc_final: 0.7917 (mp0) outliers start: 27 outliers final: 13 residues processed: 116 average time/residue: 0.2390 time to fit residues: 41.2685 Evaluate side-chains 82 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 1.710 ------------------------------------------------------------------------------- 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 632 MET Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 1393 LYS 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 1586 ASP Chi-restraints excluded: chain B residue 1589 GLU Chi-restraints excluded: chain B residue 1629 LEU Chi-restraints excluded: chain B residue 1647 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 HIS B 112 ASN B 150 ASN ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 HIS B 784 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11637 Z= 0.369 Angle : 0.676 9.152 15953 Z= 0.350 Chirality : 0.044 0.227 1743 Planarity : 0.005 0.054 1855 Dihedral : 18.132 175.219 2223 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.04 % Favored : 91.64 % Rotamer: Outliers : 3.24 % Allowed : 14.34 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.23), residues: 1244 helix: 0.47 (0.29), residues: 322 sheet: -1.50 (0.36), residues: 189 loop : -2.19 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1616 HIS 0.005 0.001 HIS B1418 PHE 0.021 0.002 PHE B1520 TYR 0.020 0.002 TYR B 558 ARG 0.005 0.001 ARG B 130 *********************** 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 103 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 68 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 166 ASP cc_start: 0.8379 (m-30) cc_final: 0.8047 (t0) REVERT: B 178 PHE cc_start: 0.8102 (t80) cc_final: 0.7565 (t80) REVERT: B 343 GLN cc_start: 0.8658 (tp40) cc_final: 0.7827 (mp10) REVERT: B 458 ASP cc_start: 0.8362 (t0) cc_final: 0.8160 (t0) REVERT: B 608 ASP cc_start: 0.7817 (t0) cc_final: 0.7609 (t0) REVERT: B 652 CYS cc_start: 0.8396 (m) cc_final: 0.7958 (t) REVERT: B 742 HIS cc_start: 0.6294 (OUTLIER) cc_final: 0.5592 (t-170) REVERT: B 950 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7949 (pp) REVERT: B 1028 LEU cc_start: 0.8181 (pt) cc_final: 0.7794 (pp) REVERT: B 1401 LYS cc_start: 0.7946 (tptt) cc_final: 0.7740 (mtpp) REVERT: B 1474 GLU cc_start: 0.7894 (pm20) cc_final: 0.7594 (tt0) REVERT: B 1512 MET cc_start: 0.7670 (mmm) cc_final: 0.7435 (mmm) REVERT: B 1600 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8122 (tt0) outliers start: 35 outliers final: 22 residues processed: 100 average time/residue: 0.2030 time to fit residues: 31.4223 Evaluate side-chains 80 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 742 HIS Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 779 GLU Chi-restraints excluded: chain B residue 950 LEU 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 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 116 optimal weight: 0.1980 chunk 88 optimal weight: 0.4980 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 125 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 561 HIS ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11637 Z= 0.173 Angle : 0.563 9.446 15953 Z= 0.290 Chirality : 0.040 0.218 1743 Planarity : 0.004 0.050 1855 Dihedral : 18.003 177.096 2223 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.63 % Favored : 94.05 % Rotamer: Outliers : 2.87 % Allowed : 15.