Starting phenix.real_space_refine on Tue Jul 29 22:07:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d8n_27252/07_2025/8d8n_27252.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d8n_27252/07_2025/8d8n_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_27252/07_2025/8d8n_27252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d8n_27252/07_2025/8d8n_27252.map" model { file = "/net/cci-nas-00/data/ceres_data/8d8n_27252/07_2025/8d8n_27252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d8n_27252/07_2025/8d8n_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.52, per 1000 atoms: 0.67 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: 2.53 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: 3.52 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: 4.48 Time building geometry restraints manager: 3.06 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: 1.070 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 33.280 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.140 ------------------------------------------------------------------------------- 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 0.141 11647 Z= 0.366 Angle : 0.986 55.277 15959 Z= 0.491 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 Details of bonding type rmsd hydrogen bonds : bond 0.20375 ( 318) hydrogen bonds : angle 8.40446 ( 926) metal coordination : bond 0.06410 ( 10) metal coordination : angle 26.48146 ( 6) covalent geometry : bond 0.00778 (11637) covalent geometry : angle 0.84145 (15953) *********************** 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 : 1.234 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: 0.2576 time to fit residues: 61.4200 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 : 1.232 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.117099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.086726 restraints weight = 20316.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.090130 restraints weight = 10230.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.092402 restraints weight = 6895.141| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 11647 Z= 0.142 Angle : 0.628 9.195 15959 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 Details of bonding type rmsd hydrogen bonds : bond 0.06316 ( 318) hydrogen bonds : angle 5.31155 ( 926) metal coordination : bond 0.00662 ( 10) metal coordination : angle 3.98895 ( 6) covalent geometry : bond 0.00309 (11637) covalent geometry : angle 0.62306 (15953) *********************** 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 : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 LEU cc_start: 0.7925 (tp) cc_final: 0.7636 (tp) REVERT: B 166 ASP cc_start: 0.8409 (m-30) cc_final: 0.8024 (t0) REVERT: B 178 PHE cc_start: 0.7713 (t80) cc_final: 0.7383 (t80) REVERT: B 213 LYS cc_start: 0.8164 (mtmt) cc_final: 0.7639 (pttp) REVERT: B 343 GLN cc_start: 0.8729 (tp40) cc_final: 0.8399 (mp10) REVERT: B 362 TYR cc_start: 0.8390 (t80) cc_final: 0.8085 (t80) REVERT: B 608 ASP cc_start: 0.7197 (t0) cc_final: 0.6899 (t70) REVERT: B 618 LYS cc_start: 0.9027 (tppt) cc_final: 0.8688 (ttpt) REVERT: B 632 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7051 (ptm) REVERT: B 652 CYS cc_start: 0.8131 (m) cc_final: 0.7508 (t) REVERT: B 874 MET cc_start: 0.5109 (mtp) cc_final: 0.4894 (mtp) REVERT: B 1028 LEU cc_start: 0.8343 (pt) cc_final: 0.7876 (pp) REVERT: B 1571 LYS cc_start: 0.8217 (mtmm) cc_final: 0.7929 (mttt) outliers start: 27 outliers final: 13 residues processed: 116 average time/residue: 0.2389 time to fit residues: 41.2154 Evaluate side-chains 80 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 88 optimal weight: 0.2980 chunk 115 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 105 optimal weight: 0.0170 chunk 36 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.4624 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.111591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.080394 restraints weight = 20490.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.083632 restraints weight = 10610.