Starting phenix.real_space_refine on Thu Jul 31 06:20:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ckm_30388/07_2025/7ckm_30388.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ckm_30388/07_2025/7ckm_30388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ckm_30388/07_2025/7ckm_30388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ckm_30388/07_2025/7ckm_30388.map" model { file = "/net/cci-nas-00/data/ceres_data/7ckm_30388/07_2025/7ckm_30388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ckm_30388/07_2025/7ckm_30388.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 4 6.06 5 S 94 5.16 5 C 8358 2.51 5 N 2205 2.21 5 O 2452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 121 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13114 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1603, 12702 Classifications: {'peptide': 1603} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 47, 'TRANS': 1555} Chain breaks: 16 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MN': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2171 SG CYS A 284 51.305 69.871 26.726 1.00 33.30 S ATOM 2195 SG CYS A 287 54.815 70.105 24.870 1.00 35.01 S ATOM 3474 SG CYS A 470 51.367 70.972 22.964 1.00 81.64 S ATOM 11406 SG CYS A1650 41.739 16.812 43.377 1.00 82.16 S ATOM 11419 SG CYS A1652 38.652 16.222 44.857 1.00 81.31 S ATOM 11438 SG CYS A1655 40.724 20.132 43.603 1.00 64.80 S ATOM 11510 SG CYS A1664 40.880 17.040 46.700 1.00 55.65 S ATOM 12763 SG CYS B 39 23.850 80.360 54.941 1.00 42.32 S ATOM 12784 SG CYS B 42 26.136 82.388 53.549 1.00 34.63 S ATOM 12918 SG CYS B 58 23.069 83.737 54.842 1.00 57.08 S ATOM 12943 SG CYS B 61 22.984 81.129 51.433 1.00 56.47 S ATOM 12866 SG CYS B 52 16.451 73.693 57.557 1.00 73.10 S ATOM 13033 SG CYS B 72 18.354 72.080 55.250 1.00 57.48 S ATOM 13057 SG CYS B 75 18.227 70.906 58.418 1.00 46.83 S Time building chain proxies: 7.72, per 1000 atoms: 0.59 Number of scatterers: 13114 At special positions: 0 Unit cell: (122.04, 114.48, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 Mn 1 24.99 S 94 16.00 O 2452 8.00 N 2205 7.00 C 8358 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 60 " distance=2.04 Simple disulfide: pdb=" SG CYS A1691 " - pdb=" SG CYS A1776 " distance=2.03 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: 3.37 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" ND1 HIS A 472 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 287 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 284 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 470 " pdb=" ZN A2303 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1650 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1652 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1655 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1664 " pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 39 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 58 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 61 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 42 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" NE2 HIS B 55 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 75 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 72 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 52 " Number of angles added : 18 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3152 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 10 sheets defined 52.7% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 3.751A pdb=" N GLU A 7 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 10 " --> pdb=" O GLN A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.700A pdb=" N GLY A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR A 28 " --> pdb=" O HIS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 57 removed outlier: 4.035A pdb=" N LEU A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 41 " --> pdb=" O PRO A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 76 removed outlier: 4.412A pdb=" N ASN A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 125 removed outlier: 4.347A pdb=" N SER A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 removed outlier: 3.763A pdb=" N LYS A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 171 removed outlier: 4.206A pdb=" N ARG A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.733A pdb=" N LEU A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 188 " --> pdb=" O TYR A 184 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 232 through 248 removed outlier: 3.844A pdb=" N ASP A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.886A pdb=" N ASN A 288 " --> pdb=" O CYS A 284 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 289' Processing helix chain 'A' and resid 289 through 303 Processing helix chain 'A' and resid 322 through 338 Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 346 through 365 Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 412 through 421 removed outlier: 3.520A pdb=" N CYS A 417 " --> pdb=" O TRP A 413 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.736A pdb=" N LEU A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 481 through 501 Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.561A pdb=" N ARG A 577 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 578 " --> pdb=" O PRO A 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 574 through 578' Processing helix chain 'A' and resid 586 through 598 Processing helix chain 'A' and resid 605 through 623 Proline residue: A 611 - end of helix Processing helix chain 'A' and resid 625 through 644 removed outlier: 3.665A pdb=" N GLN A 629 " --> pdb=" O SER A 625 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 644 " --> pdb=" O MET A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 680 removed outlier: 3.926A pdb=" N VAL A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 701 Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 712 through 732 Proline residue: A 727 - end of helix Processing helix chain 'A' and resid 745 through 760 Processing helix chain 'A' and resid 776 through 789 removed outlier: 3.824A pdb=" N ARG A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 852 Processing helix chain 'A' and resid 863 through 872 removed outlier: 3.586A pdb=" N TYR A 867 " --> pdb=" O ASP