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.23), residues: 1244 helix: 1.04 (0.30), residues: 325 sheet: -1.13 (0.36), residues: 189 loop : -2.04 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1530 HIS 0.003 0.001 HIS B 722 PHE 0.017 0.001 PHE B1520 TYR 0.008 0.001 TYR B 803 ARG 0.003 0.000 ARG B1528 *********************** 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 99 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 68 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 166 ASP cc_start: 0.8335 (m-30) cc_final: 0.7985 (t0) REVERT: B 178 PHE cc_start: 0.7943 (t80) cc_final: 0.7443 (t80) REVERT: B 343 GLN cc_start: 0.8715 (tp40) cc_final: 0.8007 (mp10) REVERT: B 458 ASP cc_start: 0.8447 (t0) cc_final: 0.8211 (t0) REVERT: B 618 LYS cc_start: 0.9027 (tppt) cc_final: 0.8558 (ttpt) REVERT: B 652 CYS cc_start: 0.8420 (m) cc_final: 0.8012 (t) REVERT: B 864 ASP cc_start: 0.8114 (t70) cc_final: 0.7774 (t70) REVERT: B 950 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8110 (pp) REVERT: B 972 GLU cc_start: 0.8643 (tp30) cc_final: 0.8197 (tp30) REVERT: B 1028 LEU cc_start: 0.8006 (pt) cc_final: 0.7632 (pp) REVERT: B 1474 GLU cc_start: 0.7871 (pm20) cc_final: 0.7570 (tt0) REVERT: B 1512 MET cc_start: 0.7800 (mmm) cc_final: 0.7364 (mmm) REVERT: B 1600 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8147 (tt0) outliers start: 31 outliers final: 22 residues processed: 98 average time/residue: 0.2233 time to fit residues: 33.3761 Evaluate side-chains 83 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 230 CYS 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 779 GLU Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain B residue 1006 MET Chi-restraints excluded: chain B residue 1024 GLU 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 1522 VAL Chi-restraints excluded: chain B residue 1586 ASP 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 104 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B 991 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11637 Z= 0.292 Angle : 0.602 9.417 15953 Z= 0.310 Chirality : 0.042 0.219 1743 Planarity : 0.005 0.051 1855 Dihedral : 17.958 176.566 2221 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.04 % Favored : 91.64 % Rotamer: Outliers : 3.61 % Allowed : 15.36 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.23), residues: 1244 helix: 1.09 (0.30), residues: 324 sheet: -1.24 (0.35), residues: 189 loop : -2.03 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1616 HIS 0.005 0.001 HIS B 722 PHE 0.020 0.001 PHE B1520 TYR 0.013 0.001 TYR B 558 ARG 0.002 0.000 ARG B 464 *********************** 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 98 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 59 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 TRP cc_start: 0.7723 (t-100) cc_final: 0.7310 (t-100) REVERT: B 166 ASP cc_start: 0.8339 (m-30) cc_final: 0.7953 (t0) REVERT: B 178 PHE cc_start: 0.7931 (t80) cc_final: 0.7426 (t80) REVERT: B 343 GLN cc_start: 0.8594 (tp40) cc_final: 0.8200 (tm-30) REVERT: B 458 ASP cc_start: 0.8565 (t0) cc_final: 0.8292 (t0) REVERT: B 608 ASP cc_start: 0.7988 (t0) cc_final: 0.7720 (t0) REVERT: B 618 LYS cc_start: 0.9077 (tppt) cc_final: 0.8648 (ttpt) REVERT: B 652 CYS cc_start: 0.8430 (m) cc_final: 0.8038 (t) REVERT: B 742 HIS cc_start: 0.5897 (OUTLIER) cc_final: 0.5359 (t-170) REVERT: B 864 ASP cc_start: 0.8175 (t70) cc_final: 0.7154 (p0) REVERT: B 950 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7968 (pp) REVERT: B 972 GLU cc_start: 0.8548 (tp30) cc_final: 0.8098 (tp30) REVERT: B 1028 LEU cc_start: 0.7625 (pt) cc_final: 0.7379 (pp) REVERT: B 1474 GLU cc_start: 0.8002 (pm20) cc_final: 0.7570 (tt0) REVERT: B 1538 SER cc_start: 0.9220 (t) cc_final: 0.8788 (p) REVERT: B 1600 GLU cc_start: 0.8470 (tm-30) cc_final: 0.7953 (tt0) REVERT: B 1651 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8521 (pp20) REVERT: B 1672 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6789 (tt) outliers start: 39 outliers final: 28 residues processed: 95 average time/residue: 0.2108 time to fit residues: 31.2182 Evaluate side-chains 