Starting phenix.real_space_refine on Sat Sep 12 02:39:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ckm_30388/09_2026/7ckm_30388.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ckm_30388/09_2026/7ckm_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7ckm_30388/09_2026/7ckm_30388.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ckm_30388/09_2026/7ckm_30388.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ckm_30388/09_2026/7ckm_30388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ckm_30388/09_2026/7ckm_30388.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ckm_30388/09_2026/7ckm_30388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ckm_30388/09_2026/7ckm_30388.map" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 'ARG:plan': 7, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 7, 'HIS:plan': 2, 'PHE:plan': 3} 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: 3.30, per 1000 atoms: 0.25 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: 1.02 Conformation dependent library (CDL) restraints added in 615.0 milliseconds 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: 0.64 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: 2.53 Time building geometry restraints manager: 1.42 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: 0.980 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.400 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 7.21 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (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 ARG 0.005 0.000 ARG A1741 TYR 0.009 0.001 TYR A 572 PHE 0.013 0.001 PHE A 533 TRP 0.009 0.001 TRP A 155 HIS 0.004 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (13341) covalent geometry : angle 0.58106 / 0.33 (18001) SS BOND : bond 0.00690 / 0.36 ( 2) SS BOND : angle 2.25990 / 1.27 ( 4) hydrogen bonds : bond 0.15744 / 9.98 ( 605) hydrogen bonds : angle 5.45285 / 3.88 ( 1752) metal coordination : bond 0.06848 / 4.22 ( 16) metal coordination : angle 19.15173 / 11.21 ( 18) *********************** 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 : 0.436 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: 0.7359 (pp30) REVERT: A 183 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: A 204 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6649 (pp) REVERT: A 209 ARG cc_start: 0.7371 (ttt-90) cc_final: 0.7121 (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: 0.6932 (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: 0.7388 (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: 0.7821 (m-30) REVERT: B 60 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7589 (ppt-90) outliers start: 53 outliers final: 35 residues processed: 312 average time/residue: 0.1295 time to fit residues: 57.1303 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 : 0.513 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 149 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 62.8727 > 50:) overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 HIS A 628 ASN A 647 HIS A 704 HIS A 788 ASN A1013 ASN A1124 GLN A1128 ASN A1308 GLN A1358 HIS A1429 ASN A1542 ASN A1611 GLN A1726 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 = 0.3874 r_free = 0.3874 target = 0.163351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123448 restraints weight = 16553.878| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.81 r_work: 0.3070 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13359 Z= 0.203 Angle : 0.670 19.892 18023 Z= 0.334 Chirality : 0.043 0.204 2073 Planarity : 0.004 0.050 2274 Dihedral : 7.384 59.405 1823 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 4.97 % Allowed : 16.38 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.20), residues: 1616 helix: 0.39 (0.18), residues: 822 sheet: -1.28 (0.47), residues: 123 loop : -3.49 (0.20), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1448 TYR 0.014 0.002 TYR A 572 PHE 0.019 0.002 PHE A 475 TRP 0.008 0.001 TRP A1549 HIS 0.006 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (13341) covalent geometry : angle 0.63968 / 0.33 (18001) SS BOND : bond 0.00542 / 0.26 ( 2) SS BOND : angle 2.32691 / 1.67 ( 4) hydrogen bonds : bond 0.05606 / 3.75 ( 605) hydrogen bonds : angle 4.29327 / 3.02 ( 1752) metal coordination : bond 0.01461 / 1.09 ( 16) metal coordination : angle 6.28771 / 3.24 ( 18) *********************** 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 289 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 215 time to evaluate : 0.474 Fit side-chains REVERT: A 125 ASN cc_start: 0.8538 (t0) cc_final: 0.8253 (t0) REVERT: A 131 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7395 (pp30) REVERT: A 183 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: A 204 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6612 (pp) REVERT: A 209 ARG cc_start: 0.7385 (ttt-90) cc_final: 0.7042 (ttm-80) REVERT: A 537 GLU cc_start: 0.7250 (tp30) cc_final: 0.7012 (tp30) REVERT: A 606 MET cc_start: 0.8715 (ptm) cc_final: 0.8421 (ptt) REVERT: A 838 GLU cc_start: 0.7692 (tp30) cc_final: 0.6873 (tp30) REVERT: A 980 TYR cc_start: 0.6050 (OUTLIER) cc_final: 0.5272 (t80) REVERT: A 1196 MET cc_start: 0.8384 (mmt) cc_final: 0.7926 (mmt) REVERT: A 1216 ARG cc_start: 0.7633 (mmt90) cc_final: 0.7343 (mmt-90) REVERT: A 1461 GLU cc_start: 0.7814 (pt0) cc_final: 0.7407 (pt0) REVERT: A 1462 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8108 (m-30) REVERT: A 1741 ARG cc_start: 0.7967 (ptm160) cc_final: 0.7320 (ttp80) outliers start: 74 outliers final: 43 residues processed: 273 average time/residue: 0.1189 time to fit residues: 47.2495 Evaluate side-chains 238 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 113 GLU 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 302 CYS 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 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 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 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 1149 SER 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 1462 ASP 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 1654 ILE Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1746 VAL 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 19 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 0.0270 chunk 136 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN A 737 ASN A 901 GLN A1296 HIS A1743 ASN A1783 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.166815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.126738 restraints weight = 16618.566| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.80 r_work: 0.3117 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13359 Z= 0.121 Angle : 0.596 13.841 18023 Z= 0.297 Chirality : 0.040 0.172 2073 Planarity : 0.004 0.046 2274 Dihedral : 6.678 59.429 1804 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 4.63 % Allowed : 17.99 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.21), residues: 1616 helix: 0.84 (0.18), residues: 826 sheet: -0.97 (0.48), residues: 116 loop : -3.30 (0.20), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 231 TYR 0.018 0.001 TYR A1097 PHE 0.011 0.001 PHE A 533 TRP 0.009 0.001 TRP A 155 HIS 0.003 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (13341) covalent geometry : angle 0.56761 / 0.29 (18001) SS BOND : bond 0.00238 / 0.11 ( 2) SS BOND : angle 6.29889 / 3.84 ( 4) hydrogen bonds : bond 0.04220 / 2.85 ( 605) hydrogen bonds : angle 3.98982 / 2.81 ( 1752) metal coordination : bond 0.01300 / 1.03 ( 16) metal coordination : angle 4.99918 / 2.70 ( 18) *********************** 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 283 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 214 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8509 (t0) cc_final: 0.8224 (t0) REVERT: A 131 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7300 (pp30) REVERT: A 183 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: A 204 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6711 (pp) REVERT: A 209 ARG cc_start: 0.7339 (ttt-90) cc_final: 0.7019 (ttm-80) REVERT: A 537 GLU cc_start: 0.7152 (tp30) cc_final: 0.6923 (tp30) REVERT: A 606 MET cc_start: 0.8733 (ptm) cc_final: 0.8432 (ptt) REVERT: A 771 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8025 (tp40) REVERT: A 980 TYR cc_start: 0.6075 (OUTLIER) cc_final: 0.5249 (t80) REVERT: A 1196 MET cc_start: 0.8318 (mmt) cc_final: 0.7909 (mmt) REVERT: A 1216 ARG cc_start: 0.7582 (mmt90) cc_final: 0.7331 (mmt90) REVERT: A 1461 GLU cc_start: 0.7717 (pt0) cc_final: 0.6739 (tt0) REVERT: A 1782 MET cc_start: 0.7392 (mtp) cc_final: 0.7175 (ppp) outliers start: 69 outliers final: 47 residues processed: 270 average time/residue: 0.1063 time to fit residues: 42.2748 Evaluate side-chains 241 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 190 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 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 382 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 421 LEU 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 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 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 1445 GLN Chi-restraints excluded: chain A residue 1460 ILE 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 1700 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 54 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 124 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 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 = 0.3919 r_free = 0.3919 target = 0.167511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.127361 restraints weight = 16735.367| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.73 r_work: 0.3140 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13359 Z= 0.117 Angle : 0.588 13.570 18023 Z= 0.289 Chirality : 0.040 0.171 2073 Planarity : 0.004 0.045 2274 Dihedral : 6.399 59.212 1798 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 4.97 % Allowed : 18.59 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.21), residues: 1616 helix: 1.16 (0.18), residues: 817 sheet: -0.91 (0.48), residues: 116 loop : -3.14 (0.21), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1742 TYR 0.017 0.001 TYR A1302 PHE 0.027 0.001 PHE A 91 TRP 0.013 0.001 TRP A1717 HIS 0.003 0.001 HIS A1791 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (13341) covalent geometry : angle 0.55476 / 0.28 (18001) SS BOND : bond 0.01405 / 0.67 ( 2) SS BOND : angle 4.32328 / 3.24 ( 4) hydrogen bonds : bond 0.03955 / 2.65 ( 605) hydrogen bonds : angle 3.84829 / 2.72 ( 1752) metal coordination : bond 0.01336 / 1.00 ( 16) metal coordination : angle 5.87798 / 3.02 ( 18) *********************** 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 275 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 201 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8500 (t0) cc_final: 0.8207 (t0) REVERT: A 131 GLN cc_start: 0.7840 (tm-30) cc_final: 0.7344 (pp30) REVERT: A 183 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: A 204 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.6888 (pp) REVERT: A 212 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8360 (tp) REVERT: A 537 GLU cc_start: 0.7186 (tp30) cc_final: 0.6984 (tp30) REVERT: A 606 MET cc_start: 0.8742 (ptm) cc_final: 0.8437 (ptt) REVERT: A 687 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7096 (mp) REVERT: A 771 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8024 (tp40) REVERT: A 980 TYR cc_start: 0.6049 (OUTLIER) cc_final: 0.5077 (t80) REVERT: A 1196 MET cc_start: 0.8341 (mmt) cc_final: 0.7948 (mmt) REVERT: A 1461 GLU cc_start: 0.7721 (pt0) cc_final: 0.6721 (tt0) REVERT: A 1741 ARG cc_start: 0.7733 (ptm-80) cc_final: 0.7359 (ttp80) outliers start: 74 outliers final: 53 residues processed: 263 average time/residue: 0.1056 time to fit residues: 41.4662 Evaluate side-chains 247 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 188 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 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 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 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 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 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 1700 THR Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1776 CYS 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 117 optimal weight: 0.0870 chunk 98 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.0020 chunk 99 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.8172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1711 ASN 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 = 0.3914 r_free = 0.3914 target = 0.167150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.127707 restraints weight = 16953.187| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.89 r_work: 0.3127 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1864 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= 0.121 Angle : 0.578 12.056 18023 Z= 0.288 Chirality : 0.040 0.168 2073 Planarity : 0.004 0.045 2274 Dihedral : 6.363 58.985 1798 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 5.30 % Allowed : 19.40 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.21), residues: 1616 helix: 1.26 (0.18), residues: 819 sheet: -0.99 (0.48), residues: 118 loop : -3.08 (0.21), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 404 TYR 0.018 0.001 TYR A1302 PHE 0.024 0.001 PHE A 91 TRP 0.015 0.001 TRP A1717 HIS 0.003 0.001 HIS A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (13341) covalent geometry : angle 0.55034 / 0.28 (18001) SS BOND : bond 0.01183 / 0.57 ( 2) SS BOND : angle 4.87013 / 3.81 ( 4) hydrogen bonds : bond 0.03954 / 2.66 ( 605) hydrogen bonds : angle 3.83555 / 2.71 ( 1752) metal coordination : bond 0.01154 / 0.89 ( 16) metal coordination : angle 5.15457 / 2.72 ( 18) *********************** 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 282 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 203 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8486 (t0) cc_final: 0.8177 (t0) REVERT: A 131 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7414 (pp30) REVERT: A 149 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8006 (p0) REVERT: A 183 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: A 204 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.6889 (pp) REVERT: A 231 ARG cc_start: 0.7972 (mtp85) cc_final: 0.7568 (ttp80) REVERT: A 406 LYS cc_start: 0.8798 (ttmt) cc_final: 0.8349 (ttpp) REVERT: A 606 MET cc_start: 0.8779 (ptm) cc_final: 0.8473 (ptt) REVERT: A 687 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6919 (mp) REVERT: A 771 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8040 (tp40) REVERT: A 980 TYR cc_start: 0.6113 (OUTLIER) cc_final: 0.5180 (t80) REVERT: A 1196 MET cc_start: 0.8349 (mmt) cc_final: 0.7902 (mmt) REVERT: A 1461 GLU cc_start: 0.7769 (pt0) cc_final: 0.6754 (tt0) REVERT: A 1493 PHE cc_start: 0.8509 (t80) cc_final: 0.8289 (t80) REVERT: A 1695 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7777 (pp20) outliers start: 79 outliers final: 55 residues processed: 268 average time/residue: 0.1148 time to fit