A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 895 Processing helix chain 'A' and resid 898 through 921 Processing helix chain 'A' and resid 963 through 968 removed outlier: 4.429A pdb=" N VAL A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS A 968 " --> pdb=" O LEU A 964 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 963 through 968' Processing helix chain 'A' and resid 971 through 975 removed outlier: 3.541A pdb=" N LEU A 975 " --> pdb=" O PRO A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 980 removed outlier: 3.871A pdb=" N VAL A 979 " --> pdb=" O PRO A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 989 removed outlier: 4.158A pdb=" N ASP A 985 " --> pdb=" O LYS A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 3.756A pdb=" N ASP A1021 " --> pdb=" O SER A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1035 Processing helix chain 'A' and resid 1135 through 1156 Processing helix chain 'A' and resid 1163 through 1181 Processing helix chain 'A' and resid 1197 through 1208 removed outlier: 3.823A pdb=" N PHE A1201 " --> pdb=" O SER A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1233 removed outlier: 3.660A pdb=" N HIS A1233 " --> pdb=" O LYS A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1249 Processing helix chain 'A' and resid 1264 through 1275 removed outlier: 4.679A pdb=" N GLN A1275 " --> pdb=" O HIS A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1319 Processing helix chain 'A' and resid 1351 through 1365 Processing helix chain 'A' and resid 1395 through 1405 removed outlier: 3.749A pdb=" N PHE A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1429 removed outlier: 3.914A pdb=" N ASN A1429 " --> pdb=" O GLN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1450 removed outlier: 3.624A pdb=" N SER A1450 " --> pdb=" O LEU A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1485 removed outlier: 3.744A pdb=" N PHE A1485 " --> pdb=" O ILE A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1507 Processing helix chain 'A' and resid 1513 through 1520 removed outlier: 3.771A pdb=" N ASN A1517 " --> pdb=" O GLU A1513 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A1518 " --> pdb=" O ASN A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1535 Processing helix chain 'A' and resid 1537 through 1545 removed outlier: 3.677A pdb=" N LEU A1545 " --> pdb=" O VAL A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1590 removed outlier: 3.839A pdb=" N LYS A1583 " --> pdb=" O PRO A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1625 Processing helix chain 'A' and resid 1639 through 1645 removed outlier: 3.602A pdb=" N VAL A1643 " --> pdb=" O TYR A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1664 through 1669 removed outlier: 3.800A pdb=" N ASN A1669 " --> pdb=" O ASN A1666 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1694 removed outlier: 3.827A pdb=" N GLY A1694 " --> pdb=" O ALA A1690 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1699 removed outlier: 3.822A pdb=" N PHE A1698 " --> pdb=" O GLU A1695 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER A1699 " --> pdb=" O TRP A1696 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1695 through 1699' Processing helix chain 'A' and resid 1735 through 1744 Processing helix chain 'A' and resid 1744 through 1750 Processing helix chain 'A' and resid 1758 through 1764 removed outlier: 3.977A pdb=" N SER A1762 " --> pdb=" O ASP A1758 " (cutoff:3.500A) Processing helix chain 'A' and resid 1778 through 1783 removed outlier: 3.678A pdb=" N MET A1782 " --> pdb=" O ALA A1778 " (cutoff:3.500A) Processing helix chain 'A' and resid 1788 through 1793 removed outlier: 3.758A pdb=" N LEU A1793 " --> pdb=" O ILE A1789 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 69 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 94 removed outlier: 6.771A pdb=" N LEU A 98 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 100 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ASP A 142 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU A 102 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ARG A 144 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 387 Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 534 removed outlier: 6.032A pdb=" N LEU A 559 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU A 567 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1129 through 1132 removed outlier: 3.833A pdb=" N LEU A1119 " --> pdb=" O GLU A1237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1379 through 1381 Processing sheet with id=AA7, first strand: chain 'A' and resid 1548 through 1549 Processing sheet with id=AA8, first strand: chain 'A' and resid 1630 through 1631 Processing sheet with id=AA9, first strand: chain 'A' and resid 1716 through 1719 Processing sheet with id=AB1, first strand: chain 'B' and resid 50 through 51 605 hydrogen bonds defined for protein. 1752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.28 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4235 1.35 - 1.46: 2978 1.46 - 1.58: 5996 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 13341 Sorted by residual: bond pdb=" N ILE B 50 " pdb=" CA ILE B 50 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.20e-02 6.94e+03 1.04e+01 bond pdb=" N LYS B 40 " pdb=" CA LYS B 40 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.28e-02 6.10e+03 8.40e+00 bond pdb=" N LEU B 57 " pdb=" CA LEU B 57 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.21e-02 6.83e+03 7.85e+00 bond pdb=" N CYS B 58 " pdb=" CA CYS B 58 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.31e-02 5.83e+03 7.66e+00 bond pdb=" N ARG B 60 " pdb=" CA ARG B 60 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.28e-02 6.10e+03 6.86e+00 ... (remaining 13336 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 17710 1.88 - 3.77: 245 3.77 - 5.65: 40 5.65 - 7.54: 2 7.54 - 9.42: 4 Bond angle restraints: 18001 Sorted by residual: angle pdb=" N ILE A1654 " pdb=" CA ILE A1654 " pdb=" C ILE A1654 " ideal model delta sigma weight residual 113.71 108.31 5.40 9.50e-01 1.11e+00 3.23e+01 angle pdb=" C LYS B 40 " pdb=" CA LYS B 40 " pdb=" CB LYS B 40 " ideal model delta sigma weight residual 109.83 115.39 -5.56 9.90e-01 1.02e+00 3.15e+01 angle pdb=" CA CYS B 39 " pdb=" C CYS B 39 " pdb=" O CYS B 39 " ideal model delta sigma weight residual 