Starting phenix.real_space_refine on Thu Sep 18 04:11:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cap_45399/09_2025/9cap_45399.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cap_45399/09_2025/9cap_45399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cap_45399/09_2025/9cap_45399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cap_45399/09_2025/9cap_45399.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cap_45399/09_2025/9cap_45399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cap_45399/09_2025/9cap_45399.map" } resolution = 2.7 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= 0.007 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: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 74 5.16 5 C 8979 2.51 5 N 2217 2.21 5 O 2495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13783 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 11425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1432, 11425 Classifications: {'peptide': 1432} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 68, 'TRANS': 1362} Chain breaks: 8 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1479 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 5, 'TRANS': 175} Chain: "A" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 879 Unusual residues: {'PEE': 18, 'R16': 12} Classifications: {'undetermined': 30} Link IDs: {None: 29} Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 231 Time building chain proxies: 3.53, per 1000 atoms: 0.26 Number of scatterers: 13783 At special positions: 0 Unit cell: (102.44, 104.804, 194.636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 18 15.00 O 2495 8.00 N 2217 7.00 C 8979 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 901 " - pdb=" SG CYS A 915 " distance=2.03 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A1047 " distance=2.04 Simple disulfide: pdb=" SG CYS A1047 " - pdb=" SG CYS A1049 " distance=2.04 Simple disulfide: pdb=" SG CYS A1281 " - pdb=" SG CYS A1610 " distance=2.06 Simple disulfide: pdb=" SG CYS A1281 " - pdb=" SG CYS A1613 " distance=2.02 Simple disulfide: pdb=" SG CYS A1610 " - pdb=" SG CYS A1613 " distance=2.02 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: 1.15 Conformation dependent library (CDL) restraints added in 553.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3072 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 2 sheets defined 35.6% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 21 through 42 removed outlier: 3.640A pdb=" N THR A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.960A pdb=" N VAL A 46 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 56 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 57 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 80 Processing helix chain 'A' and resid 141 through 152 removed outlier: 3.611A pdb=" N TYR A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 161 removed outlier: 3.545A pdb=" N GLU A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 193 Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.892A pdb=" N GLY A 274 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 340 Processing helix chain 'A' and resid 472 through 488 removed outlier: 3.521A pdb=" N LYS A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 519 through 521 No H-bonds generated for 'chain 'A' and resid 519 through 521' Processing helix chain 'A' and resid 583 through 594 Processing helix chain 'A' and resid 637 through 641 removed outlier: 3.527A pdb=" N ILE A 641 " --> pdb=" O LYS A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 654 removed outlier: 4.443A pdb=" N ASP A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 664 Processing helix chain 'A' and resid 683 through 698 removed outlier: 4.054A pdb=" N VAL A 687 " --> pdb=" O THR A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 726 removed outlier: 3.571A pdb=" N THR A 725 " --> pdb=" O SER A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 731 Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'A' and resid 859 through 878 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.563A pdb=" N GLN A 890 " --> pdb=" O ASP A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 907 removed outlier: 3.503A pdb=" N LYS A 907 " --> pdb=" O ILE A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 917 through 922 removed outlier: 3.501A pdb=" N MET A 921 " --> pdb=" O THR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1028 Processing helix chain 'A' and resid 1035 through 1039 Processing helix chain 'A' and resid 1060 through 1065 removed outlier: 3.995A pdb=" N THR A1065 " --> pdb=" O GLU A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1160 removed outlier: 3.582A pdb=" N PHE A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1189 Processing helix chain 'A' and resid 1247 through 1264 removed outlier: 3.605A pdb=" N SER A1264 " --> pdb=" O ALA A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1268 Processing helix chain 'A' and resid 1269 through 1284 removed outlier: 4.051A pdb=" N LEU A1273 " --> pdb=" O ASN A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1295 Processing helix chain 'A' and resid 1536 through 1582 Proline residue: A1542 - end of helix removed outlier: 3.761A pdb=" N SER A1549 " --> pdb=" O VAL A1545 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1601 removed outlier: 3.685A pdb=" N ARG A1599 " --> pdb=" O ARG A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1608 Processing helix chain 'A' and resid 1610 through 1626 removed outlier: 4.203A pdb=" N LEU A1616 " --> pdb=" O SER A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1633 Processing helix chain 'A' and resid 1640 through 1644 removed outlier: 3.609A pdb=" N PHE A1643 " --> pdb=" O ARG A1640 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU A1644 " --> pdb=" O PRO A1641 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1640 through 1644' Processing helix chain 'A' and resid 1645 through 1666 removed outlier: 3.550A pdb=" N LEU A1653 " --> pdb=" O ARG A1649 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER A1662 " --> pdb=" O SER A1658 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP A1663 " --> pdb=" O HIS A1659 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS A1666 " --> pdb=" O SER A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1674 through 1679 Processing helix chain 'B' and resid 8 through 38 Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 55 through 76 Processing helix chain 'B' and resid 82 through 88 removed outlier: 3.734A pdb=" N PHE B 88 " --> pdb=" O