residues: 45.4985 Evaluate side-chains 249 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 187 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 149 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 375 LEU 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 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 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 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 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 1746 VAL Chi-restraints excluded: chain A residue 1776 CYS 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 15 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 156 optimal weight: 0.1980 chunk 123 optimal weight: 0.4980 chunk 21 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3913 r_free = 0.3913 target = 0.167161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127267 restraints weight = 16781.132| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.73 r_work: 0.3139 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13359 Z= 0.124 Angle : 0.580 11.308 18023 Z= 0.290 Chirality : 0.040 0.168 2073 Planarity : 0.004 0.045 2274 Dihedral : 6.249 59.035 1796 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 4.83 % Allowed : 20.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.21), residues: 1616 helix: 1.35 (0.18), residues: 819 sheet: -0.97 (0.48), residues: 118 loop : -3.03 (0.21), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 404 TYR 0.019 0.001 TYR A1302 PHE 0.018 0.001 PHE A 91 TRP 0.017 0.001 TRP A1717 HIS 0.003 0.001 HIS A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (13341) covalent geometry : angle 0.55735 / 0.29 (18001) SS BOND : bond 0.01173 / 0.56 ( 2) SS BOND : angle 4.55621 / 3.57 ( 4) hydrogen bonds : bond 0.03950 / 2.65 ( 605) hydrogen bonds : angle 3.81084 / 2.70 ( 1752) metal coordination : bond 0.01050 / 0.82 ( 16) metal coordination : angle 4.65415 / 2.44 ( 18) *********************** 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 268 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 196 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8472 (t0) cc_final: 0.8152 (t0) REVERT: A 131 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7436 (pp30) REVERT: A 149 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.7764 (p0) REVERT: A 183 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: A 204 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.6918 (pp) REVERT: A 231 ARG cc_start: 0.7938 (mtp85) cc_final: 0.7530 (ttp80) REVERT: A 406 LYS cc_start: 0.8741 (ttmt) cc_final: 0.8329 (ttpp) REVERT: A 412 ASN cc_start: 0.8575 (t0) cc_final: 0.8024 (t0) REVERT: A 606 MET cc_start: 0.8779 (ptm) cc_final: 0.8470 (ptt) REVERT: A 687 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6912 (mp) REVERT: A 771 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8039 (tp40) REVERT: A 980 TYR cc_start: 0.6066 (OUTLIER) cc_final: 0.5176 (t80) REVERT: A 1196 MET cc_start: 0.8341 (mmt) cc_final: 0.7920 (mmt) REVERT: A 1461 GLU cc_start: 0.7743 (pt0) cc_final: 0.6726 (tt0) REVERT: A 1493 PHE cc_start: 0.8455 (t80) cc_final: 0.8119 (t80) REVERT: A 1695 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7669 (pp20) REVERT: A 1741 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7264 (ttp80) outliers start: 72 outliers final: 60 residues processed: 257 average time/residue: 0.1138 time to fit residues: 43.2206 Evaluate side-chains 256 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 188 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 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 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 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 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 1221 LEU 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 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 1513 GLU 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 1741 ARG Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1776 CYS Chi-restraints excluded: chain A residue 1783 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 119 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 121 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 73 optimal weight: 0.0570 chunk 18 optimal weight: 7.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3926 r_free = 0.3926 target = 0.168348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128504 restraints weight = 16694.215| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.70 r_work: 0.3155 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13359 Z= 0.110 Angle : 0.560 10.052 18023 Z= 0.282 Chirality : 0.039 0.166 2073 Planarity : 0.003 0.043 2274 Dihedral : 6.172 58.955 1796 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 5.23 % Allowed : 20.07 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.21), residues: 1616 helix: 1.43 (0.18), residues: 820 sheet: -1.00 (0.47), residues: 118 loop : -2.99 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 404 TYR 0.021 0.001 TYR A1302 PHE 0.020 