120.63 116.18 4.45 1.08e+00 8.57e-01 1.70e+01 angle pdb=" N CYS B 41 " pdb=" CA CYS B 41 " pdb=" C CYS B 41 " ideal model delta sigma weight residual 113.88 108.87 5.01 1.23e+00 6.61e-01 1.66e+01 angle pdb=" O CYS B 39 " pdb=" C CYS B 39 " pdb=" N LYS B 40 " ideal model delta sigma weight residual 122.12 126.03 -3.91 1.06e+00 8.90e-01 1.36e+01 ... (remaining 17996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7375 17.97 - 35.95: 572 35.95 - 53.92: 127 53.92 - 71.89: 22 71.89 - 89.87: 13 Dihedral angle restraints: 8109 sinusoidal: 3274 harmonic: 4835 Sorted by residual: dihedral pdb=" CA THR A1753 " pdb=" C THR A1753 " pdb=" N PRO A1754 " pdb=" CA PRO A1754 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" C LYS B 40 " pdb=" N LYS B 40 " pdb=" CA LYS B 40 " pdb=" CB LYS B 40 " ideal model delta harmonic sigma weight residual -122.60 -133.40 10.80 0 2.50e+00 1.60e-01 1.86e+01 dihedral pdb=" N LYS B 40 " pdb=" C LYS B 40 " pdb=" CA LYS B 40 " pdb=" CB LYS B 40 " ideal model delta harmonic sigma weight residual 122.80 133.35 -10.55 0 2.50e+00 1.60e-01 1.78e+01 ... (remaining 8106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1897 0.069 - 0.138: 169 0.138 - 0.207: 6 0.207 - 0.275: 0 0.275 - 0.344: 1 Chirality restraints: 2073 Sorted by residual: chirality pdb=" CA LYS B 40 " pdb=" N LYS B 40 " pdb=" C LYS B 40 " pdb=" CB LYS B 40 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA ILE B 50 " pdb=" N ILE B 50 " pdb=" C ILE B 50 " pdb=" CB ILE B 50 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" CB VAL A1465 " pdb=" CA VAL A1465 " pdb=" CG1 VAL A1465 " pdb=" CG2 VAL A1465 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.11e-01 ... (remaining 2070 not shown) Planarity restraints: 2274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A1393 " -0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO A1394 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A1394 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1394 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 39 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C CYS B 39 " 0.029 2.00e-02 2.50e+03 pdb=" O CYS B 39 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS B 40 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 737 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.45e+00 pdb=" N PRO A 738 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 738 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 738 " 0.022 5.00e-02 4.00e+02 ... (remaining 2271 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2992 2.78 - 3.31: 12415 3.31 - 3.84: 19912 3.84 - 4.37: 22789 4.37 - 4.90: 40391 Nonbonded interactions: 98499 Sorted by model distance: nonbonded pdb=" O VAL A 27 " pdb=" OG SER A 31 " model vdw 2.250 3.040 nonbonded pdb=" OD2 ASP A1173 " pdb=" OH TYR A1325 " model vdw 2.277 3.040 nonbonded pdb=" O THR A1377 " pdb=" OG1 THR A1377 " model vdw 2.284 3.040 nonbonded pdb=" ND2 ASN A 788 " pdb=" OE1 GLU A1209 " model vdw 2.300 3.120 nonbonded pdb=" O ASN A 412 " pdb=" ND2 ASN A 416 " model vdw 2.303 3.120 ... (remaining 98494 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: 0.740 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: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.130 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 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 : 0.004 0.117 13359 Z= 0.179 Angle : 0.839 38.791 18023 Z= 0.353 Chirality : 0.041 0.344 2073 Planarity : 0.004 0.043 2274 Dihedral : 14.022 89.867 4951 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 3.56 % Allowed : 10.60 % Favored : 85.84 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.19), residues: 1616 helix: -0.54 (0.17), residues: 805 sheet: -1.61 (0.44), residues: 121 loop : -3.86 (0.18), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 155 HIS 0.004 0.001 HIS A 647 PHE 0.013 0.001 PHE A 533 TYR 0.009 0.001 TYR A 572 ARG 0.005 0.000 ARG A1741 Details of bonding type rmsd hydrogen bonds : bond 0.15744 ( 605) hydrogen bonds : angle 5.45285 ( 1752) metal coordination : bond 0.06848 ( 16) metal coordination : angle 19.15173 ( 18) SS BOND : bond 0.00690 ( 2) SS BOND : angle 2.25990 ( 4) covalent geometry : bond 0.00315 (13341) covalent geometry : angle 0.58106 (18001) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 270 time to evaluate : 1.482 Fit side-chains REVERT: A 125 ASN cc_start: 0.8330 (t0) cc_final: 0.8063 (t0) REVERT: A 131 GLN cc_start: 0.7639 (tm-30) cc_final: 0.7357 (pp30) REVERT: A 183 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: A 204 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6647 (pp) REVERT: A 209 ARG cc_start: 0.7371 (ttt-90) cc_final: 0.7123 (ttm-80) REVERT: A 292 MET cc_start: 0.8030 (mtp) cc_final: 0.7796 (mtm) REVERT: A 606 MET cc_start: 0.8275 (ptm) cc_final: 0.8047 (ptt) REVERT: A 838 GLU cc_start: 0.7657 (tp30) cc_final: 0.6928 (tp30) REVERT: A 980 TYR cc_start: 0.6245 (OUTLIER) cc_final: 0.5567 (t80) REVERT: A 1216 ARG cc_start: 0.7644 (mmt90) cc_final: 0.7389 (mmt-90) REVERT: A 1461 GLU cc_start: 0.7530 (pt0) cc_final: 0.7068 (pt0) REVERT: A 1462 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7819 (m-30) REVERT: B 60 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7590 (ppt-90) outliers start: 53 outliers final: 35 residues processed: 312 average time/residue: 0.2972 time to fit residues: 129.4788 Evaluate side-chains 241 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 155 TRP Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1462 ASP Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1566 LEU Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1795 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 60 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 128 optimal weight: 0.0070 chunk 49 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 148 optimal weight: 0.5980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 HIS A 628 ASN A 647 HIS A 737 ASN A 788 ASN A 901 GLN A1124 GLN A1128 ASN A1308 GLN A1414 GLN A1429 ASN A1542 ASN A1611 GLN A1783 ASN ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.168730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.128862 restraints weight = 16488.257| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.85 r_work: 0.3133 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13359 