91 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 162 LEU Chi-restraints excluded: chain B residue 229 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 451 THR Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 610 ASN 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 950 LEU 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 1489 ILE 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 Chi-restraints excluded: chain B residue 1651 GLU Chi-restraints excluded: chain B residue 1672 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1483 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11637 Z= 0.340 Angle : 0.632 9.141 15953 Z= 0.326 Chirality : 0.043 0.219 1743 Planarity : 0.005 0.054 1855 Dihedral : 17.971 178.507 2221 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.56 % Favored : 92.12 % Rotamer: Outliers : 3.98 % Allowed : 15.73 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.23), residues: 1244 helix: 1.09 (0.30), residues: 317 sheet: -1.32 (0.35), residues: 184 loop : -2.01 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1601 HIS 0.006 0.001 HIS B 722 PHE 0.022 0.002 PHE B1520 TYR 0.015 0.002 TYR B 558 ARG 0.004 0.000 ARG B 523 *********************** 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: 43 poor density : 62 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 TRP cc_start: 0.7813 (t-100) cc_final: 0.7396 (t-100) REVERT: B 67 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7541 (mt-10) REVERT: B 166 ASP cc_start: 0.8346 (m-30) cc_final: 0.7959 (t0) REVERT: B 178 PHE cc_start: 0.7974 (t80) cc_final: 0.7424 (t80) REVERT: B 343 GLN cc_start: 0.8680 (tp40) cc_final: 0.8273 (tm-30) REVERT: B 608 ASP cc_start: 0.8387 (t0) cc_final: 0.8081 (t0) REVERT: B 618 LYS cc_start: 0.9062 (tppt) cc_final: 0.8632 (ttpt) REVERT: B 652 CYS cc_start: 0.8473 (m) cc_final: 0.8120 (t) REVERT: B 688 GLU cc_start: 0.8336 (tp30) cc_final: 0.7328 (tm-30) REVERT: B 742 HIS cc_start: 0.5909 (OUTLIER) cc_final: 0.5305 (t-170) REVERT: B 864 ASP cc_start: 0.8269 (t70) cc_final: 0.7283 (p0) REVERT: B 865 ASP cc_start: 0.8741 (p0) cc_final: 0.8351 (p0) REVERT: B 972 GLU cc_start: 0.8472 (tp30) cc_final: 0.8024 (tp30) REVERT: B 1474 GLU cc_start: 0.8099 (pm20) cc_final: 0.7598 (mt-10) REVERT: B 1538 SER cc_start: 0.9245 (t) cc_final: 0.8826 (p) REVERT: B 1651 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8410 (pp20) REVERT: B 1672 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6791 (tt) outliers start: 43 outliers final: 30 residues processed: 102 average time/residue: 0.2240 time to fit residues: 34.6270 Evaluate side-chains 91 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 58 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 101 ARG Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 229 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 570 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 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 1522 VAL Chi-restraints excluded: chain B residue 1582 VAL Chi-restraints excluded: chain B residue 1586 ASP Chi-restraints excluded: chain B residue 1651 GLU 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: 4.9990 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 125 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 561 HIS ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11637 Z= 0.200 Angle : 0.566 9.349 15953 Z= 0.291 Chirality : 0.041 0.224 1743 Planarity : 0.004 0.050 1855 Dihedral : 17.849 178.987 2221 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.27 % Favored : 93.41 % Rotamer: Outliers : 3.33 % Allowed : 17.85 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.23), residues: 1244 helix: 1.33 (0.30), residues: 321 sheet: -1.24 (0.35), residues: 181 loop : -1.87 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 39 HIS 0.004 0.001 HIS B 722 PHE 0.018 0.001 PHE B1520 TYR 0.009 0.001 TYR B 845 ARG 0.004 0.000 ARG B 140 *********************** 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: 36 poor density : 64 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: B 39 TRP cc_start: 0.7724 (t-100) cc_final: 0.7289 (t-100) REVERT: B 67 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7487 (mt-10) REVERT: B 166 ASP cc_start: 0.8281 (m-30) cc_final: 0.7964 (t0) REVERT: B 178 PHE cc_start: 0.7937 (t80) cc_final: 0.7420 (t80) REVERT: B 232 ILE cc_start: 0.8766 (mt) cc_final: 0.8208 (tt) REVERT: B 343 GLN cc_start: 0.8656 (tp40) cc_final: 0.8304 (tm-30) REVERT: B 458 ASP cc_start: 0.8533 (t0) cc_final: 0.8276 (t0) REVERT: B 608 ASP cc_start: 0.8366 (t0) cc_final: 0.8085 (t0) REVERT: B 618 LYS cc_start: 0.8955 (tppt) cc_final: 0.8510 (ttpt) REVERT: B 630 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8796 (tp) REVERT: B 652 CYS cc_start: 0.8414 (m) cc_final: 0.8137 (t) REVERT: B 688 GLU cc_start: 0.8277 (tp30) cc_final: 0.7239 (tm-30) REVERT: B 742 HIS cc_start: 0.5856 (OUTLIER) cc_final: 0.5209 (t-170) REVERT: B 864 ASP cc_start: 0.8264 (t70) cc_final: 0.7972 (t70) REVERT: B 972 GLU cc_start: 0.8473 (tp30) cc_final: 0.8016 (tp30) REVERT: B 1474 GLU cc_start: 0.8052 (pm20) cc_final: 0.7528 (mt-10) REVERT: B 1538 SER cc_start: 0.9267 (t) cc_final: 0.8829 (p) REVERT: B 1672 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6904 (tt) outliers start: 36 outliers final: 28 residues processed: 96 average time/residue: 0.2189 time to fit residues: 32.2608 Evaluate side-chains 93 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 62 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 101 ARG Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 229 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 451 THR Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 630 LEU 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 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 1520 PHE Chi-restraints excluded: chain B residue 1522 VAL Chi-restraints excluded: chain B residue 1572 ILE Chi-restraints excluded: chain B residue 1582 VAL 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 50 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 98 optimal weight: 0.1980 chunk 113 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 561 HIS ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11637 Z= 0.169 Angle : 0.560 11.183 15953 Z= 0.284 Chirality : 0.040 0.218 1743 Planarity : 0.004 0.049 1855 Dihedral : 17.750 179.802 2221 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.27 % Favored : 93.41 % Rotamer: Outliers : 3.24 % Allowed : 18.22 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.23), residues: 1244 helix: 1.49 (0.31), residues: 322 sheet: -1.06 (0.35), residues: 181 loop : -1.75 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 39 HIS 0.003 0.001 HIS B 155 PHE 0.016 0.001 PHE B1520 TYR 0.009 0.001 TYR B 803 ARG 0.002 0.000 ARG B1505 *********************** 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 101 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 66 time to evaluate : 1.270 Fit side-chains revert: symmetry clash REVERT: B 39 TRP cc_start: 0.7301 (t-100) cc_final: 0.6792 (t-100) REVERT: B 67 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7468 (mt-10) REVERT: B 166 ASP cc_start: 0.8215 (m-30) cc_final: 0.7921 (t0) REVERT: B 178 PHE cc_start: 0.7924 (t80) cc_final: 0.7331 (t80) REVERT: B 232 ILE cc_start: 0.8803 (mt) cc_final: 0.8265 (tt) REVERT: B 343 GLN cc_start: 0.8640 (tp40) cc_final: 0.8297 (tm-30) REVERT: B 362 TYR cc_start: 0.8202 (t80) cc_final: 0.7999 (t80) REVERT: B 608 ASP cc_start: 0.8356 (t0) cc_final: 0.8076 (t0) REVERT: B 652 CYS cc_start: 0.8389 (m) cc_final: 0.8131 (t) REVERT: B 688 GLU cc_start: 0.8219 (tp30) cc_final: 0.7010 (pp20) REVERT: B 720 GLU cc_start: 0.8505 (mp0) cc_final: 0.8224 (mp0) REVERT: B 742 HIS cc_start: 0.5823 (OUTLIER) cc_final: 0.5205 (t-170) REVERT: B 864 ASP cc_start: 0.8357 (t70) cc_final: 0.8030 (t70) REVERT: B 972 GLU cc_start: 0.8454 (tp30) cc_final: 0.7988 (tp30) REVERT: B 1474 GLU cc_start: 0.8093 (pm20) cc_final: 0.7484 (mt-10) REVERT: B 1538 SER cc_start: 0.9266 (t) cc_final: 0.8816 (p) outliers start: 35 outliers final: 28 residues processed: 97 average time/residue: 0.2103 time to fit residues: 32.1885 Evaluate side-chains 91 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 434 ILE 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 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 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 1522 VAL Chi-restraints excluded: chain B residue 1572 ILE Chi-restraints excluded: chain B residue 1582 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 91 optimal weight: 0.0870 chunk 35 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 123 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 561 HIS ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11637 Z= 0.166 Angle : 0.559 10.486 15953 Z= 0.282 Chirality : 0.039 0.218 1743 Planarity : 0.004 0.053 1855 Dihedral : 17.602 179.753 2217 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.79 % Favored : 93.89 % Rotamer: Outliers : 3.15 % Allowed : 18.50 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.24), residues: 1244 helix: 1.60 (0.31), residues: 322 sheet: -0.89 (0.35), residues: 180 loop : -1.68 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 585 HIS 0.004 0.001 HIS B 104 PHE 0.012 0.001 PHE B1520 TYR 0.009 0.001 TYR B 803 ARG 0.002 0.000 ARG B 101 *********************** 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 99 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 65 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: B 39 TRP cc_start: 0.7407 (t-100) cc_final: 0.6915 (t-100) REVERT: B 67 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7471 (mt-10) REVERT: B 166 ASP cc_start: 0.8113 (m-30) cc_final: 0.7838 (t0) REVERT: B 178 PHE cc_start: 0.7903 (t80) cc_final: 0.7331 (t80) REVERT: B 232 ILE cc_start: 0.8800 (mt) cc_final: 0.8298 (tt) REVERT: B 263 ASP cc_start: 0.8833 (t0) cc_final: 0.8630 (m-30) REVERT: B 343 GLN cc_start: 0.8613 (tp40) cc_final: 0.8286 (tm-30) REVERT: B 362 TYR cc_start: 0.8271 (t80) cc_final: 0.8067 (t80) REVERT: B 618 LYS cc_start: 0.8928 (tppt) cc_final: 0.8507 (ttpt) REVERT: B 688 GLU cc_start: 0.8163 (tp30) cc_final: 0.6998 (pp20) REVERT: B 720 GLU cc_start: 0.8498 (mp0) cc_final: 0.8226 (mp0) REVERT: B 742 HIS cc_start: 0.5838 (OUTLIER) cc_final: 0.5233 (t-170) REVERT: B 864 ASP cc_start: 0.8373 (t70) cc_final: 0.8040 (t70) REVERT: B 972 GLU cc_start: 0.8414 (tp30) cc_final: 0.7999 (tp30) REVERT: B 1474 GLU cc_start: 0.8094 (pm20) cc_final: 0.7448 (mt-10) REVERT: B 1538 SER cc_start: 0.9262 (t) cc_final: 0.8810 (p) outliers start: 34 outliers final: 30 residues processed: 93 average time/residue: 0.1896 time to fit residues: 28.4124 Evaluate side-chains 92 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 54 THR 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 434 ILE 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 632 MET 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 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 1582 VAL Chi-restraints excluded: chain B residue 1586 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 561 HIS ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11637 