0.001 PHE A 91 TRP 0.019 0.001 TRP A1717 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (13341) covalent geometry : angle 0.54127 / 0.28 (18001) SS BOND : bond 0.01019 / 0.49 ( 2) SS BOND : angle 4.02922 / 3.17 ( 4) hydrogen bonds : bond 0.03665 / 2.47 ( 605) hydrogen bonds : angle 3.74784 / 2.66 ( 1752) metal coordination : bond 0.00958 / 0.76 ( 16) metal coordination : angle 4.19808 / 2.21 ( 18) *********************** 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 274 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 196 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8463 (t0) cc_final: 0.8140 (t0) REVERT: A 131 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7441 (pp30) REVERT: A 149 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.7621 (p0) REVERT: A 183 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: A 204 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.6921 (pp) REVERT: A 231 ARG cc_start: 0.7913 (mtp85) cc_final: 0.7531 (ttp80) REVERT: A 406 LYS cc_start: 0.8747 (ttmt) cc_final: 0.8305 (ttpp) REVERT: A 606 MET cc_start: 0.8756 (ptm) cc_final: 0.8444 (ptt) REVERT: A 650 ASP cc_start: 0.8262 (t0) cc_final: 0.8029 (t0) REVERT: A 687 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6859 (mp) REVERT: A 771 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7995 (tp40) REVERT: A 980 TYR cc_start: 0.6080 (OUTLIER) cc_final: 0.5208 (t80) REVERT: A 1196 MET cc_start: 0.8318 (mmt) cc_final: 0.7910 (mmt) REVERT: A 1493 PHE cc_start: 0.8417 (t80) cc_final: 0.8086 (t80) REVERT: A 1695 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7585 (pp20) REVERT: A 1741 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7306 (ttp80) outliers start: 78 outliers final: 59 residues processed: 260 average time/residue: 0.1136 time to fit residues: 43.3847 Evaluate side-chains 251 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 184 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 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 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 900 GLU Chi-restraints excluded: chain A residue 973 ASP 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 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 1513 GLU 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 1741 ARG Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1776 CYS Chi-restraints excluded: chain A residue 1783 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 153 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN 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 = 0.3914 r_free = 0.3914 target = 0.167153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.127404 restraints weight = 16682.903| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.71 r_work: 0.3133 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2122 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= 0.128 Angle : 0.574 10.326 18023 Z= 0.289 Chirality : 0.040 0.161 2073 Planarity : 0.004 0.044 2274 Dihedral : 6.164 59.018 1794 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 5.03 % Allowed : 20.27 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.21), residues: 1616 helix: 1.48 (0.18), residues: 819 sheet: -0.98 (0.47), residues: 120 loop : -2.95 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 404 TYR 0.021 0.001 TYR A1302 PHE 0.020 0.001 PHE A 91 TRP 0.020 0.001 TRP A1717 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (13341) covalent geometry : angle 0.55526 / 0.29 (18001) SS BOND : bond 0.01167 / 0.56 ( 2) SS BOND : angle 4.48691 / 3.54 ( 4) hydrogen bonds : bond 0.03958 / 2.65 ( 605) hydrogen bonds : angle 3.77227 / 2.68 ( 1752) metal coordination : bond 0.00951 / 0.74 ( 16) metal coordination : angle 4.18082 / 2.18 ( 18) *********************** 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 267 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 192 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8477 (t0) cc_final: 0.8159 (t0) REVERT: A 131 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7504 (pp30) REVERT: A 149 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.7758 (p0) REVERT: A 183 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: A 204 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.6950 (pp) REVERT: A 212 LEU cc_start: 0.8535 (tp) cc_final: 0.8323 (pt) REVERT: A 231 ARG cc_start: 0.7924 (mtp85) cc_final: 0.7510 (ttp80) REVERT: A 406 LYS cc_start: 0.8757 (ttmt) cc_final: 0.8344 (ttpp) REVERT: A 606 MET cc_start: 0.8769 (ptm) cc_final: 0.8462 (ptt) REVERT: A 650 ASP cc_start: 0.8284 (t0) cc_final: 0.8054 (t0) REVERT: A 687 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6922 (mp) REVERT: A 771 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7986 (tp40) REVERT: A 980 TYR cc_start: 0.6151 (OUTLIER) cc_final: 0.5239 (t80) REVERT: A 1097 TYR cc_start: 0.7298 (t80) cc_final: 0.6978 (t80) REVERT: A 1148 PHE cc_start: 0.8901 (t80) cc_final: 0.8626 (t80) REVERT: A 1196 MET cc_start: 0.8318 (mmt) cc_final: 0.7893 (mmt) REVERT: A 1493 PHE cc_start: 0.8430 (t80) cc_final: 0.8098 (t80) REVERT: A 1695 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7616 (pp20) REVERT: A 1741 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7179 (ttp80) outliers start: 75 outliers final: 60 residues processed: 254 average time/residue: 0.1128 time to fit residues: 41.7520 Evaluate side-chains 251 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 183 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 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 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 539 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 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 900 GLU Chi-restraints excluded: chain A residue 973 ASP 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 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 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 1513 GLU 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 1741 ARG Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1775 VAL Chi-restraints excluded: chain A residue 1776 CYS Chi-restraints excluded: chain A residue 1783 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 73 optimal weight: 0.3980 chunk 82 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 138 optimal weight: 0.0970 chunk 101 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3915 r_free = 0.3915 target = 0.167378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.127917 restraints weight = 16759.373| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.86 r_work: 0.3127 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13359 Z= 0.121 Angle : 0.570 9.945 18023 Z= 0.287 Chirality : 0.040 0.160 2073 Planarity : 0.003 0.044 2274 Dihedral : 6.161 58.882 1794 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 4.70 % Allowed : 20.54 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.21), residues: 1616 helix: 1.52 (0.18), residues: 820 sheet: -0.93 (0.48), residues: 120 loop : -2.94 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 404 TYR 0.023 0.001 TYR A1302 PHE 0.020 0.001 PHE A 91 TRP 0.022 0.001 TRP A1717 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (13341) covalent geometry : angle 0.55215 / 0.28 (18001) SS BOND : bond 0.01112 / 0.53 ( 2) SS BOND : angle 4.28963 / 3.41 ( 4) hydrogen bonds : bond 0.03869 / 2.59 ( 605) hydrogen bonds : angle 3.76761 / 2.68 ( 1752) metal coordination : bond 0.00880 / 0.68 ( 16) metal coordination : angle 4.06339 / 2.12 ( 18) *********************** 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 263 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 193 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8489 (t0) cc_final: 0.8176 (t0) REVERT: A 131 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7514 (pp30) REVERT: A 149 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.7838 (p0) REVERT: A 183 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: A 204 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7010 (pp) REVERT: A 212 LEU cc_start: 0.8549 (tp) cc_final: 0.8316 (pt) REVERT: A 231 ARG cc_start: 0.7935 (mtp85) cc_final: 0.7569 (ttp80) REVERT: A 406 LYS cc_start: 0.8755 (ttmt) cc_final: 0.8350 (ttpp) REVERT: A 606 MET cc_start: 0.8773 (ptm) cc_final: 0.8459 (ptt) REVERT: A 650 ASP cc_start: 0.8301 (t0) cc_final: 0.8077 (t0) REVERT: A 687 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6897 (mp) REVERT: A 771 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8027 (tp40) REVERT: A 980 TYR cc_start: 0.6166 (OUTLIER) cc_final: 0.5141 (t80) REVERT: A 1097 TYR cc_start: 0.7353 (t80) cc_final: 0.7090 (t80) REVERT: A 1148 PHE cc_start: 0.8901 (t80) cc_final: 0.8673 (t80) REVERT: A 1196 MET cc_start: 0.8349 (mmt) cc_final: 0.7970 (mmt) REVERT: A 1493 PHE cc_start: 0.8431 (t80) cc_final: 0.8091 (t80) REVERT: A 1695 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7617 (pp20) REVERT: A 1741 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7178 (ttp80) outliers start: 70 outliers final: 59 residues processed: 252 average time/residue: 0.1129 time to fit residues: 41.6054 Evaluate side-chains 254 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 187 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 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 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 539 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 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 786 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 973 ASP 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 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 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 1513 GLU 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 1741 ARG Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1775 VAL Chi-restraints excluded: chain A residue 1776 CYS Chi-restraints excluded: chain A residue 1783 ASN 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 151 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 134 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 64 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 129 optimal weight: 0.2980 chunk 104 optimal weight: 0.2980 chunk 82 optimal weight: 7.