Starting phenix.real_space_refine on Fri Sep 11 18:39:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y80_33676/09_2026/7y80_33676.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y80_33676/09_2026/7y80_33676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y80_33676/09_2026/7y80_33676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y80_33676/09_2026/7y80_33676.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y80_33676/09_2026/7y80_33676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y80_33676/09_2026/7y80_33676.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7y80_33676/09_2026/7y80_33676.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y80_33676/09_2026/7y80_33676.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.247 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 35 5.49 5 Mg 1 5.21 5 S 31 5.16 5 C 6594 2.51 5 N 1837 2.21 5 O 2070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10572 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1218, 9832 Classifications: {'peptide': 1218} Link IDs: {'PTRANS': 57, 'TRANS': 1160} Chain breaks: 10 Chain: "B" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 735 Classifications: {'RNAv2': 35} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 10, 'rna3p_pur': 3, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 14} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 1, ' ZN': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 668 SG CYS A 88 35.620 35.249 135.776 1.00 72.95 S ATOM 939 SG CYS A 121 36.951 37.298 138.799 1.00 74.43 S ATOM 985 SG CYS A 127 38.897 37.300 135.687 1.00 72.08 S ATOM 1009 SG CYS A 130 35.463 38.963 135.715 1.00 73.29 S ATOM 3461 SG CYS A 491 24.588 27.235 105.428 1.00 73.76 S ATOM 3529 SG CYS A 501 24.398 26.705 108.953 1.00 62.37 S ATOM 3543 SG CYS A 503 26.629 24.554 106.979 1.00 57.38 S ATOM 3565 SG CYS A 506 27.764 28.201 107.340 1.00 54.05 S ATOM 5536 SG CYS A 750 14.102 26.248 78.183 1.00 74.12 S ATOM 5549 SG CYS A 752 16.917 24.350 76.482 1.00 61.92 S ATOM 5571 SG CYS A 755 17.736 27.469 78.478 1.00 49.45 S ATOM 7462 SG CYS A1018 20.064 39.786 44.131 1.00 60.25 S ATOM 7658 SG CYS A1406 17.803 39.491 47.070 1.00 63.96 S ATOM 7709 SG CYS A1414 19.126 36.419 44.933 1.00 57.16 S ATOM 7726 SG CYS A1417 21.343 38.015 47.417 1.00 53.11 S Time building chain proxies: 2.45, per 1000 atoms: 0.23 Number of scatterers: 10572 At special positions: 0 Unit cell: (73.7, 80.3, 154, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 31 16.00 P 35 15.00 Mg 1 11.99 O 2070 8.00 N 1837 7.00 C 6594 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: 0.88 Conformation dependent library (CDL) restraints added in 471.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 121 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 88 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 501 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 506 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 755 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 750 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1417 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1406 " Number of angles added : 21 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 20 sheets defined 32.5% alpha, 23.7% beta 0 base pairs and 9 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 59 through 78 Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 225 removed outlier: 3.592A pdb=" N LEU A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 287 removed outlier: 3.594A pdb=" N ASN A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 303 removed outlier: 3.670A pdb=" N ILE A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 removed outlier: 4.030A pdb=" N GLY A 307 " --> pdb=" O ARG A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 307' Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 354 through 374 Processing helix chain 'A' and resid 471 through 487 Processing helix chain 'A' and resid 503 through 511 removed outlier: 3.821A pdb=" N ARG A 511 " --> pdb=" O ILE A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 630 through 637 removed outlier: 3.743A pdb=" N GLU A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 663 Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 723 through 740 removed outlier: 3.826A pdb=" N ARG A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 744 Processing helix chain 'A' and resid 752 through 759 Processing helix chain 'A' and resid 800 through 804 removed outlier: 3.510A pdb=" N LYS A 804 " --> pdb=" O ASP A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 847 removed outlier: 3.555A pdb=" N LEU A 836 " --> pdb=" O GLY A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 913 removed outlier: 3.761A pdb=" N LYS A 912 " --> pdb=" O HIS A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1015 Processing helix chain 'A' and resid 1394 through 1399 Processing helix chain 'A' and resid 1414 through 1420 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 3.818A pdb=" N SER A1467 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1493 removed outlier: 3.824A pdb=" N ILE A1489 " --> pdb=" O ASN A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1493 through 1501 removed outlier: 3.745A pdb=" N ARG A1498 " --> pdb=" O GLN A1494 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU A1499 " --> pdb=" O LEU A1495 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A1501 " --> pdb=" O ILE A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1540 removed outlier: 3.780A pdb=" N GLY A1533 " --> pdb=" O GLU A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1556 Processing helix chain 'A' and resid 1583 through 1603 Processing helix chain 'A' and resid 1615 through 1618 removed outlier: 3.609A pdb=" N VAL A1618 " --> pdb=" O GLN A1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1615 through 1618' Processing helix chain 'A' and resid 1619 