ILE B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 109 removed outlier: 3.576A pdb=" N ASP B 102 " --> pdb=" O MET B 98 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 138 removed outlier: 3.506A pdb=" N LYS B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.751A pdb=" N VAL B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 186 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 73 removed outlier: 5.752A pdb=" N ASN A 87 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE A 73 " --> pdb=" O PHE A 85 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE A 85 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS A 82 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 105 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N MET A 84 " --> pdb=" O HIS A 103 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N HIS A 103 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG A 86 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP A 101 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY A 133 " --> pdb=" O ASN A 100 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY A 102 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU A 131 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU A 104 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU A 129 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N PHE A 106 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 127 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N HIS A 128 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 10.056A pdb=" N VAL A 199 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N VAL A 130 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N ALA A 201 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASN A 132 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N CYS A 203 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 134 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU A 205 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL A 136 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N HIS A 196 " --> pdb=" O LYS A 225 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS A 225 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU A 198 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN A 223 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N SER A 200 " --> pdb=" O ASN A 221 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN A 246 " --> pdb=" O GLU A 220 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU A 222 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR A 244 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER A 224 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY A 242 " --> pdb=" O SER A 224 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A 226 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N PHE A 240 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL A 228 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 238 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL A 247 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLN A 279 " --> pdb=" O VAL A 247 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 275 through 280 current: chain 'A' and resid 310 through 316 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 310 through 316 current: chain 'A' and resid 385 through 393 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 385 through 393 current: chain 'A' and resid 412 through 421 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 412 through 421 current: chain 'A' and resid 433 through 436 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 433 through 436 current: chain 'A' and resid 456 through 471 removed outlier: 4.434A pdb=" N THR A 457 " --> pdb=" O ARG A 501 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N HIS A 503 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR A 459 " --> pdb=" O HIS A 503 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ARG A 505 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP A 461 " --> pdb=" O ARG A 505 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS A 507 " --> pdb=" O ASP A 461 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 463 " --> pdb=" O LYS A 507 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A 509 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR A 465 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY A 511 " --> pdb=" O THR A 465 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A 517 " --> pdb=" O PHE A 471 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 535 through 540 current: chain 'A' and resid 559 through 567 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 559 through 567 current: chain 'A' and resid 615 through 621 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 615 through 621 current: chain 'A' and resid 667 through 675 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 667 through 675 current: chain 'A' and resid 739 through 754 removed outlier: 6.665A pdb=" N GLU A 776 " --> pdb=" O ASN A 749 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG A 751 " --> pdb=" O PHE A 774 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE A 774 " --> pdb=" O ARG A 751 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLU A 753 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL A 772 " --> pdb=" O GLU A 753 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 788 through 795 current: chain 'A' and resid 812 through 816 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 812 through 816 current: chain 'A' and resid 839 through 857 removed outlier: 6.520A pdb=" N ASP A 851 " --> pdb=" O ASP A 931 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 933 " --> pdb=" O ASP A 851 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA A 853 " --> pdb=" O VAL A 933 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU A 935 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR A 855 " --> pdb=" O LEU A 935 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE A 937 " --> pdb=" O THR A 855 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP A 857 " --> pdb=" O PHE A 937 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 933 " --> pdb=" O ALA A 948 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 942 through 948 current: chain 'A' and resid 966 through 982 removed outlier: 6.122A pdb=" N GLY A 973 " --> pdb=" O GLU A 999 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU A 999 " --> pdb=" O GLY A 973 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER A 975 " --> pdb=" O ALA A 997 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA A 997 " --> pdb=" O SER A 975 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG A 977 " --> pdb=" O ASN A 995 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN A 995 " --> pdb=" O ARG A 977 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ALA A 979 " --> pdb=" O GLY A 993 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY A 993 " --> pdb=" O ALA A 979 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ARG A 981 " --> pdb=" O ILE A 991 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE A 991 " --> pdb=" O ARG A 981 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TRP A 990 " --> pdb=" O VAL A1163 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1193 through 1196 current: chain 'A' and resid 1341 through 1348 Processing sheet with id=AA2, first strand: chain 'A' and resid 523 through 524 450 hydrogen bonds defined for protein. 