Z= 0.119 Angle : 0.595 19.665 18023 Z= 0.290 Chirality : 0.040 0.192 2073 Planarity : 0.004 0.041 2274 Dihedral : 6.972 59.236 1823 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 4.50 % Allowed : 14.56 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.20), residues: 1616 helix: 0.51 (0.18), residues: 824 sheet: -1.24 (0.47), residues: 116 loop : -3.40 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 155 HIS 0.002 0.001 HIS A 450 PHE 0.014 0.001 PHE A 475 TYR 0.009 0.001 TYR A1302 ARG 0.004 0.000 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.04321 ( 605) hydrogen bonds : angle 4.04161 ( 1752) metal coordination : bond 0.01577 ( 16) metal coordination : angle 6.52714 ( 18) SS BOND : bond 0.00990 ( 2) SS BOND : angle 1.73818 ( 4) covalent geometry : bond 0.00251 (13341) covalent geometry : angle 0.55758 (18001) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 230 time to evaluate : 1.804 Fit side-chains revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8481 (t0) cc_final: 0.8210 (t0) REVERT: A 131 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7406 (pp30) REVERT: A 183 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: A 204 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6632 (pp) REVERT: A 209 ARG cc_start: 0.7414 (ttt-90) cc_final: 0.7037 (ttm-80) REVERT: A 268 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8285 (mt-10) REVERT: A 606 MET cc_start: 0.8703 (ptm) cc_final: 0.8411 (ptt) REVERT: A 838 GLU cc_start: 0.7598 (tp30) cc_final: 0.6822 (tp30) REVERT: A 980 TYR cc_start: 0.5833 (OUTLIER) cc_final: 0.5232 (t80) REVERT: A 1141 MET cc_start: 0.8393 (mmt) cc_final: 0.8164 (mmt) REVERT: A 1196 MET cc_start: 0.8352 (mmt) cc_final: 0.7828 (mmt) REVERT: A 1216 ARG cc_start: 0.7582 (mmt90) cc_final: 0.7173 (mmt-90) REVERT: A 1461 GLU cc_start: 0.7683 (pt0) cc_final: 0.7315 (pt0) REVERT: A 1741 ARG cc_start: 0.7969 (ptm160) cc_final: 0.7351 (ttm170) REVERT: A 1742 ARG cc_start: 0.7042 (mtm-85) cc_final: 0.6663 (ttm170) outliers start: 67 outliers final: 38 residues processed: 283 average time/residue: 0.3267 time to fit residues: 137.2060 Evaluate side-chains 241 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 155 TRP Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1542 ASN Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1566 LEU Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1795 THR Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 108 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN A 431 HIS ** A 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1726 GLN A1783 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.163737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124174 restraints weight = 16671.974| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.89 r_work: 0.3068 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 13359 Z= 0.189 Angle : 0.637 14.463 18023 Z= 0.318 Chirality : 0.042 0.175 2073 Planarity : 0.004 0.050 2274 Dihedral : 6.948 59.218 1803 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 4.97 % Allowed : 16.98 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.21), residues: 1616 helix: 0.71 (0.18), residues: 831 sheet: -1.00 (0.47), residues: 126 loop : -3.41 (0.20), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1717 HIS 0.005 0.001 HIS A 647 PHE 0.018 0.002 PHE A 533 TYR 0.012 0.001 TYR A 572 ARG 0.006 0.001 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.05176 ( 605) hydrogen bonds : angle 4.14001 ( 1752) metal coordination : bond 0.01438 ( 16) metal coordination : angle 5.10102 ( 18) SS BOND : bond 0.00734 ( 2) SS BOND : angle 4.14025 ( 4) covalent geometry : bond 0.00455 (13341) covalent geometry : angle 0.61326 (18001) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 214 time to evaluate : 4.250 Fit side-chains revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8551 (t0) cc_final: 0.8255 (t0) REVERT: A 131 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7487 (pp30) REVERT: A 183 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: A 204 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6663 (pp) REVERT: A 209 ARG cc_start: 0.7303 (ttt-90) cc_final: 0.7098 (ttm-80) REVERT: A 212 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8290 (tp) REVERT: A 458 MET cc_start: 0.7615 (tpp) cc_final: 0.7326 (tpp) REVERT: A 606 MET cc_start: 0.8733 (ptm) cc_final: 0.8444 (ptt) REVERT: A 980 TYR cc_start: 0.6086 (OUTLIER) cc_final: 0.5255 (t80) REVERT: A 1196 MET cc_start: 0.8424 (mmt) cc_final: 0.7875 (mmt) REVERT: A 1216 ARG cc_start: 0.7608 (mmt90) cc_final: 0.7311 (mmt-90) REVERT: A 1461 GLU cc_start: 0.7818 (pt0) cc_final: 0.7456 (pt0) REVERT: A 1741 ARG cc_start: 0.7980 (ptm160) cc_final: 0.7349 (ttp80) REVERT: A 1742 ARG cc_start: 0.7064 (mtm-85) cc_final: 0.6835 (ttm170) outliers start: 74 outliers final: 48 residues processed: 269 average time/residue: 0.3958 time to fit residues: 158.3094 Evaluate side-chains 247 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 195 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 155 TRP Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1486 HIS Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1566 LEU Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1700 THR Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1783 ASN Chi-restraints excluded: chain A residue 1795 THR Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 92 optimal weight: 10.0000 chunk 69 optimal weight: 0.1980 chunk 5 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN A 800 ASN A1542 ASN A1743 ASN A1783 ASN ** B 55 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 = 0.3909 r_free = 0.3909 target = 0.166556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.126199 restraints weight = 16500.863| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.64 r_work: 0.3131 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13359 Z= 0.122 Angle : 0.587 14.289 18023 Z= 0.288 Chirality : 0.040 0.166 2073 Planarity : 0.004 0.045 2274 Dihedral : 6.428 59.309 1798 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 5.10 % Allowed : 17.79 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.21), residues: 1616 helix: 1.04 (0.18), residues: 829 sheet: -0.95 (0.48), residues: 116 loop : -3.19 (0.21), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 