through 1629 Processing helix chain 'A' and resid 1662 through 1668 removed outlier: 3.703A pdb=" N LEU A1666 " --> pdb=" O THR A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1673 through 1683 Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 removed outlier: 6.988A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG A 19 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N TRP A 44 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL A 21 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N TRP A 46 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N GLU A 22 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 12.598A pdb=" N ARG A 193 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.612A pdb=" N VAL A 85 " --> pdb=" O TRP A 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.584A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181 removed outlier: 7.036A pdb=" N ARG A 180 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 333 through 334 Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.490A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.490A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 431 through 432 removed outlier: 4.330A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE A 460 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.665A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.665A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N GLN A 673 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE A 868 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR A 675 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE A 866 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU A 677 " --> pdb=" O ALA A 864 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 699 through 700 removed outlier: 7.082A pdb=" N ALA A 699 " --> pdb=" O TYR A 808 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AB6, first strand: chain 'A' and resid 920 through 921 removed outlier: 3.807A pdb=" N TYR A 921 " --> pdb=" O ASP A1642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 924 through 927 removed outlier: 3.777A pdb=" N ARG A1478 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 991 through 992 removed outlier: 3.621A pdb=" N GLU A 995 " --> pdb=" O ILE A 992 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL A1517 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A1517 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N THR A 960 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N SER A1519 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU A 958 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP A1521 " --> pdb=" O CYS A 956 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N CYS A 956 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ARG A1523 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE A 954 " --> pdb=" O ARG A1523 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLU A1525 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY A 952 " --> pdb=" O GLU A1525 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 6.900A pdb=" N VAL A1517 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N THR A 960 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N SER A1519 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU A 958 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP A1521 " --> pdb=" O CYS A 956 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N CYS A 956 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ARG A1523 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE A 954 " --> pdb=" O ARG A1523 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLU A1525 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY A 952 " --> pdb=" O GLU A1525 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 967 through 968 removed outlier: 4.240A pdb=" N LYS A 988 " --> pdb=" O ASP A 968 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N TYR A 987 " --> pdb=" O GLU A1510 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A1509 " --> pdb=" O LEU A1454 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1421 through 1422 361 hydrogen bonds defined for protein. 996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1686 1.27 - 1.41: 2789 1.41 - 1.55: 6245 1.55 - 1.68: 117 1.68 - 1.82: 42 Bond restraints: 10879 Sorted by residual: bond pdb=" C PRO A 648 " pdb=" O PRO A 648 " ideal model delta sigma weight residual 1.233 1.129 0.104 1.19e-02 7.06e+03 7.70e+01 bond pdb=" C LEU A1443 " pdb=" O LEU A1443 " ideal model delta sigma weight residual 1.235 1.166 0.069 1.19e-02 7.06e+03 3.39e+01 bond pdb=" C PRO A1440 " pdb=" O PRO A1440 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.23e-02 6.61e+03 2.10e+01 bond pdb=" C ASN A1438 " pdb=" O ASN A1438 " ideal model delta sigma weight residual 1.235 1.180 0.054 1.22e-02 6.72e+03 1.97e+01 bond pdb=" N PRO A1440 " pdb=" CD PRO A1440 " ideal model delta sigma weight residual 1.473 1.420 0.053 1.40e-02 5.10e+03 1.46e+01 ... (remaining 10874 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 14290 2.40 - 4.80: 446 4.80 - 7.21: 69 7.21 - 9.61: 14 9.61 - 12.01: 7 Bond angle restraints: 14826 Sorted by residual: angle pdb=" N GLU A1441 " pdb=" CA GLU A1441 " pdb=" C GLU A1441 " ideal model delta sigma weight residual 108.00 97.11 10.89 1.48e+00 4.57e-01 5.41e+01 angle pdb=" C PRO A1440 " pdb=" CA PRO A1440 " pdb=" CB PRO A1440 " ideal model delta sigma weight residual 110.88 101.76 9.12 1.41e+00 5.03e-01 4.18e+01 angle pdb=" C PRO A 648 " pdb=" CA PRO A 648 " pdb=" CB PRO A 648 " ideal model delta sigma weight residual 111.23 104.23 7.00 1.28e+00 6.10e-01 2.99e+01 angle pdb=" C GLU A1441 " pdb=" CA GLU A1441 " pdb=" CB GLU A1441 " ideal model delta sigma weight residual 116.34 123.97 -7.63 1.40e+00 5.10e-01 2.97e+01 angle pdb=" CA PRO A 648 " pdb=" C PRO A 648 " pdb=" O PRO A 648 " ideal model delta sigma weight residual 121.56 116.03 5.53 1.16e+00 