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.085795 restraints weight = 7295.352| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11647 Z= 0.181 Angle : 0.611 9.439 15959 Z= 0.314 Chirality : 0.042 0.226 1743 Planarity : 0.005 0.051 1855 Dihedral : 18.038 176.660 2223 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.67 % Favored : 93.01 % Rotamer: Outliers : 2.96 % Allowed : 14.15 % Favored : 82.89 % 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: -1.72 (0.23), residues: 1244 helix: 0.76 (0.29), residues: 324 sheet: -1.27 (0.36), residues: 197 loop : -2.10 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 190 HIS 0.005 0.001 HIS B 104 PHE 0.020 0.002 PHE B1520 TYR 0.015 0.002 TYR B 558 ARG 0.005 0.000 ARG B 130 Details of bonding type rmsd hydrogen bonds : bond 0.06450 ( 318) hydrogen bonds : angle 4.86839 ( 926) metal coordination : bond 0.00569 ( 10) metal coordination : angle 3.28341 ( 6) covalent geometry : bond 0.00407 (11637) covalent geometry : angle 0.60813 (15953) *********************** 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 101 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 166 ASP cc_start: 0.8360 (m-30) cc_final: 0.7979 (t0) REVERT: B 178 PHE cc_start: 0.7954 (t80) cc_final: 0.7499 (t80) REVERT: B 213 LYS cc_start: 0.8416 (mtmt) cc_final: 0.7989 (pttp) REVERT: B 343 GLN cc_start: 0.8779 (tp40) cc_final: 0.8251 (mp10) REVERT: B 652 CYS cc_start: 0.8240 (m) cc_final: 0.7835 (t) REVERT: B 742 HIS cc_start: 0.6019 (OUTLIER) cc_final: 0.5617 (t-170) REVERT: B 1027 THR cc_start: 0.8931 (m) cc_final: 0.8731 (t) REVERT: B 1028 LEU cc_start: 0.8598 (pt) cc_final: 0.8195 (pp) REVERT: B 1401 LYS cc_start: 0.8227 (tptt) cc_final: 0.7798 (mtpp) outliers start: 32 outliers final: 20 residues processed: 98 average time/residue: 0.2078 time to fit residues: 31.6452 Evaluate side-chains 78 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 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 779 GLU 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 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 64 optimal weight: 0.0020 chunk 58 optimal weight: 2.9990 chunk 116 optimal weight: 0.0570 chunk 100 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.5506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 ASN B 561 HIS ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.114527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.083608 restraints weight = 20385.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.086977 restraints weight = 10417.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.089217 restraints weight = 7084.790| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11647 Z= 0.108 Angle : 0.548 9.556 15959 Z= 0.281 Chirality : 0.040 0.227 1743 Planarity : 0.004 0.046 1855 Dihedral : 17.919 178.695 2223 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.23 % Favored : 94.45 % Rotamer: Outliers : 2.68 % Allowed : 15.91 % Favored : 81.41 % 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: -1.30 (0.23), residues: 1244 helix: 1.19 (0.30), residues: 327 sheet: -0.85 (0.37), residues: 184 loop : -1.93 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 585 HIS 0.002 0.000 HIS B 722 PHE 0.015 0.001 PHE B1520 TYR 0.009 0.001 TYR B 803 ARG 0.003 0.000 ARG B1528 Details of bonding type rmsd hydrogen bonds : bond 0.05544 ( 318) hydrogen bonds : angle 4.46442 ( 926) metal coordination : bond 0.00191 ( 10) metal coordination : angle 1.85508 ( 6) covalent geometry : bond 0.00237 (11637) covalent geometry : angle 0.54687 (15953) *********************** 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 98 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 166 ASP cc_start: 0.8343 (m-30) cc_final: 0.7993 (t0) REVERT: B 178 PHE cc_start: 0.7995 (t80) cc_final: 0.7623 (t80) REVERT: B 343 GLN cc_start: 0.8689 (tp40) cc_final: 0.8274 (mp10) REVERT: B 608 ASP cc_start: 0.7509 (t0) cc_final: 0.7192 (t70) REVERT: B 618 LYS cc_start: 0.9014 (tppt) cc_final: 0.8664 (ttpt) REVERT: B 632 MET cc_start: 0.7527 (ptp) cc_final: 0.7193 (ptm) REVERT: B 652 CYS cc_start: 0.8169 (m) cc_final: 0.7842 (t) REVERT: B 972 GLU cc_start: 0.8597 (tp30) cc_final: 0.8353 (tp30) REVERT: B 1027 THR cc_start: 0.8820 (m) cc_final: 0.8542 (t) REVERT: B 1028 LEU cc_start: 0.8543 (pt) cc_final: 0.8148 (pp) REVERT: B 1401 LYS cc_start: 0.8151 (tptt) cc_final: 0.7840 (mtpp) outliers start: 29 outliers final: 16 residues processed: 96 average time/residue: 0.2018 time to fit residues: 30.0137 Evaluate side-chains 77 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 101 ARG Chi-restraints excluded: chain B residue 146 ILE 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 920 ILE Chi-restraints excluded: chain B residue 1006 MET Chi-restraints excluded: chain B residue 1024 GLU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 112 optimal weight: 1.9990 chunk 42 optimal weight: 0.0030 chunk 108 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 7 optimal weight: 0.0370 chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.4668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 991 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.115164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.083485 restraints weight = 20314.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.086889 restraints weight = 10471.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.089158 restraints weight = 7178.242| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11647 Z= 0.103 Angle : 0.536 9.778 15959 Z= 0.273 Chirality : 0.039 0.217 1743 Planarity : 0.004 0.045 1855 Dihedral : 17.781 179.387 2221 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.23 % Favored : 94.45 % Rotamer: Outliers : 2.22 % Allowed : 17.30 % Favored : 80.48 % 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: -1.06 (0.24), residues: 1244 helix: 1.42 (0.30), residues: 328 sheet: -0.71 (0.35), residues: 192 loop : -1.81 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 585 HIS 0.002 0.000 HIS B1621 PHE 0.016 0.001 PHE B1520 TYR 0.009 0.001 TYR B 362 ARG 0.002 0.000 ARG B1505 Details of bonding type rmsd hydrogen bonds : bond 0.05423 ( 318) hydrogen bonds : angle 4.22540 ( 926) metal coordination : bond 0.00211 ( 10) metal coordination : angle 2.83601 ( 6) covalent geometry : bond 0.00226 (11637) covalent geometry : angle 0.53328 (15953) *********************** 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 96 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.7879 (tpp) cc_final: 0.7071 (mmm) REVERT: B 166 ASP cc_start: 0.8270 (m-30) cc_final: 0.7931 (t0) REVERT: B 178 PHE cc_start: 0.8017 (t80) cc_final: 0.7651 (t80) REVERT: B 343 GLN cc_start: 0.8712 (tp40) cc_final: 0.8252 (mp10) REVERT: B 362 TYR cc_start: 0.8412 (t80) cc_final: 0.8185 (t80) REVERT: B 608 ASP cc_start: 0.7576 (t0) cc_final: 0.7166 (t70) REVERT: B 618 LYS cc_start: 0.9022 (tppt) cc_final: 0.8671 (ttpt) REVERT: B 652 CYS cc_start: 0.8133 (m) cc_final: 0.7781 (t) REVERT: B 864 ASP cc_start: 0.8165 (t70) cc_final: 0.7129 (p0) REVERT: B 972 GLU cc_start: 0.8551 (tp30) cc_final: 0.8252 (tp30) REVERT: B 1027 THR cc_start: 0.8797 (m) cc_final: 0.8528 (t) REVERT: B 1028 LEU cc_start: 0.8549 (pt) cc_final: 0.8167 (pp) REVERT: B 1401 LYS cc_start: 0.8143 (tptt) cc_final: 0.7935 (mtpp) outliers start: 24 outliers final: 18 residues processed: 93 average time/residue: 0.2039 time to fit residues: 29.2100 Evaluate side-chains 78 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP 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 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 1006 MET Chi-restraints excluded: chain B residue 1024 GLU Chi-restraints excluded: chain B residue 1441 GLU 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 50 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 0.0040 chunk 64 optimal weight: 5.9990 chunk 29 optimal weight: 0.0020 chunk 37 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.7202 ------------------------------------------------------------------------------- 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** B1671 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.114232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.083097 restraints weight = 20569.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.086450 restraints weight = 10500.