155 HIS 0.007 0.001 HIS A 431 PHE 0.030 0.001 PHE A 91 TYR 0.018 0.001 TYR A1097 ARG 0.005 0.000 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 605) hydrogen bonds : angle 3.89684 ( 1752) metal coordination : bond 0.01564 ( 16) metal coordination : angle 6.19056 ( 18) SS BOND : bond 0.00391 ( 2) SS BOND : angle 1.14864 ( 4) covalent geometry : bond 0.00269 (13341) covalent geometry : angle 0.55383 (18001) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 203 time to evaluate : 2.344 Fit side-chains revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8500 (t0) cc_final: 0.8204 (t0) REVERT: A 131 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7395 (pp30) REVERT: A 183 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: A 204 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6809 (pp) REVERT: A 412 ASN cc_start: 0.8546 (t0) cc_final: 0.8003 (t0) REVERT: A 458 MET cc_start: 0.7619 (tpp) cc_final: 0.7344 (tpp) REVERT: A 606 MET cc_start: 0.8795 (ptm) cc_final: 0.8492 (ptt) REVERT: A 771 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8054 (tp40) REVERT: A 980 TYR cc_start: 0.6039 (OUTLIER) cc_final: 0.5151 (t80) REVERT: A 1097 TYR cc_start: 0.7230 (t80) cc_final: 0.6806 (t80) REVERT: A 1196 MET cc_start: 0.8341 (mmt) cc_final: 0.7942 (mmt) REVERT: A 1461 GLU cc_start: 0.7728 (pt0) cc_final: 0.7352 (pt0) REVERT: A 1695 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7739 (pp20) REVERT: A 1741 ARG cc_start: 0.7968 (ptm160) cc_final: 0.7379 (ttm170) outliers start: 76 outliers final: 53 residues processed: 265 average time/residue: 0.2572 time to fit residues: 99.9504 Evaluate side-chains 247 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 189 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 155 TRP Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1445 GLN Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1486 HIS Chi-restraints excluded: chain A residue 1542 ASN Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1566 LEU Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1587 SER Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1695 GLU Chi-restraints excluded: chain A residue 1700 THR Chi-restraints excluded: chain A residue 1783 ASN Chi-restraints excluded: chain A residue 1795 THR Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 13 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 80 optimal weight: 0.0670 chunk 20 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 89 optimal weight: 0.0980 chunk 3 optimal weight: 8.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 HIS A1296 HIS A1711 ASN A1783 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.168072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128151 restraints weight = 16674.602| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.78 r_work: 0.3144 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13359 Z= 0.109 Angle : 0.561 11.929 18023 Z= 0.277 Chirality : 0.039 0.166 2073 Planarity : 0.004 0.061 2274 Dihedral : 6.275 59.054 1798 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 4.90 % Allowed : 18.39 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.21), residues: 1616 helix: 1.29 (0.19), residues: 825 sheet: -1.01 (0.48), residues: 118 loop : -3.09 (0.21), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1717 HIS 0.003 0.001 HIS B 73 PHE 0.023 0.001 PHE A 91 TYR 0.018 0.001 TYR A1302 ARG 0.006 0.000 ARG A1543 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 605) hydrogen bonds : angle 3.77504 ( 1752) metal coordination : bond 0.00881 ( 16) metal coordination : angle 5.11091 ( 18) SS BOND : bond 0.00653 ( 2) SS BOND : angle 1.26533 ( 4) covalent geometry : bond 0.00235 (13341) covalent geometry : angle 0.53677 (18001) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 202 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8485 (t0) cc_final: 0.8188 (t0) REVERT: A 131 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7461 (pp30) REVERT: A 183 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: A 204 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6788 (pp) REVERT: A 231 ARG cc_start: 0.7989 (mtp85) cc_final: 0.7612 (ttp80) REVERT: A 406 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8296 (ttpp) REVERT: A 412 ASN cc_start: 0.8562 (t0) cc_final: 0.8034 (t0) REVERT: A 458 MET cc_start: 0.7590 (tpp) cc_final: 0.7285 (tpp) REVERT: A 606 MET cc_start: 0.8772 (ptm) cc_final: 0.8467 (ptt) REVERT: A 771 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8041 (tp40) REVERT: A 980 TYR cc_start: 0.6042 (OUTLIER) cc_final: 0.5089 (t80) REVERT: A 1116 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8351 (mtmm) REVERT: A 1196 MET cc_start: 0.8335 (mmt) cc_final: 0.7896 (mmt) REVERT: A 1461 GLU cc_start: 0.7686 (pt0) cc_final: 0.6701 (tt0) REVERT: A 1493 PHE cc_start: 0.8444 (t80) cc_final: 0.8222 (t80) REVERT: A 1695 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7845 (pp20) REVERT: A 1741 ARG cc_start: 0.8063 (ptm160) cc_final: 0.7292 (ttm170) outliers start: 73 outliers final: 54 residues processed: 263 average time/residue: 0.2642 time to fit residues: 101.5419 Evaluate side-chains 255 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 195 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 155 TRP Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1266 SER Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1414 GLN Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1445 GLN Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1486 HIS Chi-restraints excluded: chain A residue 1560 LEU Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1587 SER Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1695 GLU Chi-restraints excluded: chain A residue 1700 THR Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1783 ASN Chi-restraints excluded: chain A residue 1795 THR Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 99 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 HIS ** A 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 HIS A1783 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.160224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.120997 restraints weight = 17030.745| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.34 r_work: 0.3014 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 