7.43e-01 2.27e+01 ... (remaining 14821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 5156 17.67 - 35.35: 833 35.35 - 53.02: 294 53.02 - 70.69: 123 70.69 - 88.36: 33 Dihedral angle restraints: 6439 sinusoidal: 2966 harmonic: 3473 Sorted by residual: dihedral pdb=" C4' G B 33 " pdb=" C3' G B 33 " pdb=" C2' G B 33 " pdb=" C1' G B 33 " ideal model delta sinusoidal sigma weight residual 36.34 -37.89 74.24 1 3.10e+00 1.04e-01 7.28e+02 dihedral pdb=" C4' G B 32 " pdb=" C3' G B 32 " pdb=" C2' G B 32 " pdb=" C1' G B 32 " ideal model delta sinusoidal sigma weight residual 36.34 -37.25 73.60 1 3.10e+00 1.04e-01 7.17e+02 dihedral pdb=" C4' C B 50 " pdb=" C3' C B 50 " pdb=" C2' C B 50 " pdb=" C1' C B 50 " ideal model delta sinusoidal sigma weight residual 36.34 -36.18 72.52 1 3.10e+00 1.04e-01 6.99e+02 ... (remaining 6436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1204 0.062 - 0.124: 265 0.124 - 0.185: 44 0.185 - 0.247: 39 0.247 - 0.309: 47 Chirality restraints: 1599 Sorted by residual: chirality pdb=" CG LEU A 221 " pdb=" CB LEU A 221 " pdb=" CD1 LEU A 221 " pdb=" CD2 LEU A 221 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA GLU A1441 " pdb=" N GLU A1441 " pdb=" C GLU A1441 " pdb=" CB GLU A1441 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA THR A1445 " pdb=" N THR A1445 " pdb=" C THR A1445 " pdb=" CB THR A1445 " both_signs ideal model delta sigma weight residual False 2.53 2.83 -0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 1596 not shown) Planarity restraints: 1785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A1439 " 0.020 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C GLY A1439 " -0.067 2.00e-02 2.50e+03 pdb=" O GLY A1439 " 0.024 2.00e-02 2.50e+03 pdb=" N PRO A1440 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 962 " -0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO A 963 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 963 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 963 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1437 " -0.015 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C GLU A1437 " 0.055 2.00e-02 2.50e+03 pdb=" O GLU A1437 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN A1438 " -0.019 2.00e-02 2.50e+03 ... (remaining 1782 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 179 2.60 - 3.18: 8146 3.18 - 3.75: 18811 3.75 - 4.33: 26266 4.33 - 4.90: 42152 Nonbonded interactions: 95554 Sorted by model distance: nonbonded pdb=" OP2 U B 26 " pdb="MG MG A1805 " model vdw 2.031 2.170 nonbonded pdb=" OD1 ASP A 137 " pdb="MG MG A1805 " model vdw 2.032 2.170 nonbonded pdb=" O GLY A 134 " pdb="MG MG A1805 " model vdw 2.116 2.170 nonbonded pdb=" O ILE A 940 " pdb=" OH TYR A1425 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR A 337 " pdb=" OG1 THR A 341 " model vdw 2.271 3.040 ... (remaining 95549 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.400 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 : 0.005 0.104 10895 Z= 0.273 Angle : 1.000 12.008 14847 Z= 0.510 Chirality : 0.076 0.309 1599 Planarity : 0.008 0.111 1785 Dihedral : 21.080 88.365 4215 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.77 % Allowed : 31.26 % Favored : 64.97 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.20), residues: 1196 helix: -1.63 (0.22), residues: 341 sheet: -0.56 (0.35), residues: 184 loop : -0.65 (0.20), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 484 TYR 0.035 0.003 TYR A 903 PHE 0.018 0.003 PHE A 129 TRP 0.034 0.002 TRP A1442 HIS 0.007 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.27 (10879) covalent geometry : angle 0.98454 / 0.51 (14826) hydrogen bonds : bond 0.16244 / 10.86 ( 331) hydrogen bonds : angle 7.67375 / 5.61 ( 996) metal coordination : bond 0.00954 / 0.58 ( 16) metal coordination : angle 4.82838 / 2.94 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.354 Fit side-chains REVERT: A 229 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7278 (tppp) REVERT: A 308 GLU cc_start: 0.6390 (mt-10) cc_final: 0.6073 (mp0) REVERT: A 361 MET cc_start: 0.6807 (mtp) cc_final: 0.6567 (ttp) REVERT: A 1441 GLU cc_start: 0.5883 (OUTLIER) cc_final: 0.5579 (mm-30) REVERT: A 1563 LYS cc_start: 0.7910 (pptt) cc_final: 0.7666 (pptt) REVERT: A 1596 GLN cc_start: 0.6346 (mm-40) cc_final: 0.5425 (mt0) REVERT: A 1644 ARG cc_start: 0.7169 (pmm-80) cc_final: 0.6533 (ptt90) outliers start: 40 outliers final: 29 residues processed: 169 average time/residue: 0.5585 time to fit residues: 102.0610 Evaluate side-chains 162 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1566 SER Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS A 459 ASN A 712 ASN A 762 HIS A 978 GLN A 984 HIS ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1418 HIS A1494 GLN ** A1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1592 ASN A1671 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.174555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.147096 restraints weight = 10397.618| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.55 r_work: 0.3555 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10895 Z= 0.221 Angle : 1.121 26.817 14847 Z= 0.463 Chirality : 0.104 1.094 1599 Planarity : 0.005 0.060 1785 Dihedral : 15.697 143.126 1787 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 5.37 % Allowed : 27.31 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.22), residues: 1196 helix: -0.45 (0.25), residues: 354 sheet: -0.95 (0.33), residues: 184 loop : -0.32 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 484 TYR 0.012 0.002 TYR A 934 PHE 0.017 0.002 PHE A 15 TRP 0.021 0.002 TRP A 612 HIS 0.005 0.001 HIS A1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.22 (10879) covalent geometry : angle 1.11060 / 0.46 (14826) hydrogen bonds : bond 0.04536 / 3.09 ( 331) hydrogen bonds : angle 5.91021 / 4.31 ( 996) metal coordination : bond 0.00634 / 0.37 ( 16) metal coordination : angle 4.25324 / 2.66 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 150 time to evaluate : 0.361 Fit side-chains REVERT: A 25 ASP cc_start: 0.7077 (OUTLIER) cc_final: 0.6288 (p0) REVERT: A 168 ARG cc_start: 0.8158 (mtm180) cc_final: 0.7915 (mtm110) REVERT: A 218 LYS cc_start: 0.7042 (mmpt) cc_final: 0.6306 (mmmt) REVERT: A 229 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7480 (tppp) REVERT: A 1499 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7175 (pm20) REVERT: A 1563 LYS cc_start: 0.8031 (pptt) cc_final: 0.7745 (pptt) REVERT: A 1570 PHE cc_start: 0.6970 (OUTLIER) cc_final: 0.6560 (p90) REVERT: A 1585 SER cc_start: 0.7087 (OUTLIER) cc_final: 0.6856 (t) REVERT: A 1644 ARG cc_start: 0.7435 (pmm-80) cc_final: 0.6773 (ptt90) outliers start: 57 outliers final: 25 residues processed: 193 average time/residue: 0.6006 time to fit residues: 124.5557 Evaluate side-chains 161 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1570 PHE Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 712 ASN A 762 HIS A 778 ASN ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1418 HIS A1484 HIS ** A1494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1516 ASN ** A1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1592 ASN A1621 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.168170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.139834 restraints weight = 10489.664| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.56 r_work: 0.3480 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 10895 Z= 0.259 Angle : 0.945 18.861 14847 Z= 0.414 Chirality : 0.082 0.808 1599 Planarity : 0.005 0.054 1785 Dihedral : 17.184 171.311 1761 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 6.31 % Allowed : 25.89 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.22), residues: 1196 helix: -0.08 (0.26), residues: 353 sheet: -1.03 (0.33), residues: 179 loop : -0.27 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 484 TYR 0.016 0.002 TYR A 529 PHE 0.015 0.002 PHE A 546 TRP 0.020 0.002 TRP A 612 HIS 0.006 0.001 HIS A1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.26 (10879) covalent geometry : angle 0.93166 / 0.41 (14826) hydrogen bonds : bond 0.04452 / 3.03 ( 331) hydrogen bonds : angle 5.71497 / 4.12 ( 996) metal coordination : bond 0.00740 / 0.49 ( 16) metal coordination : angle 4.36609 / 2.88 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 140 time to evaluate : 0.345 Fit side-chains REVERT: A 11 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7534 (tt0) REVERT: A 25 ASP cc_start: 0.7077 (OUTLIER) cc_final: 0.6310 (p0) REVERT: A 68 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7310 (mp) REVERT: A 620 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7140 (pm20) REVERT: A 636 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: A 697 ARG cc_start: 0.6536 (OUTLIER) cc_final: 0.5766 (mpp-170) REVERT: A 899 ILE cc_start: 0.4223 (OUTLIER) cc_final: 0.3800 (pt) REVERT: A 938 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7244 (t70) REVERT: A 976 LYS cc_start: 0.7900 (mmtt) cc_final: 0.7511 (mmtm) REVERT: A 1452 ARG cc_start: 0.8171 (mtm-85) cc_final: 0.7923 (mtm-85) REVERT: A 1478 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7251 (mtp85) REVERT: A 1499 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7192 (pm20) REVERT: A 1563 LYS cc_start: 0.8151 (pptt) cc_final: 0.7815 (pptt) REVERT: A 1570 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.6771 (p90) REVERT: A 1619 ILE cc_start: 0.7196 (OUTLIER) cc_final: 0.6890 (mt) REVERT: A 1644 ARG cc_start: 0.7746 (pmm-80) cc_final: 0.7098 (ptt90) outliers start: 67 outliers final: 33 residues processed: 187 average time/residue: 0.6035 time to fit residues: 121.0394 Evaluate side-chains 174 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 779 GLU Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1407 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1478 ARG Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1570 PHE Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 ASN A 762 HIS ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN A 986 ASN ** A1494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1592 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.171890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.144154 restraints weight = 10531.978| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.55 r_work: 0.3519 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10895 Z= 0.174 Angle : 0.792 12.356 14847 Z= 0.351 Chirality : 0.069 0.679 1599 Planarity : 0.004 0.052 1785 Dihedral : 17.450 176.760 1753 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 6.21 % Allowed : 26.37 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.23), residues: 1196 helix: 0.43 (0.27), residues: 353 sheet: -0.79 (0.35), residues: 163 loop : -0.19 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 106 TYR 0.012 0.002 TYR A 934 PHE 0.014 0.002 PHE A 15 TRP 0.018 0.001 TRP A 612 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (10879) covalent geometry : angle 0.78084 / 0.35 (14826) hydrogen bonds : bond 0.03922 / 2.68 ( 331) hydrogen bonds : angle 5.40982 / 3.90 ( 996) metal coordination : bond 0.00479 / 0.28 ( 16) metal coordination : angle 3.66543 / 2.26 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 137 time to evaluate : 0.367 Fit side-chains REVERT: A 11 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7412 (tt0) REVERT: A 25 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.6330 (p0) REVERT: A 68 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7221 (mp) REVERT: A 308 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6561 (mp0) REVERT: A 325 LYS cc_start: 0.6227 (pptt) cc_final: 0.5958 (pptt) REVERT: A 456 THR cc_start: 0.7556 (OUTLIER) cc_final: 0.7156 (p) REVERT: A 620 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7166 (pm20) REVERT: A 636 