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.088641 restraints weight = 7149.810| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11647 Z= 0.115 Angle : 0.541 9.699 15959 Z= 0.276 Chirality : 0.039 0.214 1743 Planarity : 0.004 0.045 1855 Dihedral : 17.733 179.674 2221 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.79 % Favored : 93.89 % Rotamer: Outliers : 2.68 % Allowed : 17.76 % Favored : 79.56 % 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: -0.94 (0.24), residues: 1244 helix: 1.53 (0.30), residues: 328 sheet: -0.57 (0.36), residues: 184 loop : -1.75 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 607 HIS 0.003 0.001 HIS B 722 PHE 0.017 0.001 PHE B1520 TYR 0.008 0.001 TYR B 362 ARG 0.002 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.05370 ( 318) hydrogen bonds : angle 4.18116 ( 926) metal coordination : bond 0.00264 ( 10) metal coordination : angle 2.61326 ( 6) covalent geometry : bond 0.00260 (11637) covalent geometry : angle 0.53871 (15953) *********************** 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 92 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.7923 (tpp) cc_final: 0.7139 (mmm) REVERT: B 67 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7361 (mt-10) REVERT: B 139 GLU cc_start: 0.7122 (pp20) cc_final: 0.6789 (pp20) REVERT: B 166 ASP cc_start: 0.8251 (m-30) cc_final: 0.7926 (t0) REVERT: B 178 PHE cc_start: 0.7850 (t80) cc_final: 0.7461 (t80) REVERT: B 343 GLN cc_start: 0.8679 (tp40) cc_final: 0.8272 (mp10) REVERT: B 608 ASP cc_start: 0.7774 (t0) cc_final: 0.7355 (t70) REVERT: B 618 LYS cc_start: 0.8977 (tppt) cc_final: 0.8583 (ttpt) REVERT: B 639 ASP cc_start: 0.8172 (p0) cc_final: 0.7505 (t70) REVERT: B 652 CYS cc_start: 0.8177 (m) cc_final: 0.7833 (t) REVERT: B 688 GLU cc_start: 0.8173 (tp30) cc_final: 0.7357 (pp20) REVERT: B 864 ASP cc_start: 0.8248 (t70) cc_final: 0.7727 (p0) REVERT: B 972 GLU cc_start: 0.8540 (tp30) cc_final: 0.8235 (tp30) REVERT: B 1027 THR cc_start: 0.8860 (m) cc_final: 0.8600 (t) REVERT: B 1028 LEU cc_start: 0.8541 (pt) cc_final: 0.8181 (pp) REVERT: B 1672 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7636 (tt) outliers start: 29 outliers final: 23 residues processed: 90 average time/residue: 0.1949 time to fit residues: 27.4006 Evaluate side-chains 85 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP 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 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 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 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 115 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 116 optimal weight: 0.0770 chunk 32 optimal weight: 0.0870 chunk 106 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- 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** B1671 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.115061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.083799 restraints weight = 20630.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.087211 restraints weight = 10457.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.089464 restraints weight = 7102.572| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 11647 Z= 0.104 Angle : 0.521 9.675 15959 Z= 0.266 Chirality : 0.039 0.216 1743 Planarity : 0.004 0.044 1855 Dihedral : 17.629 179.532 2221 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.31 % Favored : 94.37 % Rotamer: Outliers : 2.96 % Allowed : 17.76 % Favored : 79.28 % 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: -0.83 (0.24), residues: 1244 helix: 1.63 (0.30), residues: 328 sheet: -0.49 (0.37), residues: 181 loop : -1.68 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 607 HIS 0.002 0.000 HIS B 722 PHE 0.015 0.001 PHE B1520 TYR 0.008 0.001 TYR B 362 ARG 0.002 0.000 ARG B1505 Details of bonding type rmsd hydrogen bonds : bond 0.05103 ( 318) hydrogen bonds : angle 4.05213 ( 926) metal coordination : bond 0.00205 ( 10) metal coordination : angle 2.63764 ( 6) covalent geometry : bond 0.00234 (11637) covalent geometry : angle 0.51848 (15953) *********************** 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 104 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: B 31 MET cc_start: 0.7902 (tpp) cc_final: 0.7138 (mmm) REVERT: B 67 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7367 (mt-10) REVERT: B 139 GLU cc_start: 0.6968 (pp20) cc_final: 0.6728 (pp20) REVERT: B 166 ASP cc_start: 0.8179 (m-30) cc_final: 0.7863 (t0) REVERT: B 178 PHE cc_start: 0.7810 (t80) cc_final: 0.7406 (t80) REVERT: B 232 ILE cc_start: 0.9002 (mt) cc_final: 0.8453 (tt) REVERT: B 308 LYS cc_start: 0.8903 (mtmt) cc_final: 0.8613 (mtpt) REVERT: B 343 GLN cc_start: 0.8662 (tp40) cc_final: 0.8284 (mp10) REVERT: B 362 TYR cc_start: 0.8431 (t80) cc_final: 0.8211 (t80) REVERT: B 583 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7631 (tpp) REVERT: B 618 LYS cc_start: 0.8934 (tppt) cc_final: 0.8532 (ttpt) REVERT: B 639 ASP cc_start: 0.8047 (p0) cc_final: 0.7411 (t70) REVERT: B 652 CYS cc_start: 0.8202 (m) cc_final: 0.7878 (t) REVERT: B 688 GLU cc_start: 0.8166 (tp30) cc_final: 0.7298 (pp20) REVERT: B 864 ASP cc_start: 0.8306 (t70) cc_final: 0.7848 (p0) REVERT: B 972 GLU cc_start: 0.8528 (tp30) cc_final: 0.8224 (tp30) REVERT: B 1027 THR cc_start: 0.8861 (m) cc_final: 0.8607 (t) REVERT: B 1028 LEU cc_start: 0.8544 (pt) cc_final: 0.8197 (pp) REVERT: B 1538 SER cc_start: 0.9437 (t) cc_final: 0.8972 (p) REVERT: B 1672 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7617 (tt) outliers start: 32 outliers final: 21 residues processed: 99 average time/residue: 0.1805 time to fit residues: 28.9925 Evaluate side-chains 90 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 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 583 MET 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 1467 SER Chi-restraints excluded: chain B residue 1522 VAL Chi-restraints excluded: chain B residue 1572 ILE Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1671 ASN 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 55 optimal weight: 0.0470 chunk 5 optimal weight: 0.2980 chunk 121 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 67 optimal weight: 0.1980 chunk 60 optimal weight: 0.6980 overall best weight: 0.6480 ------------------------------------------------------------------------------- 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** B1671 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.114541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.083348 restraints weight = 20499.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.086731 restraints weight = 10443.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.088977 restraints weight = 7097.603| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11647 Z= 0.109 Angle : 0.535 9.683 15959 Z= 0.271 Chirality : 0.039 0.214 1743 Planarity : 0.004 0.044 1855 Dihedral : 17.560 179.623 2217 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.55 % Favored : 94.13 % Rotamer: Outliers : 2.68 % Allowed : 18.22 % Favored : 79.09 % 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: -0.78 (0.24), residues: 1244 helix: 1.67 (0.30), residues: 328 sheet: -0.49 (0.36), residues: 181 loop : -1.65 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 607 HIS 0.002 0.000 HIS B1621 PHE 0.016 0.001 PHE B1520 TYR 0.007 0.001 TYR B 362 ARG 0.002 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.05100 ( 318) hydrogen bonds : angle 4.06059 ( 926) metal coordination : bond 0.00239 ( 10) metal coordination : angle 2.54479 ( 6) covalent geometry : bond 0.00246 (11637) covalent geometry : angle 0.53233 (15953) *********************** 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: 29 poor density : 68 time to evaluate : 1.365 Fit side-chains REVERT: B 31 MET cc_start: 0.7927 (tpp) cc_final: 0.7171 (mmm) REVERT: B 67 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7376 (mt-10) REVERT: B 139 GLU cc_start: 0.6971 (pp20) cc_final: 0.6723 (pp20) REVERT: B 166 ASP cc_start: 0.8155 (m-30) cc_final: 0.7850 (t0) REVERT: B 178 PHE cc_start: 0.7827 (t80) cc_final: 0.7413 (t80) REVERT: B 308 LYS cc_start: 0.8895 (mtmt) cc_final: 0.8609 (mtpt) REVERT: B 343 GLN cc_start: 0.8666 (tp40) cc_final: 0.8441 (tm-30) REVERT: B 583 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7624 (tpp) REVERT: B 618 LYS cc_start: 0.8918 (tppt) cc_final: 0.8518 (ttpt) REVERT: B 639 ASP cc_start: 0.8022 (p0) cc_final: 0.7395 (t70) REVERT: B 652 CYS cc_start: 0.8130 (m) cc_final: 0.7911 (t) REVERT: B 688 GLU cc_start: 0.8182 (tp30) cc_final: 0.7283 (pp20) REVERT: B 864 ASP cc_start: 0.8344 (t70) cc_final: 0.7790 (p0) REVERT: B 865 ASP cc_start: 0.8545 (p0) cc_final: 0.7712 (p0) REVERT: B 972 GLU cc_start: 0.8516 (tp30) cc_final: 0.8210 (tp30) REVERT: B 1027 THR cc_start: 0.8868 (m) cc_final: 0.8624 (t) REVERT: B 1028 LEU cc_start: 0.8515 (pt) cc_final: 0.8177 (pp) REVERT: B 1538 SER cc_start: 0.9436 (t) cc_final: 0.8976 (p) outliers start: 29 outliers final: 22 residues processed: 93 average time/residue: 0.1942 time to fit residues: 29.2379 Evaluate side-chains 88 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 162 LEU 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 583 MET 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 1024 GLU 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 1520 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 30 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 74 optimal weight: 0.0870 chunk 85 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 7 optimal weight: 0.0370 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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** B1671 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.113992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.082644 restraints weight = 20583.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.086025 restraints weight = 10510.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.088242 restraints weight = 7148.045| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11647 Z= 0.112 Angle : 0.531 9.678 15959 Z= 0.270 Chirality : 0.039 0.214 1743 Planarity : 0.004 0.044 1855 Dihedral : 17.488 179.783 2217 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.39 % Favored : 94.29 % Rotamer: Outliers : 2.87 % Allowed : 18.22 % Favored : 78.91 % 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: -0.74 (0.24), residues: 1244 helix: 1.71 (0.30), residues: 329 sheet: -0.48 (0.36), residues: 180 loop : -1.63 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 607 HIS 0.003 0.001 HIS B 722 PHE 0.016 0.001 PHE B1520 TYR 0.009 0.001 TYR B 558 ARG 0.002 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.05073 ( 318) hydrogen bonds : angle 4.04716 ( 926) metal coordination : bond 0.00257 ( 10) metal coordination : angle 2.51140 ( 6) covalent geometry : bond 0.00253 (11637) covalent geometry : angle 0.52926 (15953) *********************** 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 97 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: B 31 MET cc_start: 0.7937 (tpp) cc_final: 0.7182 (mmm) REVERT: B 67 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7407 (mt-10) REVERT: B 139 GLU cc_start: 0.6983 (pp20) cc_final: 0.6757 (pp20) REVERT: B 166 ASP cc_start: 0.8172 (m-30) cc_final: 0.7889 (t0) REVERT: B 178 PHE cc_start: 0.7825 (t80) cc_final: 0.7326 (t80) REVERT: B 232 ILE cc_start: 0.8968 (mt) cc_final: 0.8381 (tt) REVERT: B 308 LYS cc_start: 0.8857 (mtmt) cc_final: 0.8554 (mtpt) REVERT: B 343 GLN cc_start: 0.8718 (tp40) cc_final: 0.8441 (tm-30) REVERT: B 583 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7629 (tpp) REVERT: B 618 LYS cc_start: 0.8912 (tppt) cc_final: 0.8485 (ttpt) REVERT: B 639 ASP cc_start: 0.7878 (p0) cc_final: 0.7309 (t70) REVERT: B 688 GLU cc_start: 0.8209 (tp30) cc_final: 0.7254 (pp20) REVERT: B 864 ASP cc_start: 0.8369 (t70) cc_final: 0.7871 (p0) REVERT: B 865 ASP cc_start: 0.8639 (p0) cc_final: 0.7872 (p0) REVERT: B 972 GLU cc_start: 0.8472 (tp30) cc_final: 0.8179 (tp30) REVERT: B 1027 THR cc_start: 0.8899 (m) cc_final: 0.8668 (t) REVERT: B 1028 LEU cc_start: 0.8562 (pt) cc_final: 0.8250 (pp) REVERT: B 1538 SER cc_start: 0.9440 (t) cc_final: 0.8984 (p) outliers start: 31 outliers final: 24 residues processed: 93 average time/residue: 0.1867 time to fit residues: 28.1009 Evaluate side-chains 86 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 162 LEU Chi-restraints excluded: chain B residue 229 LEU 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 583 MET 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 920 ILE Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 1006 MET 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 1647 VAL Chi-restraints excluded: chain B residue 1671 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 23 optimal weight: 0.7980 chunk 123 optimal weight: 0.0980 chunk 20 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.113349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.081891 restraints weight = 20437.