13359 Z= 0.283 Angle : 0.736 16.020 18023 Z= 0.367 Chirality : 0.046 0.184 2073 Planarity : 0.005 0.065 2274 Dihedral : 6.870 59.672 1796 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 5.10 % Allowed : 19.53 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.21), residues: 1616 helix: 0.92 (0.18), residues: 832 sheet: -0.93 (0.47), residues: 128 loop : -3.33 (0.21), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 43 HIS 0.008 0.002 HIS A 647 PHE 0.023 0.002 PHE A 533 TYR 0.017 0.002 TYR A 572 ARG 0.005 0.001 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.06215 ( 605) hydrogen bonds : angle 4.32471 ( 1752) metal coordination : bond 0.01393 ( 16) metal coordination : angle 6.43069 ( 18) SS BOND : bond 0.01000 ( 2) SS BOND : angle 2.04847 ( 4) covalent geometry : bond 0.00692 (13341) covalent geometry : angle 0.70706 (18001) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 199 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8596 (t0) cc_final: 0.8342 (t0) REVERT: A 131 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7581 (pp30) REVERT: A 183 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7741 (mp0) REVERT: A 204 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6771 (pp) REVERT: A 406 LYS cc_start: 0.8727 (ttmt) cc_final: 0.8213 (ttpp) REVERT: A 412 ASN cc_start: 0.8498 (t0) cc_final: 0.7978 (t0) REVERT: A 458 MET cc_start: 0.7678 (tpp) cc_final: 0.7473 (tpp) REVERT: A 606 MET cc_start: 0.8790 (ptm) cc_final: 0.8497 (ptt) REVERT: A 771 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8027 (tp40) REVERT: A 980 TYR cc_start: 0.6179 (OUTLIER) cc_final: 0.5101 (t80) REVERT: A 1097 TYR cc_start: 0.7353 (t80) cc_final: 0.6968 (t80) REVERT: A 1461 GLU cc_start: 0.7927 (pt0) cc_final: 0.7045 (tt0) REVERT: A 1463 GLN cc_start: 0.8347 (tp40) cc_final: 0.7592 (tm-30) REVERT: A 1695 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7983 (pp20) REVERT: A 1741 ARG cc_start: 0.8030 (ptm160) cc_final: 0.7200 (ttp80) outliers start: 76 outliers final: 61 residues processed: 261 average time/residue: 0.2723 time to fit residues: 102.5592 Evaluate side-chains 258 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 192 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 155 TRP Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1266 SER Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1414 GLN Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1486 HIS Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1587 SER Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1695 GLU Chi-restraints excluded: chain A residue 1700 THR Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1783 ASN Chi-restraints excluded: chain A residue 1795 THR Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 119 optimal weight: 0.0980 chunk 43 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 HIS A1783 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.163773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124158 restraints weight = 16612.121| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.70 r_work: 0.3089 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13359 Z= 0.147 Angle : 0.609 12.739 18023 Z= 0.304 Chirality : 0.041 0.166 2073 Planarity : 0.004 0.050 2274 Dihedral : 6.596 59.990 1794 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 4.63 % Allowed : 20.34 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.21), residues: 1616 helix: 1.24 (0.18), residues: 825 sheet: -0.86 (0.47), residues: 128 loop : -3.17 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1717 HIS 0.003 0.001 HIS A 647 PHE 0.018 0.001 PHE A 91 TYR 0.021 0.001 TYR A1302 ARG 0.006 0.000 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 605) hydrogen bonds : angle 3.96848 ( 1752) metal coordination : bond 0.01051 ( 16) metal coordination : angle 5.32340 ( 18) SS BOND : bond 0.00780 ( 2) SS BOND : angle 1.69616 ( 4) covalent geometry : bond 0.00344 (13341) covalent geometry : angle 0.58519 (18001) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 204 time to evaluate : 1.656 Fit side-chains revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8547 (t0) cc_final: 0.8278 (t0) REVERT: A 131 GLN cc_start: 0.8000 (tm-30) cc_final: 0.7524 (pp30) REVERT: A 183 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: A 204 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.6874 (pp) REVERT: A 212 LEU cc_start: 0.8497 (pt) cc_final: 0.8218 (tp) REVERT: A 231 ARG cc_start: 0.8223 (mtm110) cc_final: 0.7689 (ttp80) REVERT: A 406 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8233 (ttpp) REVERT: A 412 ASN cc_start: 0.8522 (t0) cc_final: 0.7990 (t0) REVERT: A 458 MET cc_start: 0.7710 (tpp) cc_final: 0.7376 (tpp) REVERT: A 606 MET cc_start: 0.8793 (ptm) cc_final: 0.8493 (ptt) REVERT: A 771 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7977 (tp40) REVERT: A 980 TYR cc_start: 0.6135 (OUTLIER) cc_final: 0.5072 (t80) REVERT: A 1097 TYR cc_start: 0.7278 (t80) cc_final: 0.6872 (t80) REVERT: A 1148 PHE cc_start: 0.8924 (t80) cc_final: 0.8627 (t80) REVERT: A 1196 MET cc_start: 0.8355 (mmt) cc_final: 0.8050 (mmt) REVERT: A 1461 GLU cc_start: 0.7769 (pt0) cc_final: 0.6836 (tt0) REVERT: A 1463 GLN cc_start: 0.8236 (tp40) cc_final: 0.7564 (tm-30) REVERT: A 1695 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7884 (pp20) REVERT: A 1741 ARG cc_start: 0.8053 (ptm160) cc_final: 0.7221 (ttp80) outliers start: 69 outliers final: 54 residues processed: 261 average time/residue: 0.2615 time to fit residues: 99.0614 Evaluate side-chains 255 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 196 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 155 TRP Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1414 GLN Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1445 GLN Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1486 HIS Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1587 SER Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1695 GLU Chi-restraints excluded: chain A residue 1700 THR Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1783 ASN Chi-restraints excluded: chain A residue 1795 THR Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 156 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 139 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 0.1980 chunk 40 