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: A 899 ILE cc_start: 0.4126 (OUTLIER) cc_final: 0.3705 (pt) REVERT: A 918 LYS cc_start: 0.7282 (pptt) cc_final: 0.6740 (pmmt) REVERT: A 938 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7209 (t0) REVERT: A 976 LYS cc_start: 0.7858 (mmtt) cc_final: 0.7490 (mmtm) REVERT: A 1452 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7704 (mtm-85) REVERT: A 1489 ILE cc_start: 0.8063 (mt) cc_final: 0.7655 (mp) REVERT: A 1499 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7131 (pm20) REVERT: A 1563 LYS cc_start: 0.8167 (pptt) cc_final: 0.7835 (pptt) REVERT: A 1619 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6819 (mt) REVERT: A 1644 ARG cc_start: 0.7697 (pmm-80) cc_final: 0.6975 (ptt90) REVERT: A 1650 GLU cc_start: 0.7274 (tt0) cc_final: 0.6729 (tp30) outliers start: 66 outliers final: 27 residues processed: 186 average time/residue: 0.5915 time to fit residues: 118.4260 Evaluate side-chains 169 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 779 GLU Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1407 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1656 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 55 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 44 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS A 179 ASN A 335 GLN A 712 ASN A 762 HIS ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN A 986 ASN ** A1494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1516 ASN ** A1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.173233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.145920 restraints weight = 10439.830| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.53 r_work: 0.3537 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10895 Z= 0.161 Angle : 0.762 11.143 14847 Z= 0.336 Chirality : 0.067 0.556 1599 Planarity : 0.004 0.051 1785 Dihedral : 17.602 176.642 1753 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 5.46 % Allowed : 27.21 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.23), residues: 1196 helix: 0.71 (0.27), residues: 354 sheet: -0.79 (0.35), residues: 163 loop : -0.10 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 484 TYR 0.012 0.001 TYR A 934 PHE 0.012 0.001 PHE A 15 TRP 0.018 0.001 TRP A 612 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (10879) covalent geometry : angle 0.75028 / 0.34 (14826) hydrogen bonds : bond 0.03712 / 2.55 ( 331) hydrogen bonds : angle 5.24319 / 3.77 ( 996) metal coordination : bond 0.00483 / 0.29 ( 16) metal coordination : angle 3.55642 / 2.08 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 142 time to evaluate : 0.371 Fit side-chains REVERT: A 68 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7174 (mp) REVERT: A 301 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.6832 (ttp80) REVERT: A 456 THR cc_start: 0.7500 (OUTLIER) cc_final: 0.7097 (p) REVERT: A 503 CYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7722 (p) REVERT: A 620 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7143 (pm20) REVERT: A 636 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7409 (mp0) REVERT: A 899 ILE cc_start: 0.4175 (OUTLIER) cc_final: 0.3768 (pt) REVERT: A 938 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7400 (t0) REVERT: A 976 LYS cc_start: 0.7854 (mmtt) cc_final: 0.7473 (mmtm) REVERT: A 995 GLU cc_start: 0.8535 (pt0) cc_final: 0.8314 (pt0) REVERT: A 1489 ILE cc_start: 0.8024 (mt) cc_final: 0.7625 (mp) REVERT: A 1499 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7209 (pm20) REVERT: A 1563 LYS cc_start: 0.8080 (pttt) cc_final: 0.7800 (pptt) REVERT: A 1619 ILE cc_start: 0.7172 (OUTLIER) cc_final: 0.6843 (mt) REVERT: A 1644 ARG cc_start: 0.7663 (pmm-80) cc_final: 0.6929 (ptt90) REVERT: A 1650 GLU cc_start: 0.7206 (tt0) cc_final: 0.6649 (tp30) REVERT: A 1666 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6872 (mm) outliers start: 58 outliers final: 25 residues processed: 184 average time/residue: 0.6035 time to fit residues: 119.3485 Evaluate side-chains 167 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 503 CYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 779 GLU Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1407 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1666 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 74 optimal weight: 0.0670 chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 ASN A 762 HIS ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 ASN ** A1494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.172809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.145322 restraints weight = 10487.156| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.54 r_work: 0.3531 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10895 Z= 0.165 Angle : 0.763 10.908 14847 Z= 0.337 Chirality : 0.067 0.557 1599 Planarity : 0.004 0.050 1785 Dihedral : 17.518 177.141 1752 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.90 % Allowed : 27.31 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.23), residues: 1196 helix: 0.78 (0.27), residues: 354 sheet: -0.75 (0.35), residues: 163 loop : -0.06 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1488 TYR 0.012 0.001 TYR A 934 PHE 0.024 0.001 PHE A 659 TRP 0.018 0.001 TRP A 612 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (10879) covalent geometry : angle 0.74977 / 0.34 (14826) hydrogen bonds : bond 0.03717 / 2.55 ( 331) hydrogen bonds : angle 5.18008 / 3.72 ( 996) metal coordination : bond 0.00546 / 0.34 ( 16) metal coordination : angle 3.88142 / 2.39 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 140 time to evaluate : 0.391 Fit side-chains REVERT: A 11 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7308 (tt0) REVERT: A 68 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7163 (mp) REVERT: A 301 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.6875 (ttp80) REVERT: A 325 LYS cc_start: 0.6256 (pptt) cc_final: 0.6014 (pptt) REVERT: A 456 THR cc_start: 0.7601 (t) cc_final: 0.7189 (p) REVERT: A 491 CYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7250 (p) REVERT: A 503 CYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7526 (p) REVERT: A 585 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7766 (ttpp) REVERT: A 620 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7161 (pm20) REVERT: A 636 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: A 899 ILE cc_start: 0.4203 (OUTLIER) cc_final: 0.3777 (pt) REVERT: A 908 HIS cc_start: 0.7544 (t-90) cc_final: 0.7037 (t70) REVERT: A 976 LYS cc_start: 0.7858 (mmtt) cc_final: 0.7478 (mmtm) REVERT: A 995 GLU cc_start: 0.8542 (pt0) cc_final: 0.8298 (pt0) REVERT: A 1460 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6702 (mm-30) REVERT: A 1463 ARG cc_start: 0.7865 (mmt90) cc_final: 0.7395 (mmm160) REVERT: A 1478 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7019 (mtp85) REVERT: A 1489 ILE cc_start: 0.8218 (mt) cc_final: 0.7814 (mp) REVERT: A 1499 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7203 (pm20) REVERT: A 1619 ILE cc_start: 0.7176 (OUTLIER) cc_final: 0.6850 (mt) REVERT: A 1644 ARG cc_start: 0.7652 (pmm-80) cc_final: 0.6938 (ptt90) REVERT: A 1650 GLU cc_start: 0.7189 (tt0) cc_final: 0.6565 (tp30) outliers start: 52 outliers final: 24 residues processed: 178 average time/residue: 0.6274 time to fit residues: 119.7591 Evaluate side-chains 171 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 503 CYS Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 779 GLU Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1407 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1460 GLU Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1478 ARG Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1643 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 335 GLN ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 ASN A 762 HIS ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN A 986 ASN ** A1494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.171644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.144119 restraints weight = 10522.160| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.54 r_work: 0.3518 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10895 Z= 0.180 Angle : 0.773 10.951 14847 Z= 0.341 Chirality : 0.068 0.561 1599 Planarity : 0.004 0.049 1785 Dihedral : 17.455 177.812 1746 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 5.84 % Allowed : 26.55 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.23), residues: 1196 helix: 0.81 (0.27), residues: 354 sheet: -0.77 (0.35), residues: 163 loop : -0.04 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1488 TYR 0.011 0.002 TYR A 903 PHE 0.012 0.001 PHE A 15 TRP 0.018 0.001 TRP A 612 HIS 0.004 0.001 HIS A1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (10879) covalent geometry : angle 0.76071 / 0.34 (14826) hydrogen bonds : bond 0.03824 / 2.63 ( 331) hydrogen bonds : angle 5.20481 / 3.74 ( 996) metal coordination : bond 0.00567 / 0.33 ( 16) metal coordination : angle 3.76550 / 2.34 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 137 time to evaluate : 0.383 Fit side-chains REVERT: A 68 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7158 (mp) REVERT: A 196 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7587 (mt-10) REVERT: A 301 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.6944 (ttp80) REVERT: A 456 THR cc_start: 0.7604 (t) cc_final: 0.7174 (p) REVERT: A 491 CYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7207 (p) REVERT: A 503 CYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7538 (p) REVERT: A 585 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7757 (ttpp) REVERT: A 620 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7215 (pm20) REVERT: A 636 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: A 697 ARG cc_start: 0.6362 (OUTLIER) cc_final: 0.5633 (mpp-170) REVERT: A 908 HIS cc_start: 0.7369 (t-90) cc_final: 0.6849 (t70) REVERT: A 918 LYS cc_start: 0.7042 (pptt) cc_final: 0.6568 (pmmt) REVERT: A 938 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7421 (t0) REVERT: A 976 LYS cc_start: 0.7907 (mmtt) cc_final: 0.7635 (mmtm) REVERT: A 995 GLU cc_start: 0.8554 (pt0) cc_final: 0.8274 (pt0) REVERT: A 1463 ARG cc_start: 0.7829 (mmt90) cc_final: 0.7262 (mmm160) REVERT: A 1478 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.6979 (mtp85) REVERT: A 1489 ILE cc_start: 0.8229 (mt) cc_final: 0.7813 (mp) REVERT: A 1499 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7167 (pm20) REVERT: A 1502 GLN cc_start: 0.6563 (mm-40) cc_final: 0.6351 (mm-40) REVERT: A 1563 LYS cc_start: 0.7929 (pttp) cc_final: 0.7700 (tmtt) REVERT: A 1592 ASN cc_start: 0.7876 (t0) cc_final: 0.7639 (t0) REVERT: A 1619 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6826 (mt) REVERT: A 1644 ARG cc_start: 0.7630 (pmm-80) cc_final: 0.6896 (ptt90) REVERT: A 1650 GLU cc_start: 0.7206 (tt0) cc_final: 0.6546 (tp30) REVERT: A 1666 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6813 (mm) REVERT: A 1674 TYR cc_start: 0.8174 (m-10) cc_final: 0.7941 (m-10) outliers start: 62 outliers final: 25 residues processed: 186 average time/residue: 0.6158 time to fit residues: 122.3868 Evaluate side-chains 175 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 503 CYS Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 779 GLU Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1407 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1478 ARG Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1666 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 33 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 93 optimal weight: 0.1980 chunk 117 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS A 179 ASN A 335 GLN ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 ASN A 762 HIS ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 