1254 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: 2.72 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2235 1.32 - 1.46: 5101 1.46 - 1.60: 6562 1.60 - 1.74: 36 1.74 - 1.88: 119 Bond restraints: 14053 Sorted by residual: bond pdb=" C18 PEE A4401 " pdb=" C19 PEE A4401 " ideal model delta sigma weight residual 1.523 1.321 0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C18 PEE A4412 " pdb=" C19 PEE A4412 " ideal model delta sigma weight residual 1.523 1.323 0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C18 PEE A4413 " pdb=" C19 PEE A4413 " ideal model delta sigma weight residual 1.523 1.323 0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C18 PEE A4421 " pdb=" C19 PEE A4421 " ideal model delta sigma weight residual 1.523 1.323 0.200 2.00e-02 2.50e+03 9.99e+01 bond pdb=" C18 PEE A4405 " pdb=" C19 PEE A4405 " ideal model delta sigma weight residual 1.523 1.323 0.200 2.00e-02 2.50e+03 9.96e+01 ... (remaining 14048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.25: 18763 8.25 - 16.51: 44 16.51 - 24.76: 12 24.76 - 33.02: 0 33.02 - 41.27: 10 Bond angle restraints: 18829 Sorted by residual: angle pdb=" C38 PEE A4421 " pdb=" C39 PEE A4421 " pdb=" C40 PEE A4421 " ideal model delta sigma weight residual 112.47 153.74 -41.27 3.00e+00 1.11e-01 1.89e+02 angle pdb=" C38 PEE A4419 " pdb=" C39 PEE A4419 " pdb=" C40 PEE A4419 " ideal model delta sigma weight residual 112.47 153.05 -40.58 3.00e+00 1.11e-01 1.83e+02 angle pdb=" C38 PEE A4404 " pdb=" C39 PEE A4404 " pdb=" C40 PEE A4404 " ideal model delta sigma weight residual 112.47 153.01 -40.54 3.00e+00 1.11e-01 1.83e+02 angle pdb=" C38 PEE A4422 " pdb=" C39 PEE A4422 " pdb=" C40 PEE A4422 " ideal model delta sigma weight residual 112.47 153.00 -40.53 3.00e+00 1.11e-01 1.83e+02 angle pdb=" C38 PEE A4420 " pdb=" C39 PEE A4420 " pdb=" C40 PEE A4420 " ideal model delta sigma weight residual 112.47 152.86 -40.39 3.00e+00 1.11e-01 1.81e+02 ... (remaining 18824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 8225 35.46 - 70.93: 346 70.93 - 106.39: 66 106.39 - 141.86: 31 141.86 - 177.32: 16 Dihedral angle restraints: 8684 sinusoidal: 3971 harmonic: 4713 Sorted by residual: dihedral pdb=" CB CYS A1610 " pdb=" SG CYS A1610 " pdb=" SG CYS A1613 " pdb=" CB CYS A1613 " ideal model delta sinusoidal sigma weight residual -86.00 -6.54 -79.46 1 1.00e+01 1.00e-02 7.84e+01 dihedral pdb=" CB CYS A1281 " pdb=" SG CYS A1281 " pdb=" SG CYS A1610 " pdb=" CB CYS A1610 " ideal model delta sinusoidal sigma weight residual 93.00 170.79 -77.79 1 1.00e+01 1.00e-02 7.57e+01 dihedral pdb=" CA GLY A 567 " pdb=" C GLY A 567 " pdb=" N GLU A 568 " pdb=" CA GLU A 568 " ideal model delta harmonic sigma weight residual 180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 8681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1636 0.052 - 0.105: 297 0.105 - 0.157: 84 0.157 - 0.209: 7 0.209 - 0.261: 12 Chirality restraints: 2036 Sorted by residual: chirality pdb=" C2 PEE A4425 " pdb=" C1 PEE A4425 " pdb=" C3 PEE A4425 " pdb=" O2 PEE A4425 " both_signs ideal model delta sigma weight residual False -2.33 -2.59 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C2 PEE A4413 " pdb=" C1 PEE A4413 " pdb=" C3 PEE A4413 " pdb=" O2 PEE A4413 " both_signs ideal model delta sigma weight residual False -2.33 -2.57 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C2 PEE A4410 " pdb=" C1 PEE A4410 " pdb=" C3 PEE A4410 " pdb=" O2 PEE A4410 " both_signs ideal model delta sigma weight residual False -2.33 -2.56 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 2033 not shown) Planarity restraints: 2308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 392 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.98e+00 pdb=" C ARG A 392 " 0.042 2.00e-02 2.50e+03 pdb=" O ARG A 392 " -0.016 2.00e-02 2.50e+03 pdb=" N CYS A 393 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 81 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C GLY A 81 " -0.040 2.00e-02 2.50e+03 pdb=" O GLY A 81 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS A 82 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 394 " 0.012 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C GLY A 394 " -0.039 2.00e-02 2.50e+03 pdb=" O GLY A 394 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO A 395 " 0.013 2.00e-02 2.50e+03 ... (remaining 2305 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2618 2.78 - 3.31: 12552 3.31 - 3.84: 22788 3.84 - 4.37: 28189 4.37 - 4.90: 47586 Nonbonded interactions: 113733 Sorted by model distance: nonbonded pdb=" O ASN A 522 " pdb=" OD1 ASN A 522 " model vdw 2.249 3.040 nonbonded pdb=" OD2 ASP A 91 " pdb=" OG1 THR A 96 " model vdw 2.277 3.040 nonbonded pdb=" OG1 THR A 426 " pdb=" O THR A 432 " model vdw 2.298 3.040 nonbonded pdb=" O GLU A 940 " pdb=" NH2 ARG A 981 " model vdw 2.312 3.120 nonbonded pdb=" OE1 GLN A 896 " pdb=" N SER A 902 " model vdw 2.316 3.120 ... (remaining 113728 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: 41.190 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.590 Find NCS groups from input model: 0.060 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:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 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 : 0.012 0.202 14059 Z= 0.578 Angle : 1.488 41.269 18841 Z= 0.553 Chirality : 0.048 0.261 2036 Planarity : 0.004 0.042 2308 Dihedral : 21.876 177.321 5594 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.21 % Allowed : 9.10 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.30 (0.22), residues: 1593 helix: 1.46 (0.25), residues: 471 sheet: -0.17 (0.24), residues: 506 loop : -0.33 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1649 