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 160 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A1783 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.166432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126442 restraints weight = 16634.657| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.71 r_work: 0.3133 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13359 Z= 0.116 Angle : 0.584 11.156 18023 Z= 0.292 Chirality : 0.040 0.167 2073 Planarity : 0.004 0.048 2274 Dihedral : 6.422 59.953 1794 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 4.77 % Allowed : 20.74 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.21), residues: 1616 helix: 1.44 (0.19), residues: 825 sheet: -1.14 (0.47), residues: 123 loop : -3.04 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1717 HIS 0.003 0.001 HIS A 450 PHE 0.020 0.001 PHE A 91 TYR 0.023 0.001 TYR A1302 ARG 0.005 0.000 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 605) hydrogen bonds : angle 3.81895 ( 1752) metal coordination : bond 0.01018 ( 16) metal coordination : angle 4.66687 ( 18) SS BOND : bond 0.00408 ( 2) SS BOND : angle 2.82099 ( 4) covalent geometry : bond 0.00259 (13341) covalent geometry : angle 0.56430 (18001) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 201 time to evaluate : 1.452 Fit side-chains revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8477 (t0) cc_final: 0.8229 (t0) REVERT: A 131 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7528 (pp30) REVERT: A 149 ASN cc_start: 0.8838 (OUTLIER) cc_final: 0.8293 (p0) REVERT: A 183 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: A 204 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6875 (pp) REVERT: A 212 LEU cc_start: 0.8499 (pt) cc_final: 0.8238 (tp) REVERT: A 231 ARG cc_start: 0.8086 (mtm110) cc_final: 0.7543 (ttp80) REVERT: A 406 LYS cc_start: 0.8716 (ttmt) cc_final: 0.8283 (ttpp) REVERT: A 412 ASN cc_start: 0.8500 (t0) cc_final: 0.7969 (t0) REVERT: A 419 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8595 (mttp) REVERT: A 458 MET cc_start: 0.7809 (tpp) cc_final: 0.7436 (tpp) REVERT: A 606 MET cc_start: 0.8765 (ptm) cc_final: 0.8450 (ptt) REVERT: A 771 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8007 (tp40) REVERT: A 870 LEU cc_start: 0.6422 (OUTLIER) cc_final: 0.5911 (mm) REVERT: A 980 TYR cc_start: 0.6123 (OUTLIER) cc_final: 0.5097 (t80) REVERT: A 1097 TYR cc_start: 0.7261 (t80) cc_final: 0.6835 (t80) REVERT: A 1196 MET cc_start: 0.8296 (mmt) cc_final: 0.8046 (mmt) REVERT: A 1463 GLN cc_start: 0.8222 (tp40) cc_final: 0.7516 (tm-30) REVERT: A 1493 PHE cc_start: 0.8545 (t80) cc_final: 0.8328 (t80) REVERT: A 1513 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6693 (mp0) REVERT: A 1695 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7804 (pp20) REVERT: A 1741 ARG cc_start: 0.7981 (ptm160) cc_final: 0.7211 (ttp80) outliers start: 71 outliers final: 56 residues processed: 261 average time/residue: 0.2527 time to fit residues: 95.8344 Evaluate side-chains 256 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 192 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 155 TRP Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1266 SER Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1414 GLN Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1486 HIS Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1587 SER Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1695 GLU Chi-restraints excluded: chain A residue 1700 THR Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1783 ASN Chi-restraints excluded: chain A residue 1795 THR Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 69 optimal weight: 0.0670 chunk 78 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 122 optimal weight: 0.5980 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS A1783 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.165997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.126747 restraints weight = 16717.480| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.71 r_work: 0.3132 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13359 Z= 0.118 Angle : 0.577 10.663 18023 Z= 0.288 Chirality : 0.040 0.165 2073 Planarity : 0.004 0.047 2274 Dihedral : 6.333 59.886 1794 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 4.77 % Allowed : 20.60 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.21), residues: 1616 helix: 1.49 (0.19), residues: 827 sheet: -1.11 (0.47), residues: 123 loop : -2.99 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1717 HIS 0.004 0.001 HIS A 450 PHE 0.019 0.001 PHE A 91 TYR 0.023 0.001 TYR A1302 ARG 0.004 0.000 ARG A1742 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 605) hydrogen bonds : angle 3.78148 ( 1752) metal coordination : bond 0.00955 ( 16) metal coordination : angle 4.41938 ( 18) SS BOND : bond 0.00616 ( 2) SS BOND : angle 2.43109 ( 4) covalent geometry : bond 0.00265 (13341) covalent geometry : angle 0.55866 (18001) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 195 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8494 (t0) cc_final: 0.8241 (t0) REVERT: A 131 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7539 (pp30) REVERT: A 183 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: A 204 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.6903 (pp) REVERT: A 212 LEU cc_start: 0.8520 (pt) cc_final: 0.8251 (tp) REVERT: A 231 ARG cc_start: 0.8013 (mtm110) cc_final: 0.7521 (ttp80) REVERT: A 406 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8301 (ttpp) REVERT: A 419 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8620 (mttp) REVERT: A 458 MET cc_start: 0.7846 (tpp) cc_final: 0.7501 (tpp) REVERT: A 508 ARG cc_start: 0.7442 (mmp-170) cc_final: 0.7191 (mmp-170) REVERT: A 606 MET cc_start: 0.8774 (ptm) cc_final: 0.8470 (ptt) REVERT: A 771 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8015 (tp40) REVERT: A 870 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.5966 (mm) REVERT: A 980 TYR cc_start: 0.6122 (OUTLIER) cc_final: 0.5054 (t80) REVERT: A 1097 TYR cc_start: 0.7269 (t80) cc_final: 0.6855 (t80) REVERT: A 1463 GLN cc_start: 0.8149 (tp40) cc_final: 0.7487 (tm-30) REVERT: A 1493 PHE cc_start: 0.8448 (t80) cc_final: 0.8224 (t80) REVERT: A 1695 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7780 (pp20) REVERT: A 1741 ARG