ASN ** A1494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.172469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.145159 restraints weight = 10400.267| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.53 r_work: 0.3528 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10895 Z= 0.169 Angle : 0.764 10.942 14847 Z= 0.337 Chirality : 0.066 0.546 1599 Planarity : 0.004 0.049 1785 Dihedral : 17.452 178.249 1746 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 5.18 % Allowed : 27.02 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.23), residues: 1196 helix: 0.86 (0.28), residues: 354 sheet: -0.77 (0.35), residues: 163 loop : 0.01 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1488 TYR 0.012 0.001 TYR A 903 PHE 0.018 0.001 PHE A 659 TRP 0.018 0.001 TRP A 612 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (10879) covalent geometry : angle 0.75076 / 0.34 (14826) hydrogen bonds : bond 0.03753 / 2.58 ( 331) hydrogen bonds : angle 5.17083 / 3.72 ( 996) metal coordination : bond 0.00561 / 0.33 ( 16) metal coordination : angle 3.78756 / 2.25 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 138 time to evaluate : 0.415 Fit side-chains REVERT: A 68 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7197 (mp) REVERT: A 196 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7559 (mt-10) REVERT: A 301 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.6935 (ttp80) REVERT: A 456 THR cc_start: 0.7390 (t) cc_final: 0.7070 (p) REVERT: A 491 CYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7229 (p) REVERT: A 503 CYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7524 (p) REVERT: A 585 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7773 (ttpp) REVERT: A 620 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7227 (pm20) REVERT: A 636 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: A 697 ARG cc_start: 0.6307 (OUTLIER) cc_final: 0.5528 (mpp-170) REVERT: A 908 HIS cc_start: 0.7387 (t-90) cc_final: 0.6896 (t70) REVERT: A 938 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7412 (t0) REVERT: A 976 LYS cc_start: 0.7841 (mmtt) cc_final: 0.7523 (mmtm) REVERT: A 995 GLU cc_start: 0.8550 (pt0) cc_final: 0.8271 (pt0) REVERT: A 1460 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6799 (mm-30) REVERT: A 1463 ARG cc_start: 0.7829 (mmt90) cc_final: 0.7278 (mmm160) REVERT: A 1489 ILE cc_start: 0.8229 (mt) cc_final: 0.7830 (mp) REVERT: A 1499 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7186 (pm20) REVERT: A 1502 GLN cc_start: 0.6541 (mm-40) cc_final: 0.6337 (mm-40) REVERT: A 1563 LYS cc_start: 0.7988 (pttp) cc_final: 0.7715 (tmtt) REVERT: A 1619 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6832 (mt) REVERT: A 1644 ARG cc_start: 0.7611 (pmm-80) cc_final: 0.6890 (ptt90) REVERT: A 1650 GLU cc_start: 0.7208 (tt0) cc_final: 0.6572 (tp30) REVERT: A 1666 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6825 (mm) REVERT: A 1674 TYR cc_start: 0.8239 (m-10) cc_final: 0.8011 (m-10) outliers start: 55 outliers final: 27 residues processed: 178 average time/residue: 0.6090 time to fit residues: 116.1461 Evaluate side-chains 178 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 503 CYS Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 779 GLU Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1460 GLU Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1666 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 74 optimal weight: 0.0040 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS A 335 GLN ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 ASN A 762 HIS ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1516 ASN ** A1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.174446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.147140 restraints weight = 10478.244| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.55 r_work: 0.3550 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10895 Z= 0.149 Angle : 0.742 10.860 14847 Z= 0.328 Chirality : 0.065 0.508 1599 Planarity : 0.004 0.049 1785 Dihedral : 17.429 178.214 1746 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.71 % Allowed : 27.50 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.24), residues: 1196 helix: 0.99 (0.28), residues: 354 sheet: -0.64 (0.37), residues: 155 loop : -0.01 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1488 TYR 0.014 0.001 TYR A 903 PHE 0.012 0.001 PHE A 15 TRP 0.018 0.001 TRP A 612 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (10879) covalent geometry : angle 0.73093 / 0.33 (14826) hydrogen bonds : bond 0.03609 / 2.49 ( 331) hydrogen bonds : angle 5.10186 / 3.67 ( 996) metal coordination : bond 0.00545 / 0.35 ( 16) metal coordination : angle 3.53376 / 2.06 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 143 time to evaluate : 0.292 Fit side-chains REVERT: A 68 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7151 (mp) REVERT: A 196 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: A 301 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.6959 (ttp80) REVERT: A 335 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6988 (pt0) REVERT: A 456 THR cc_start: 0.7486 (t) cc_final: 0.7150 (p) REVERT: A 491 CYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7190 (p) REVERT: A 503 CYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7554 (p) REVERT: A 620 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7216 (pm20) REVERT: A 636 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: A 719 ARG cc_start: 0.7945 (mmm-85) cc_final: 0.7539 (tpp-160) REVERT: A 908 HIS cc_start: 0.7372 (t-90) cc_final: 0.6902 (t70) REVERT: A 976 LYS cc_start: 0.7907 (mmtt) cc_final: 0.7524 (mmtm) REVERT: A 995 GLU cc_start: 0.8503 (pt0) cc_final: 0.8232 (pt0) REVERT: A 1460 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6700 (mm-30) REVERT: A 1463 ARG cc_start: 0.7818 (mmt90) cc_final: 0.7338 (mmm160) REVERT: A 1489 ILE cc_start: 0.8206 (mt) cc_final: 0.7806 (mp) REVERT: A 1499 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7230 (pm20) REVERT: A 1563 LYS cc_start: 0.7954 (pttp) cc_final: 0.7698 (tmtt) REVERT: A 1619 ILE cc_start: 0.7195 (OUTLIER) cc_final: 0.6868 (mt) REVERT: A 1644 ARG cc_start: 0.7633 (pmm-80) cc_final: 0.6914 (ptt90) REVERT: A 1650 GLU cc_start: 0.7182 (tt0) cc_final: 0.6547 (tp30) REVERT: A 1666 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6807 (mm) REVERT: A 1674 TYR cc_start: 0.8239 (m-10) cc_final: 0.8002 (m-10) outliers start: 50 outliers final: 25 residues processed: 178 average time/residue: 0.5778 time to fit residues: 110.4326 Evaluate side-chains 172 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 503 CYS Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 779 GLU Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1460 GLU Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1666 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 0.0870 chunk 6 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS A 335 GLN ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 ASN A 762 HIS ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN ** A1494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.173854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.146734 restraints weight = 10395.167| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.53 r_work: 0.3546 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10895 Z= 0.160 Angle : 0.753 11.252 14847 Z= 0.333 Chirality : 0.065 0.517 1599 Planarity : 0.004 0.049 1785 Dihedral : 17.403 178.220 1746 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.86 % Allowed : 28.81 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1196 helix: 1.00 (0.28), residues: 354 sheet: -0.64 (0.37), residues: 155 loop : 0.01 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1488 TYR 0.014 0.001 TYR A 529 PHE 0.019 0.001 PHE A 659 TRP 0.018 0.001 TRP A 612 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (10879) covalent geometry : angle 0.74124 / 0.33 (14826) hydrogen bonds : bond 0.03645 / 2.51 ( 331) hydrogen bonds : angle 5.10843 / 3.67 ( 996) metal coordination : bond 0.00546 / 0.33 ( 16) metal coordination : angle 3.56019 / 2.07 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 0.387 Fit side-chains REVERT: A 11 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7240 (tt0) REVERT: A 68 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7168 (mp) REVERT: A 100 LYS cc_start: 0.6718 (tttm) cc_final: 0.6296 (tttm) REVERT: A 196 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: A 301 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7032 (ttp80) REVERT: A 456 THR cc_start: 0.7442 (t) cc_final: 0.7118 (p) REVERT: A 491 CYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7139 (p) REVERT: A 503 CYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7539 (p) REVERT: A 620 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7209 (pm20) REVERT: A 636 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: A 908 HIS cc_start: 0.7402 (t-90) cc_final: 0.6938 (t70) REVERT: A 976 LYS cc_start: 0.7910 (mmtt) cc_final: 0.7551 (mmtm) REVERT: A 995 GLU cc_start: 0.8514 (pt0) cc_final: 0.8238 (pt0) REVERT: A 1460 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6726 (mm-30) REVERT: A 1463 ARG cc_start: 0.7833 (mmt90) cc_final: 0.7364 (mmm160) REVERT: A 1489 ILE cc_start: 0.8206 (mt) cc_final: 0.7805 (mp) REVERT: A 1499 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: A 1563 LYS cc_start: 0.7981 (pttp) cc_final: 0.7721 (tmtt) REVERT: A 1619 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6888 (mt) REVERT: A 1644 ARG cc_start: 0.7655 (pmm-80) cc_final: 0.6936 (ptt90) REVERT: A 1650 GLU cc_start: 0.7187 (tt0) cc_final: 0.6552 (tp30) REVERT: A 1666 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6836 (mm) REVERT: A 1674 TYR cc_start: 0.8241 (m-10) cc_final: 0.7969 (m-10) outliers start: 41 outliers final: 26 residues processed: 163 average time/residue: 0.5879 time to fit residues: 103.0896 Evaluate side-chains 169 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 503 CYS Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 779 GLU Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 827 LYS Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1460 GLU Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1666 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 58 optimal weight: 0.0670 overall best weight: 0.6316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS A 335 GLN ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 ASN A 762 HIS ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN ** A1494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.174807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.147805 restraints weight = 10435.917| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.54 r_work: 0.3557 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10895 Z= 0.152 Angle : 0.742 10.820 14847 Z= 0.328 Chirality : 0.064 0.499 1599 Planarity : 0.004 0.049 1785 Dihedral : 17.393 178.578 1746 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.24 % Allowed : 28.63 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.24), residues: 1196 helix: 1.05 (0.28), residues: 354 sheet: -0.62 (0.38), residues: 155 loop : 0.03 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1488 TYR 0.013 0.001 TYR A 529 PHE 0.012 0.001 PHE A 15 TRP 0.017 0.001 TRP A 612 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (10879) covalent geometry : angle 0.73106 / 0.33 (14826) hydrogen bonds : bond 0.03591 / 2.48 ( 331) hydrogen bonds : angle 5.08146 / 3.65 ( 996) metal coordination : bond 0.00528 / 0.34 ( 16) metal coordination : angle 3.46649 / 1.98 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3782.44 seconds wall clock time: 65 minutes 31.27 seconds (3931.27 seconds total)