Z= 0.186 Angle : 0.561 10.514 15953 Z= 0.284 Chirality : 0.040 0.217 1743 Planarity : 0.004 0.054 1855 Dihedral : 17.574 179.677 2217 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.19 % Favored : 93.49 % Rotamer: Outliers : 2.96 % Allowed : 18.78 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.24), residues: 1244 helix: 1.62 (0.31), residues: 322 sheet: -0.90 (0.35), residues: 180 loop : -1.65 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 39 HIS 0.003 0.001 HIS B 722 PHE 0.014 0.001 PHE B1520 TYR 0.008 0.001 TYR B 803 ARG 0.002 0.000 ARG B 559 ********************** 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 93 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 61 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: B 39 TRP cc_start: 0.7423 (t-100) cc_final: 0.6911 (t-100) REVERT: B 67 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7476 (mt-10) REVERT: B 166 ASP cc_start: 0.8107 (m-30) cc_final: 0.7835 (t0) REVERT: B 178 PHE cc_start: 0.7900 (t80) cc_final: 0.7335 (t80) REVERT: B 232 ILE cc_start: 0.8872 (mt) cc_final: 0.8370 (tt) REVERT: B 263 ASP cc_start: 0.8829 (t0) cc_final: 0.8628 (m-30) REVERT: B 343 GLN cc_start: 0.8603 (tp40) cc_final: 0.8256 (tm-30) REVERT: B 362 TYR cc_start: 0.8278 (t80) cc_final: 0.8074 (t80) REVERT: B 618 LYS cc_start: 0.8961 (tppt) cc_final: 0.8473 (ttpt) REVERT: B 688 GLU cc_start: 0.8184 (tp30) cc_final: 0.7038 (pp20) REVERT: B 720 GLU cc_start: 0.8502 (mp0) cc_final: 0.8222 (mp0) REVERT: B 742 HIS cc_start: 0.5883 (OUTLIER) cc_final: 0.5269 (t-170) REVERT: B 864 ASP cc_start: 0.8412 (t70) cc_final: 0.8072 (t70) REVERT: B 972 GLU cc_start: 0.8379 (tp30) cc_final: 0.7978 (tp30) REVERT: B 1474 GLU cc_start: 0.8110 (pm20) cc_final: 0.7450 (mt-10) REVERT: B 1538 SER cc_start: 0.9260 (t) cc_final: 0.8807 (p) outliers start: 32 outliers final: 29 residues processed: 88 average time/residue: 0.1957 time to fit residues: 27.6121 Evaluate side-chains 91 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 54 THR 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 434 ILE 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 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 951 SER 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 1522 VAL Chi-restraints excluded: chain B residue 1572 ILE Chi-restraints excluded: chain B residue 1582 VAL Chi-restraints excluded: chain B residue 1586 ASP 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 31 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 103 optimal weight: 0.0020 chunk 43 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 561 HIS ** B 668 GLN ** 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 = 0.3537 r_free = 0.3537 target = 0.111582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.080132 restraints weight = 19107.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.083554 restraints weight = 9444.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.085841 restraints weight = 6307.519| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11637 Z= 0.175 Angle : 0.562 11.804 15953 Z= 0.282 Chirality : 0.039 0.218 1743 Planarity : 0.004 0.052 1855 Dihedral : 17.526 179.398 2217 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.63 % Favored : 94.05 % Rotamer: Outliers : 2.78 % Allowed : 19.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.23), residues: 1244 helix: 1.55 (0.30), residues: 328 sheet: -0.82 (0.35), residues: 180 loop : -1.66 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 585 HIS 0.003 0.001 HIS B1621 PHE 0.014 0.001 PHE B1520 TYR 0.009 0.001 TYR B 803 ARG 0.003 0.000 ARG B 506 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1941.02 seconds wall clock time: 36 minutes 58.08 seconds (2218.08 seconds total)