cc_start: 0.7986 (ptm160) cc_final: 0.7242 (ttp80) outliers start: 71 outliers final: 60 residues processed: 254 average time/residue: 0.2770 time to fit residues: 102.3444 Evaluate side-chains 256 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 189 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 155 TRP Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1266 SER Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1414 GLN Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1445 GLN Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1486 HIS Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1587 SER Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1695 GLU Chi-restraints excluded: chain A residue 1700 THR Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1795 THR Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 128 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 142 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 119 optimal weight: 0.0470 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 416 ASN A 431 HIS A1743 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.166161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.126670 restraints weight = 16612.866| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.72 r_work: 0.3124 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13359 Z= 0.125 Angle : 0.584 10.463 18023 Z= 0.291 Chirality : 0.040 0.165 2073 Planarity : 0.004 0.047 2274 Dihedral : 6.299 59.784 1794 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.70 % Allowed : 20.87 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.21), residues: 1616 helix: 1.49 (0.18), residues: 834 sheet: -1.10 (0.47), residues: 123 loop : -3.01 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1717 HIS 0.006 0.001 HIS A 430 PHE 0.019 0.001 PHE A 91 TYR 0.024 0.001 TYR A1302 ARG 0.006 0.000 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 605) hydrogen bonds : angle 3.78017 ( 1752) metal coordination : bond 0.00959 ( 16) metal coordination : angle 4.32745 ( 18) SS BOND : bond 0.00594 ( 2) SS BOND : angle 2.60909 ( 4) covalent geometry : bond 0.00287 (13341) covalent geometry : angle 0.56630 (18001) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 195 time to evaluate : 1.713 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.6636 (tp) cc_final: 0.6419 (tp) REVERT: A 125 ASN cc_start: 0.8523 (t0) cc_final: 0.8277 (t0) REVERT: A 131 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7538 (pp30) REVERT: A 149 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8236 (p0) REVERT: A 183 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: A 204 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.6918 (pp) REVERT: A 212 LEU cc_start: 0.8510 (pt) cc_final: 0.8255 (tp) REVERT: A 231 ARG cc_start: 0.8011 (mtm110) cc_final: 0.7519 (ttp80) REVERT: A 406 LYS cc_start: 0.8707 (ttmt) cc_final: 0.8312 (ttpp) REVERT: A 412 ASN cc_start: 0.8553 (t0) cc_final: 0.8067 (t0) REVERT: A 419 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8619 (mttp) REVERT: A 458 MET cc_start: 0.7849 (tpp) cc_final: 0.7520 (tpp) REVERT: A 508 ARG cc_start: 0.7420 (mmp-170) cc_final: 0.7189 (mmp-170) REVERT: A 606 MET cc_start: 0.8774 (ptm) cc_final: 0.8467 (ptt) REVERT: A 650 ASP cc_start: 0.8294 (t0) cc_final: 0.8080 (t0) REVERT: A 771 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8027 (tp40) REVERT: A 870 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.5926 (mm) REVERT: A 980 TYR cc_start: 0.6147 (OUTLIER) cc_final: 0.5061 (t80) REVERT: A 1097 TYR cc_start: 0.7275 (t80) cc_final: 0.6857 (t80) REVERT: A 1463 GLN cc_start: 0.8220 (tp40) cc_final: 0.7557 (tm-30) REVERT: A 1493 PHE cc_start: 0.8448 (t80) cc_final: 0.8100 (t80) REVERT: A 1521 ARG cc_start: 0.8278 (tpp80) cc_final: 0.8077 (ttp-110) REVERT: A 1695 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7788 (pp20) REVERT: A 1741 ARG cc_start: 0.8004 (ptm160) cc_final: 0.7256 (ttp80) outliers start: 70 outliers final: 60 residues processed: 255 average time/residue: 0.2639 time to fit residues: 98.0714 Evaluate side-chains 258 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 190 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 155 TRP Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 980 TYR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1266 SER Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1414 GLN Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1445 GLN Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1486 HIS Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1587 SER Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1695 GLU Chi-restraints excluded: chain A residue 1700 THR Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1795 THR Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 157 optimal weight: 0.0570 chunk 122 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 85 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 153 optimal weight: 0.3980 chunk 41 optimal weight: 6.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS A 431 HIS ** A1743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.166871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127619 restraints weight = 16796.357| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.87 r_work: 0.3129 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13359 Z= 0.115 Angle : 0.582 10.210 18023 Z= 0.290 Chirality : 0.040 0.161 2073 Planarity : 0.004 0.047 2274 Dihedral : 6.257 59.747 1794 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.56 % Allowed : 21.28 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.22), residues: 1616 helix: 1.54 (0.18), residues: 833 sheet: -1.09 (0.47), residues: 123 loop : -2.98 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 429 HIS 0.017 0.001 HIS A 431 PHE 0.020 0.001 PHE A 91 TYR 0.024 0.001 TYR A1302 ARG 0.009 0.000 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 605) hydrogen bonds : angle 3.74992 ( 1752) metal coordination : bond 0.00915 ( 16) metal coordination : angle 4.23038 ( 18) SS BOND : bond 0.00542 ( 2) SS BOND : angle 2.63518 ( 4) covalent geometry : bond 0.00249 (13341) covalent geometry : angle 0.56547 (18001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6754.93 seconds wall clock time: 119 minutes 39.88 seconds (7179.88 seconds total)