TYR 0.016 0.001 TYR A 340 PHE 0.024 0.001 PHE A1254 TRP 0.008 0.001 TRP A 473 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.01154 (14053) covalent geometry : angle 1.48186 (18829) SS BOND : bond 0.01565 ( 6) SS BOND : angle 5.42291 ( 12) hydrogen bonds : bond 0.15730 ( 450) hydrogen bonds : angle 6.35215 ( 1254) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 251 time to evaluate : 0.557 Fit side-chains REVERT: A 58 TYR cc_start: 0.8248 (t80) cc_final: 0.7912 (t80) REVERT: A 144 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7980 (mtpp) REVERT: A 150 ARG cc_start: 0.8754 (ttm170) cc_final: 0.8325 (ttm-80) REVERT: A 163 MET cc_start: 0.6628 (tpp) cc_final: 0.6342 (tmt) REVERT: A 198 GLU cc_start: 0.8749 (tt0) cc_final: 0.8443 (mt-10) REVERT: A 262 LYS cc_start: 0.9048 (tmmt) cc_final: 0.8762 (tptp) REVERT: A 279 GLN cc_start: 0.8129 (tt0) cc_final: 0.7707 (mm110) REVERT: A 496 LYS cc_start: 0.8940 (mtmt) cc_final: 0.8729 (mttm) REVERT: A 506 MET cc_start: 0.8763 (ttp) cc_final: 0.8503 (tmm) REVERT: A 714 ASP cc_start: 0.8165 (t0) cc_final: 0.7668 (t70) REVERT: A 881 ASP cc_start: 0.7356 (t70) cc_final: 0.6675 (t0) REVERT: A 919 GLU cc_start: 0.8705 (tp30) cc_final: 0.8304 (mp0) REVERT: A 1086 LYS cc_start: 0.8420 (mttt) cc_final: 0.8014 (mmmt) REVERT: A 1167 LEU cc_start: 0.8641 (mm) cc_final: 0.8422 (mt) REVERT: A 1193 ARG cc_start: 0.7918 (mtp85) cc_final: 0.7700 (mtm-85) REVERT: A 1563 HIS cc_start: 0.7514 (m-70) cc_final: 0.6644 (t-90) REVERT: A 1596 ARG cc_start: 0.8432 (mtp85) cc_final: 0.8194 (ttm110) REVERT: A 1663 ASP cc_start: 0.8795 (t0) cc_final: 0.8588 (t0) REVERT: B 30 GLN cc_start: 0.8765 (tt0) cc_final: 0.8436 (tp40) REVERT: B 39 ASN cc_start: 0.8921 (t0) cc_final: 0.8407 (t0) REVERT: B 42 ARG cc_start: 0.8565 (ttp-110) cc_final: 0.8101 (mtp180) REVERT: B 46 GLN cc_start: 0.8330 (mt0) cc_final: 0.7988 (mm-40) REVERT: B 56 LYS cc_start: 0.9185 (mptt) cc_final: 0.8932 (mptt) REVERT: B 87 GLN cc_start: 0.8950 (tt0) cc_final: 0.8750 (pp30) REVERT: B 111 GLN cc_start: 0.8622 (tp40) cc_final: 0.7945 (tm-30) outliers start: 3 outliers final: 1 residues processed: 253 average time/residue: 0.7086 time to fit residues: 193.5942 Evaluate side-chains 139 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 932 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.0270 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 728 ASN A 835 ASN A1382 ASN A1677 HIS B 113 ASN B 177 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.109739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.083463 restraints weight = 21872.557| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.23 r_work: 0.3114 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 14059 Z= 0.170 Angle : 0.605 13.426 18841 Z= 0.302 Chirality : 0.045 0.165 2036 Planarity : 0.004 0.050 2308 Dihedral : 24.125 177.652 2479 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.36 % Allowed : 13.37 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.30 (0.22), residues: 1593 helix: 1.25 (0.24), residues: 490 sheet: -0.22 (0.23), residues: 508 loop : -0.13 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1082 TYR 0.015 0.001 TYR A 340 PHE 0.019 0.001 PHE A 682 TRP 0.010 0.001 TRP B 34 HIS 0.005 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00388 (14053) covalent geometry : angle 0.58913 (18829) SS BOND : bond 0.01651 ( 6) SS BOND : angle 5.48974 ( 12) hydrogen bonds : bond 0.04090 ( 450) hydrogen bonds : angle 5.09312 ( 1254) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8361 (mmtt) cc_final: 0.8134 (mmmt) REVERT: A 158 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.6320 (m-80) REVERT: A 163 MET cc_start: 0.6780 (tpp) cc_final: 0.6485 (tmt) REVERT: A 258 ASP cc_start: 0.8513 (p0) cc_final: 0.8308 (p0) REVERT: A 279 GLN cc_start: 0.8238 (tt0) cc_final: 0.7955 (mm110) REVERT: A 410 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8936 (mtpp) REVERT: A 881 ASP cc_start: 0.7315 (t70) cc_final: 0.6620 (t0) REVERT: A 1081 GLU cc_start: 0.7656 (tp30) cc_final: 0.6845 (pp20) REVERT: A 1086 LYS cc_start: 0.8547 (mttt) cc_final: 0.7742 (mmmt) REVERT: A 1563 HIS cc_start: 0.7491 (m-70) cc_final: 0.6702 (t-90) REVERT: A 1596 ARG cc_start: 0.8538 (mtp85) cc_final: 0.8081 (ttm110) REVERT: B 30 GLN cc_start: 0.8832 (tt0) cc_final: 0.8476 (tp40) REVERT: B 39 ASN cc_start: 0.8980 (t0) cc_final: 0.8465 (t0) REVERT: B 42 ARG cc_start: 0.8608 (ttp-110) cc_final: 0.8214 (mtp180) REVERT: B 46 GLN cc_start: 0.8463 (mt0) cc_final: 0.8106 (mm-40) REVERT: B 87 GLN cc_start: 0.8880 (tt0) cc_final: 0.8624 (tm-30) REVERT: B 111 GLN cc_start: 0.8648 (tp40) cc_final: 0.7870 (tm-30) REVERT: B 167 GLN cc_start: 0.8459 (mp10) cc_final: 0.8194 (mp10) outliers start: 48 outliers final: 12 residues processed: 184 average time/residue: 0.6297 time to fit residues: 126.4957 Evaluate side-chains 146 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1047 CYS Chi-restraints excluded: chain A residue 1149 SER Chi-restraints excluded: chain A residue 1393 LEU Chi-restraints excluded: chain A residue 1433 PHE Chi-restraints excluded: chain A residue 1658 SER Chi-restraints excluded: chain B residue 18 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 83 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 156 optimal weight: 0.0010 chunk 94 optimal weight: 0.0470 chunk 36 optimal weight: 0.6980 overall best weight: 0.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 835 ASN B 113 ASN B 177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.110484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.083872 restraints weight = 21991.043| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.25 r_work: 0.3115 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 14059 Z= 0.146 Angle : 0.552 11.962 18841 Z= 0.278 Chirality : 0.044 0.161 2036 Planarity : 0.004 0.039 2308 Dihedral : 22.209 178.025 2478 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.94 % Allowed : 14.49 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.30 (0.22), residues: 1593 helix: 1.21 (0.24), residues: 496 sheet: -0.25 (0.23), residues: 506 loop : -0.06 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 355 TYR 0.013 0.001 TYR A 340 PHE 0.030 0.001 PHE A 647 TRP 0.011 0.001 TRP B 34 HIS 0.004 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00334 (14053) covalent geometry : angle 0.54041 (18829) SS BOND : bond 0.01592 ( 6) SS BOND : angle 4.42734 ( 12) hydrogen bonds : bond 0.03668 ( 450) hydrogen bonds : angle 4.88720 ( 1254) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8340 (mmtt) cc_final: 0.8129 (mmmt) REVERT: A 163 MET cc_start: 0.6804 (tpp) cc_final: 0.6512 (tmt) REVERT: A 258 ASP cc_start: 0.8502 (p0) cc_final: 0.8292 (p0) REVERT: A 279 GLN cc_start: 0.8178 (tt0) cc_final: 0.7866 (mm110) REVERT: A 330 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8414 (tm-30) REVERT: A 355 ARG cc_start: 0.8716 (tpp80) cc_final: 0.8353 (tpp80) REVERT: A 644 ASP cc_start: 0.8533 (t0) cc_final: 0.8310 (t0) REVERT: A 691 PHE cc_start: 0.8365 (m-10) cc_final: 0.8147 (m-10) REVERT: A 881 ASP cc_start: 0.7307 (t70) cc_final: 0.6617 (t0) REVERT: A 1086 LYS cc_start: 0.8542 (mttt) cc_final: 0.8134 (mmmt) REVERT: A 1152 MET cc_start: 0.7692 (mtp) cc_final: 0.7386 (mtm) REVERT: A 1390 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8112 (tt) REVERT: A 1439 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8265 (mp) REVERT: A 1563 HIS cc_start: 0.7547 (m-70) cc_final: 0.6747 (t-90) REVERT: A 1596 ARG cc_start: 0.8607 (mtp85) cc_final: 0.8070 (ttm110) REVERT: A 1637 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6681 (tm) REVERT: B 30 GLN cc_start: 0.8854 (tt0) cc_final: 0.8475 (tp40) REVERT: B 39 ASN cc_start: 0.8920 (t0) cc_final: 0.8492 (t0) REVERT: B 42 ARG cc_start: 0.8611 (ttp-110) cc_final: 0.8238 (mtp180) REVERT: B 46 GLN cc_start: 0.8427 (mt0) cc_final: 0.8048 (mm-40) REVERT: B 111 GLN cc_start: 0.8641 (tp40) cc_final: 0.7848 (tm-30) REVERT: B 167 GLN cc_start: 0.8472 (mp10) cc_final: 0.8156 (mp10) outliers start: 42 outliers final: 13 residues processed: 176 average time/residue: 0.6150 time to fit residues: 118.8202 Evaluate side-chains 142 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 952 ARG Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1047 CYS Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1342 ASN Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1658 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 16 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 135 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 95 optimal weight: 0.0020 chunk 114 optimal weight: 2.9990 chunk 36 optimal weight: 0.0770 chunk 61 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 0.4746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 728 ASN A 835 ASN A1677 HIS B 113 ASN B 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.110162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.083527 restraints weight = 21952.486| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.25 r_work: 0.3106 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 14059 Z= 0.156 Angle : 0.568 13.229 18841 Z= 0.284 Chirality : 0.044 0.165 2036 Planarity : 0.004 0.040 2308 Dihedral : 21.207 176.839 2478 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.87 % Allowed : 15.89 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.31 (0.22), residues: 1593 helix: 1.18 (0.24), residues: 498 sheet: -0.27 (0.23), residues: 505 loop : 0.00 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 150 TYR 0.012 0.001 TYR A 340 PHE 0.014 0.001 PHE A 682 TRP 0.012 0.001 TRP B 34 HIS 0.005 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00368 (14053) covalent geometry : angle 0.54945 (18829) SS BOND : bond 0.01074 ( 6) SS BOND : angle 5.77056 ( 12) hydrogen bonds : bond 0.03534 ( 450) hydrogen bonds : angle 4.83805 ( 1254) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.602 Fit side-chains REVERT: A 144 LYS cc_start: 0.8353 (mmtt) cc_final: 0.8147 (mmmt) REVERT: A 158 PHE cc_start: 0.7780 (t80) cc_final: 0.7125 (m-80) REVERT: A 163 MET cc_start: 0.6788 (tpp) cc_final: 0.6492 (tmt) REVERT: A 258 ASP cc_start: 0.8469 (p0) cc_final: 0.8257 (p0) REVERT: A 279 GLN cc_start: 0.8259 (tt0) cc_final: 0.8008 (mm110) REVERT: A 330 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8409 (tm-30) REVERT: A 355 ARG cc_start: 0.8688 (tpp80) cc_final: 0.8465 (tpp80) REVERT: A 665 GLU cc_start: 0.8455 (tm-30) cc_final: 0.7982 (tt0) REVERT: A 1086 LYS cc_start: 0.8518 (mttt) cc_final: 0.8122 (mmmt) REVERT: A 1152 MET cc_start: 0.7756 (mtp) cc_final: 0.7352 (mtm) REVERT: A 1390 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8083 (tt) REVERT: A 1563 HIS cc_start: 0.7547 (m-70) cc_final: 0.6748 (t-90) REVERT: A 1596 ARG cc_start: 0.8607 (mtp85) cc_final: 0.8058 (ttm110) REVERT: A 1637 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6691 (tm) REVERT: B 30 GLN cc_start: 0.8851 (tt0) cc_final: 0.8482 (tp40) REVERT: B 39 ASN cc_start: 0.8975 (t0) cc_final: 0.8369 (t0) REVERT: B 42 ARG cc_start: 0.8628 (ttp-110) cc_final: 0.8219 (mtp180) outliers start: 41 outliers final: 17 residues processed: 165 average time/residue: 0.5926 time to fit residues: 107.3542 Evaluate side-chains 139 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1047 CYS Chi-restraints excluded: chain A residue 1149 SER Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1342 ASN Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1658 SER Chi-restraints excluded: chain B residue 141 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 156 optimal weight: 0.0670 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 79 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 48 optimal weight: 0.0970 chunk 103 optimal weight: 0.6980 chunk 152 optimal weight: 0.0980 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 GLN B 113 ASN B 177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.110670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.084630 restraints weight = 21962.017| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.22 r_work: 0.3134 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 14059 Z= 0.112 Angle : 0.524 10.930 18841 Z= 0.263 Chirality : 0.043 0.146 2036 Planarity : 0.003 0.040 2308 Dihedral : 20.370 173.387 2478 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.10 % Allowed : 16.72 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.37 (0.22), residues: 1593 helix: 1.29 (0.24), residues: 497 sheet: -0.28 (0.23), residues: 507 loop : 0.04 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 355 TYR 0.009 0.001 TYR A 340 PHE 0.034 0.001 PHE A 647 TRP 0.013 0.001 TRP B 34 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00255 (14053) covalent geometry : angle 0.51232 (18829) SS BOND : bond 0.01402 ( 6) SS BOND : angle 4.43931 ( 12) hydrogen bonds : bond 0.03231 ( 450) hydrogen bonds : angle 4.71947 ( 1254) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.6755 (tpp) cc_final: 0.6512 (tmt) REVERT: A 258 ASP cc_start: 0.8477 (p0) cc_final: 0.8262 (p0) REVERT: A 279 GLN cc_start: 0.8201 (tt0) cc_final: 0.7905 (mm110) REVERT: A 355 ARG cc_start: 0.8681 (tpp80) cc_final: 0.8434 (tpp80) REVERT: A 557 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8311 (mp10) REVERT: A 665 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7976 (tt0) REVERT: A 723 ASP cc_start: 0.8847 (m-30) cc_final: 0.8593 (m-30) REVERT: A 724 LYS cc_start: 0.9216 (ttmm) cc_final: 0.8887 (ttpp) REVERT: A 881 ASP cc_start: 0.7231 (t70) cc_final: 0.6462 (t0) REVERT: A 1086 LYS cc_start: 0.8463 (mttt) cc_final: 0.8122 (mmmt) REVERT: A 1152 MET cc_start: 0.7784 (mtp) cc_final: 0.7432 (mtm) REVERT: A 1390 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8022 (tt) REVERT: A 1563 HIS cc_start: 0.7525 (m-70) cc_final: 0.6729 (t-90) REVERT: A 1596 ARG cc_start: 0.8599 (mtp85) cc_final: 0.8197 (ttm110) REVERT: A 1637 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6758 (tm) REVERT: B 30 GLN cc_start: 0.8860 (tt0) cc_final: 0.8480 (tp40) REVERT: B 39 ASN cc_start: 0.8936 (t0) cc_final: 0.8186 (t0) REVERT: B 42 ARG cc_start: 0.8618 (ttp-110) cc_final: 0.8162 (mtp180) REVERT: B 56 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8747 (mptt) REVERT: B 121 ARG cc_start: 0.6922 (mpp-170) cc_final: 0.6638 (pmm150) REVERT: B 130 TYR cc_start: 0.8203 (t80) cc_final: 0.7512 (t80) outliers start: 30 outliers final: 14 residues processed: 156 average time/residue: 0.6287 time to fit residues: 107.5576 Evaluate side-chains 143 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 557 GLN Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 952 ARG Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1047 CYS Chi-restraints excluded: chain A residue 1149 SER Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1342 ASN Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 141 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 19 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 110 optimal weight: 0.0980 chunk 107 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 GLN A 728 ASN A 835 ASN B 113 ASN B 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.110069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.083808 restraints weight = 21867.738| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.23 r_work: 0.3122 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.133 14059 Z= 0.142 Angle : 0.569 17.501 18841 Z= 0.282 Chirality : 0.043 0.161 2036 Planarity : 0.004 0.041 2308 Dihedral : 19.971 168.886 2478 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.24 % Allowed : 17.70 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.38 (0.22), residues: 1593 helix: 1.29 (0.24), residues: 499 sheet: -0.29 (0.24), residues: 507 loop : 0.06 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 150 TYR 0.010 0.001 TYR A 340 PHE 0.012 0.001 PHE A 682 TRP 0.015 0.001 TRP B 34 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00335 (14053) covalent geometry : angle 0.53408 (18829) SS BOND : bond 0.01623 ( 6) SS BOND : angle 7.79052 ( 12) hydrogen bonds : bond 0.03313 ( 450) hydrogen bonds : angle 4.69028 ( 1254) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 158 PHE cc_start: 0.7805 (t80) cc_final: 0.7219 (m-80) REVERT: A 163 MET cc_start: 0.6802 (tpp) cc_final: 0.6497 (tmt) REVERT: A 258 ASP cc_start: 0.8476 (p0) cc_final: 0.8258 (p0) REVERT: A 279 GLN cc_start: 0.8186 (tt0) cc_final: 0.7910 (mm110) REVERT: A 355 ARG cc_start: 0.8708 (tpp80) cc_final: 0.8146 (tpp80) REVERT: A 385 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.7936 (tm-30) REVERT: A 665 GLU cc_start: 0.8431 (tm-30) cc_final: 0.7959 (tt0) REVERT: A 723 ASP cc_start: 0.8827 (m-30) cc_final: 0.8582 (m-30) REVERT: A 724 LYS cc_start: 0.9201 (ttmm) cc_final: 0.8915 (ttpp) REVERT: A 881 ASP cc_start: 0.7243 (t70) cc_final: 0.6433 (t0) REVERT: A 1086 LYS cc_start: 0.8448 (mttt) cc_final: 0.8117 (mmmt) REVERT: A 1152 MET cc_start: 0.7788 (mtp) cc_final: 0.7440 (mtm) REVERT: A 1390 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8037 (tt) REVERT: A 1563 HIS cc_start: 0.7537 (m-70) cc_final: 0.6746 (t-90) REVERT: A 1596 ARG cc_start: 0.8611 (mtp85) cc_final: 0.8055 (ttm110) REVERT: B 30 GLN cc_start: 0.8855 (tt0) cc_final: 0.8485 (tp40) REVERT: B 39 ASN cc_start: 0.8931 (t0) cc_final: 0.8188 (t0) REVERT: B 42 ARG cc_start: 0.8640 (ttp-110) cc_final: 0.8175 (mtp180) REVERT: B 56 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8746 (mptt) REVERT: B 121 ARG cc_start: 0.6969 (mpp-170) cc_final: 0.6662 (pmm150) REVERT: B 130 TYR cc_start: 0.8209 (t80) cc_final: 0.7544 (t80) outliers start: 32 outliers final: 15 residues processed: 154 average time/residue: 0.5948 time to fit residues: 100.5892 Evaluate side-chains 139 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 952 ARG Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1047 CYS Chi-restraints excluded: chain A residue 1149 SER Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1342 ASN Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 141 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 123 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 103 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 631 HIS A 728 ASN A 820 GLN A 835 ASN B 113 ASN B 177 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.108626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.082538 restraints weight = 21986.304| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.20 r_work: 0.3100 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 14059 Z= 0.186 Angle : 0.606 22.706 18841 Z= 0.301 Chirality : 0.044 0.188 2036 Planarity : 0.004 0.041 2308 Dihedral : 19.694 166.420 2478 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.24 % Allowed : 17.84 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.36 (0.22), residues: 1593 helix: 1.26 (0.24), residues: 495 sheet: -0.31 (0.24), residues: 507 loop : 0.07 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 150 TYR 0.014 0.001 TYR A 340 PHE 0.034 0.002 PHE A 647 TRP 0.017 0.001 TRP B 34 HIS 0.005 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00441 (14053) covalent geometry : angle 0.55768 (18829) SS BOND : bond 0.02366 ( 6) SS BOND : angle 9.36840 ( 12) hydrogen bonds : bond 0.03558 ( 450) hydrogen bonds : angle 4.75675 ( 1254) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.554 Fit side-chains REVERT: A 158 PHE cc_start: 0.7829 (t80) cc_final: 0.7303 (m-80) REVERT: A 163 MET cc_start: 0.6820 (tpp) cc_final: 0.6501 (tmt) REVERT: A 258 ASP cc_start: 0.8484 (p0) cc_final: 0.8259 (p0) REVERT: A 270 MET cc_start: 0.8143 (mmt) cc_final: 0.7924 (ptp) REVERT: A 279 GLN cc_start: 0.8238 (tt0) cc_final: 0.7972 (mm110) REVERT: A 330 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8429 (tm-30) REVERT: A 355 ARG cc_start: 0.8754 (tpp80) cc_final: 0.8151 (tpp80) REVERT: A 385 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: A 665 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7957 (tt0) REVERT: A 723 ASP cc_start: 0.8852 (m-30) cc_final: 0.8594 (m-30) REVERT: A 724 LYS cc_start: 0.9214 (ttmm) cc_final: 0.8905 (ttpp) REVERT: A 881 ASP cc_start: 0.7293 (t70) cc_final: 0.6469 (t0) REVERT: A 1039 TRP cc_start: 0.8630 (OUTLIER) cc_final: 0.7996 (m100) REVERT: A 1086 LYS cc_start: 0.8455 (mttt) cc_final: 0.8115 (mmmt) REVERT: A 1152 MET cc_start: 0.7802 (mtp) cc_final: 0.7453 (mtm) REVERT: A 1350 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7842 (mtm180) REVERT: A 1390 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8082 (tt) REVERT: A 1563 HIS cc_start: 0.7557 (m-70) cc_final: 0.6770 (t-90) REVERT: A 1596 ARG cc_start: 0.8631 (mtp85) cc_final: 0.8197 (ttm110) REVERT: B 30 GLN cc_start: 0.8846 (tt0) cc_final: 0.8483 (tp40) REVERT: B 39 ASN cc_start: 0.8945 (t0) cc_final: 0.8249 (t0) REVERT: B 42 ARG cc_start: 0.8661 (ttp-110) cc_final: 0.8195 (mtp180) REVERT: B 56 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8768 (mptt) REVERT: B 130 TYR cc_start: 0.8226 (t80) cc_final: 0.7570 (t80) outliers start: 32 outliers final: 18 residues processed: 155 average time/residue: 0.5817 time to fit residues: 98.8779 Evaluate side-chains 145 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1039 TRP Chi-restraints excluded: chain A residue 1047 CYS Chi-restraints excluded: chain A residue 1149 SER Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1342 ASN Chi-restraints excluded: chain A residue 1350 ARG Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1613 CYS Chi-restraints excluded: chain A residue 1658 SER Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 141 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 156 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 62 optimal weight: 0.0030 chunk 96 optimal weight: 0.0670 chunk 22 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 111 optimal weight: 0.1980 chunk 160 optimal weight: 0.7980 overall best weight: 0.2928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 820 GLN A 835 ASN B 113 ASN B 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.110310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.084340 restraints weight = 21832.047| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.21 r_work: 0.3131 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 14059 Z= 0.124 Angle : 0.575 22.456 18841 Z= 0.285 Chirality : 0.043 0.174 2036 Planarity : 0.003 0.041 2308 Dihedral : 19.210 163.314 2478 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.75 % Allowed : 18.61 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.43 (0.22), residues: 1593 helix: 1.33 (0.24), residues: 496 sheet: -0.25 (0.24), residues: 506 loop : 0.09 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 150 TYR 0.009 0.001 TYR A 340 PHE 0.018 0.001 PHE B 88 TRP 0.021 0.001 TRP B 34 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00292 (14053) covalent geometry : angle 0.52661 (18829) SS BOND : bond 0.01907 ( 6) SS BOND : angle 9.17623 ( 12) hydrogen bonds : bond 0.03200 ( 450) hydrogen bonds : angle 4.64336 ( 1254) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.622 Fit side-chains REVERT: A 158 PHE cc_start: 0.7800 (t80) cc_final: 0.7281 (m-80) REVERT: A 163 MET cc_start: 0.6770 (tpp) cc_final: 0.6487 (tmt) REVERT: A 258 ASP cc_start: 0.8438 (p0) cc_final: 0.8212 (p0) REVERT: A 279 GLN cc_start: 0.8054 (tt0) cc_final: 0.7814 (mm110) REVERT: A 355 ARG cc_start: 0.8723 (tpp80) cc_final: 0.8116 (tpp80) REVERT: A 665 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7956 (tt0) REVERT: A 723 ASP cc_start: 0.8829 (m-30) cc_final: 0.8570 (m-30) REVERT: A 724 LYS cc_start: 0.9204 (ttmm) cc_final: 0.8887 (ttpp) REVERT: A 881 ASP cc_start: 0.7237 (t70) cc_final: 0.6425 (t0) REVERT: A 1039 TRP cc_start: 0.8638 (OUTLIER) cc_final: 0.7927 (m100) REVERT: A 1086 LYS cc_start: 0.8431 (mttt) cc_final: 0.8106 (mmmt) REVERT: A 1152 MET cc_start: 0.7714 (mtp) cc_final: 0.7317 (mtm) REVERT: A 1390 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.7990 (tt) REVERT: A 1563 HIS cc_start: 0.7525 (m-70) cc_final: 0.6731 (t-90) REVERT: A 1596 ARG cc_start: 0.8629 (mtp85) cc_final: 0.8200 (ttm110) REVERT: B 30 GLN cc_start: 0.8862 (tt0) cc_final: 0.8495 (tp40) REVERT: B 39 ASN cc_start: 0.8921 (t0) cc_final: 0.8167 (t0) REVERT: B 42 ARG cc_start: 0.8641 (ttp-110) cc_final: 0.8164 (mtp180) REVERT: B 56 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8734 (mptt) REVERT: B 130 TYR cc_start: 0.8225 (t80) cc_final: 0.7564 (t80) outliers start: 25 outliers final: 14 residues processed: 148 average time/residue: 0.6221 time to fit residues: 101.1389 Evaluate side-chains 137 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1039 TRP Chi-restraints excluded: chain A residue 1047 CYS Chi-restraints excluded: chain A residue 1149 SER Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1342 ASN Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1658 SER Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 141 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 103 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN A 728 ASN A 820 GLN A 835 ASN A 866 HIS A1199 ASN B 113 ASN B 177 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.108166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.081795 restraints weight = 21932.171| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.24 r_work: 0.3082 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 14059 Z= 0.207 Angle : 0.649 31.122 18841 Z= 0.321 Chirality : 0.045 0.166 2036 Planarity : 0.004 0.041 2308 Dihedral : 19.151 163.200 2478 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.96 % Allowed : 18.47 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.36 (0.22), residues: 1593 helix: 1.26 (0.24), residues: 493 sheet: -0.28 (0.24), residues: 507 loop : 0.03 (0.27), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 150 TYR 0.016 0.001 TYR A 340 PHE 0.038 0.002 PHE A 647 TRP 0.025 0.001 TRP B 34 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00482 (14053) covalent geometry : angle 0.57787 (18829) SS BOND : bond 0.03614 ( 6) SS BOND : angle 11.72201 ( 12) hydrogen bonds : bond 0.03639 ( 450) hydrogen bonds : angle 4.77112 ( 1254) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 PHE cc_start: 0.7819 (t80) cc_final: 0.7321 (m-80) REVERT: A 163 MET cc_start: 0.6776 (tpp) cc_final: 0.6496 (tmt) REVERT: A 258 ASP cc_start: 0.8514 (p0) cc_final: 0.8298 (p0) REVERT: A 279 GLN cc_start: 0.8235 (tt0) cc_final: 0.7993 (mm110) REVERT: A 355 ARG cc_start: 0.8766 (tpp80) cc_final: 0.8102 (tpp80) REVERT: A 665 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8002 (tt0) REVERT: A 723 ASP cc_start: 0.8844 (m-30) cc_final: 0.8591 (m-30) REVERT: A 881 ASP cc_start: 0.7312 (t70) cc_final: 0.6482 (t0) REVERT: A 1039 TRP cc_start: 0.8856 (OUTLIER) cc_final: 0.7822 (m100) REVERT: A 1086 LYS cc_start: 0.8443 (mttt) cc_final: 0.8099 (mmmt) REVERT: A 1152 MET cc_start: 0.7753 (mtp) cc_final: 0.7370 (mtm) REVERT: A 1350 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7856 (mtm180) REVERT: A 1390 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8106 (tt) REVERT: A 1563 HIS cc_start: 0.7557 (m-70) cc_final: 0.6768 (t-90) REVERT: B 30 GLN cc_start: 0.8857 (tt0) cc_final: 0.8478 (tp40) REVERT: B 56 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8782 (mptt) REVERT: B 130 TYR cc_start: 0.8196 (t80) cc_final: 0.7599 (t80) outliers start: 28 outliers final: 18 residues processed: 144 average time/residue: 0.5821 time to fit residues: 92.1007 Evaluate side-chains 138 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 952 ARG Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1039 TRP Chi-restraints excluded: chain A residue 1047 CYS Chi-restraints excluded: chain A residue 1149 SER Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1342 ASN Chi-restraints excluded: chain A residue 1350 ARG Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1613 CYS Chi-restraints excluded: chain A residue 1658 SER Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 141 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 120 optimal weight: 0.0670 chunk 62 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 135 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 820 GLN A 835 ASN A1199 ASN B 113 ASN B 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.109038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.082766 restraints weight = 21914.317| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.23 r_work: 0.3100 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 14059 Z= 0.151 Angle : 0.618 30.993 18841 Z= 0.305 Chirality : 0.044 0.160 2036 Planarity : 0.003 0.040 2308 Dihedral : 18.801 160.730 2478 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.89 % Allowed : 18.68 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.41 (0.22), residues: 1593 helix: 1.32 (0.24), residues: 493 sheet: -0.26 (0.24), residues: 506 loop : 0.06 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1596 TYR 0.024 0.001 TYR A 58 PHE 0.013 0.001 PHE A 682 TRP 0.028 0.001 TRP B 34 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00348 (14053) covalent geometry : angle 0.54375 (18829) SS BOND : bond 0.03155 ( 6) SS BOND : angle 11.63562 ( 12) hydrogen bonds : bond 0.03391 ( 450) hydrogen bonds : angle 4.69667 ( 1254) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 PHE cc_start: 0.7762 (t80) cc_final: 0.7265 (m-80) REVERT: A 163 MET cc_start: 0.6747 (tpp) cc_final: 0.6485 (tmt) REVERT: A 258 ASP cc_start: 0.8480 (p0) cc_final: 0.8259 (p0) REVERT: A 279 GLN cc_start: 0.8127 (tt0) cc_final: 0.7915 (mm110) REVERT: A 644 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8165 (t0) REVERT: A 665 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7972 (tt0) REVERT: A 723 ASP cc_start: 0.8812 (m-30) cc_final: 0.8558 (m-30) REVERT: A 724 LYS cc_start: 0.9233 (ttmm) cc_final: 0.8828 (ttpp) REVERT: A 881 ASP cc_start: 0.7301 (t70) cc_final: 0.6471 (t0) REVERT: A 1039 TRP cc_start: 0.8863 (OUTLIER) cc_final: 0.7875 (m100) REVERT: A 1086 LYS cc_start: 0.8428 (mttt) cc_final: 0.8091 (mmmt) REVERT: A 1152 MET cc_start: 0.7732 (mtp) cc_final: 0.7328 (mtm) REVERT: A 1208 PHE cc_start: 0.3856 (t80) cc_final: 0.3203 (t80) REVERT: A 1350 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7853 (mtm180) REVERT: A 1390 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8037 (tt) REVERT: A 1563 HIS cc_start: 0.7550 (m-70) cc_final: 0.6737 (t-90) REVERT: B 30 GLN cc_start: 0.8867 (tt0) cc_final: 0.8481 (tp40) REVERT: B 56 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8748 (mptt) REVERT: B 130 TYR cc_start: 0.8183 (t80) cc_final: 0.7507 (t80) outliers start: 27 outliers final: 18 residues processed: 143 average time/residue: 0.5890 time to fit residues: 92.8796 Evaluate side-chains 139 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 952 ARG Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain A residue 1039 TRP Chi-restraints excluded: chain A residue 1047 CYS Chi-restraints excluded: chain A residue 1149 SER Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1342 ASN Chi-restraints excluded: chain A residue 1350 ARG Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1613 CYS Chi-restraints excluded: chain A residue 1658 SER Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 141 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 chunk 120 optimal weight: 0.8980 chunk 134 optimal weight: 0.1980 chunk 112 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 137 optimal weight: 0.4980 chunk 125 optimal weight: 0.4980 chunk 109 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 820 GLN A 835 ASN A1199 ASN B 113 ASN B 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.109945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.083642 restraints weight = 21972.273| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.24 r_work: 0.3116 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 14059 Z= 0.131 Angle : 0.607 30.536 18841 Z= 0.300 Chirality : 0.043 0.157 2036 Planarity : 0.003 0.041 2308 Dihedral : 18.377 160.379 2478 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.68 % Allowed : 19.10 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 aren not related in a simple way. whole: 0.47 (0.22), residues: 1593 helix: 1.42 (0.24), residues: 491 sheet: -0.23 (0.24), residues: 506 loop : 0.06 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1596 TYR 0.011 0.001 TYR A 340 PHE 0.038 0.001 PHE A 647 TRP 0.028 0.001 TRP B 34 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00300 (14053) covalent geometry : angle 0.53383 (18829) SS BOND : bond 0.03036 ( 6) SS BOND : angle 11.48597 ( 12) hydrogen bonds : bond 0.03224 ( 450) hydrogen bonds : angle 4.63898 ( 1254) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6000.30 seconds wall clock time: 103 minutes 5.31 seconds (6185.31 seconds total)