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.085213 restraints weight = 10630.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.087382 restraints weight = 7323.474| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4734 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= 0.130 Angle : 0.553 9.664 15959 Z= 0.281 Chirality : 0.040 0.217 1743 Planarity : 0.004 0.045 1855 Dihedral : 17.478 179.886 2217 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.27 % Favored : 93.41 % Rotamer: Outliers : 2.31 % Allowed : 19.43 % 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: -0.78 (0.24), residues: 1244 helix: 1.69 (0.30), residues: 330 sheet: -0.62 (0.36), residues: 180 loop : -1.63 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 607 HIS 0.003 0.001 HIS B 155 PHE 0.013 0.001 PHE B1520 TYR 0.009 0.001 TYR B 558 ARG 0.002 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.05222 ( 318) hydrogen bonds : angle 4.10416 ( 926) metal coordination : bond 0.00350 ( 10) metal coordination : angle 2.44044 ( 6) covalent geometry : bond 0.00298 (11637) covalent geometry : angle 0.55073 (15953) ********************** 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 87 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: B 31 MET cc_start: 0.7890 (tpp) cc_final: 0.7136 (mmm) REVERT: B 67 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7410 (mt-10) REVERT: B 166 ASP cc_start: 0.8134 (m-30) cc_final: 0.7867 (t0) REVERT: B 178 PHE cc_start: 0.7828 (t80) cc_final: 0.7303 (t80) REVERT: B 232 ILE cc_start: 0.9017 (mt) cc_final: 0.8438 (tt) REVERT: B 308 LYS cc_start: 0.8844 (mtmt) cc_final: 0.8569 (mtpt) REVERT: B 343 GLN cc_start: 0.8714 (tp40) cc_final: 0.8426 (tm-30) REVERT: B 583 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7606 (tpp) REVERT: B 618 LYS cc_start: 0.8922 (tppt) cc_final: 0.8496 (ttpt) REVERT: B 688 GLU cc_start: 0.8224 (tp30) cc_final: 0.7271 (pp20) REVERT: B 864 ASP cc_start: 0.8372 (t70) cc_final: 0.7908 (p0) REVERT: B 865 ASP cc_start: 0.8669 (p0) cc_final: 0.7933 (p0) REVERT: B 972 GLU cc_start: 0.8479 (tp30) cc_final: 0.8173 (tp30) REVERT: B 1027 THR cc_start: 0.8898 (m) cc_final: 0.8684 (t) REVERT: B 1028 LEU cc_start: 0.8573 (pt) cc_final: 0.8278 (pp) REVERT: B 1538 SER cc_start: 0.9431 (t) cc_final: 0.8993 (p) outliers start: 25 outliers final: 23 residues processed: 83 average time/residue: 0.1919 time to fit residues: 25.8163 Evaluate side-chains 85 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 229 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 583 MET 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 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 1647 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 112 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** B1671 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.112714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.081534 restraints weight = 20171.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.084833 restraints weight = 10505.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.086994 restraints weight = 7251.075| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4806 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= 0.115 Angle : 0.543 9.635 15959 Z= 0.277 Chirality : 0.039 0.217 1743 Planarity : 0.004 0.044 1855 Dihedral : 17.468 179.943 2217 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.47 % Favored : 94.21 % Rotamer: Outliers : 2.50 % Allowed : 18.96 % 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: -0.76 (0.24), residues: 1244 helix: 1.71 (0.30), residues: 330 sheet: -0.56 (0.36), residues: 180 loop : -1.63 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 607 HIS 0.005 0.001 HIS B 561 PHE 0.013 0.001 PHE B1520 TYR 0.007 0.001 TYR B 845 ARG 0.003 0.000 ARG B 559 Details of bonding type rmsd hydrogen bonds : bond 0.05079 ( 318) hydrogen bonds : angle 4.06346 ( 926) metal coordination : bond 0.00254 ( 10) metal coordination : angle 2.42283 ( 6) covalent geometry : bond 0.00260 (11637) covalent geometry : angle 0.54072 (15953) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3511.72 seconds wall clock time: 63 minutes 2.23 seconds (3782.23 seconds total)