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3932 r_free = 0.3932 target = 0.168884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128997 restraints weight = 16813.985| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.68 r_work: 0.3167 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13359 Z= 0.108 Angle : 0.562 9.081 18023 Z= 0.283 Chirality : 0.040 0.164 2073 Planarity : 0.003 0.043 2274 Dihedral : 6.075 58.696 1793 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.36 % Allowed : 21.28 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.22), residues: 1616 helix: 1.64 (0.19), residues: 815 sheet: -0.90 (0.48), residues: 118 loop : -2.89 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 404 TYR 0.024 0.001 TYR A1302 PHE 0.021 0.001 PHE A 91 TRP 0.021 0.001 TRP A1717 HIS 0.006 0.001 HIS A1283 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (13341) covalent geometry : angle 0.54549 / 0.28 (18001) SS BOND : bond 0.00965 / 0.46 ( 2) SS BOND : angle 4.00743 / 3.16 ( 4) hydrogen bonds : bond 0.03558 / 2.40 ( 605) hydrogen bonds : angle 3.70259 / 2.64 ( 1752) metal coordination : bond 0.00884 / 0.70 ( 16) metal coordination : angle 3.82821 / 2.00 ( 18) ********************** 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 255 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 190 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8439 (t0) cc_final: 0.8124 (t0) REVERT: A 131 GLN cc_start: 0.7922 (tm-30) cc_final: 0.7505 (pp30) REVERT: A 149 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.7990 (p0) REVERT: A 183 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: A 204 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7117 (pp) REVERT: A 231 ARG cc_start: 0.7911 (mtp85) cc_final: 0.7529 (ttp80) REVERT: A 406 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8387 (ttpp) REVERT: A 508 ARG cc_start: 0.7364 (mmp-170) cc_final: 0.7084 (mmp-170) REVERT: A 606 MET cc_start: 0.8731 (ptm) cc_final: 0.8416 (ptt) REVERT: A 650 ASP cc_start: 0.8268 (t0) cc_final: 0.8047 (t0) REVERT: A 687 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6820 (mp) REVERT: A 771 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8019 (tp40) REVERT: A 980 TYR cc_start: 0.6124 (OUTLIER) cc_final: 0.5107 (t80) REVERT: A 1097 TYR cc_start: 0.7324 (t80) cc_final: 0.7070 (t80) REVERT: A 1196 MET cc_start: 0.8302 (mmt) cc_final: 0.8010 (mmt) REVERT: A 1493 PHE cc_start: 0.8410 (t80) cc_final: 0.8118 (t80) REVERT: A 1695 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7605 (pp20) REVERT: A 1741 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7156 (ttp80) outliers start: 65 outliers final: 53 residues processed: 243 average time/residue: 0.1159 time to fit residues: 41.1516 Evaluate side-chains 245 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 184 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 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 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 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 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 786 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 973 ASP 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 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 1513 GLU 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 1741 ARG Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1775 VAL Chi-restraints excluded: chain A residue 1786 LEU Chi-restraints excluded: chain A residue 1795 THR 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 135 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 145 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.164173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124452 restraints weight = 16738.401| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.98 r_work: 0.3068 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13359 Z= 0.179 Angle : 0.626 11.466 18023 Z= 0.314 Chirality : 0.042 0.161 2073 Planarity : 0.004 0.048 2274 Dihedral : 6.360 59.785 1793 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 4.03 % Allowed : 21.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.21), residues: 1616 helix: 1.44 (0.18), residues: 822 sheet: -1.03 (0.47), residues: 125 loop : -2.98 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1742 TYR 0.021 0.002 TYR A1302 PHE 0.020 0.002 PHE A 91 TRP 0.023 0.002 TRP A1717 HIS 0.004 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (13341) covalent geometry : angle 0.60409 / 0.31 (18001) SS BOND : bond 0.01417 / 0.68 ( 2) SS BOND : angle 5.02231 / 3.94 ( 4) hydrogen bonds : bond 0.04776 / 3.18 ( 605) hydrogen bonds : angle 3.96330 / 2.81 ( 1752) metal coordination : bond 0.00980 / 0.70 ( 16) metal coordination : angle 4.60817 / 2.38 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2915.59 seconds wall clock time: 50 minutes 53.51 seconds (3053.51 seconds total)