Starting phenix.real_space_refine on Tue Aug 26 15:05:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cg6_16632/08_2025/8cg6_16632_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cg6_16632/08_2025/8cg6_16632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cg6_16632/08_2025/8cg6_16632_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cg6_16632/08_2025/8cg6_16632_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cg6_16632/08_2025/8cg6_16632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cg6_16632/08_2025/8cg6_16632.map" } resolution = 3.4 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 85 5.16 5 C 11904 2.51 5 N 3360 2.21 5 O 3626 1.98 5 H 18739 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37715 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 18155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 18155 Classifications: {'peptide': 1208} Link IDs: {'PTRANS': 73, 'TRANS': 1134} Chain breaks: 4 Chain: "B" Number of atoms: 18361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1223, 18361 Classifications: {'peptide': 1223} Link IDs: {'PCIS': 1, 'PTRANS': 73, 'TRANS': 1148} Chain breaks: 3 Chain: "C" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1174 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'42X': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 5.92, per 1000 atoms: 0.16 Number of scatterers: 37715 At special positions: 0 Unit cell: (167.28, 143.5, 110.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 85 16.00 P 1 15.00 O 3626 8.00 N 3360 7.00 C 11904 6.00 H 18739 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 851.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4678 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 21 sheets defined 48.4% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 33 through 51 Proline residue: A 43 - end of helix Processing helix chain 'A' and resid 54 through 61 removed outlier: 3.801A pdb=" N GLU A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 69 through 77 removed outlier: 4.386A pdb=" N ARG A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 102 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.735A pdb=" N SER A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 137 through 163 Processing helix chain 'A' and resid 166 through 170 removed outlier: 3.633A pdb=" N ALA A 169 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN A 170 " --> pdb=" O ARG A 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 170' Processing helix chain 'A' and resid 184 through 200 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 294 through 309 removed outlier: 3.503A pdb=" N ARG A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 328 removed outlier: 4.567A pdb=" N ALA A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 353 removed outlier: 4.056A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU A 353 " --> pdb=" O VAL A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'A' and resid 467 through 485 removed outlier: 3.536A pdb=" N GLY A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 531 through 540 removed outlier: 3.981A pdb=" N VAL A 536 " --> pdb=" O ILE A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 570 removed outlier: 3.741A pdb=" N ALA A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 634 Processing helix chain 'A' and resid 664 through 676 removed outlier: 4.503A pdb=" N PHE A 668 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 682 Processing helix chain 'A' and resid 692 through 708 Processing helix chain 'A' and resid 727 through 732 Processing helix chain 'A' and resid 737 through 753 Processing helix chain 'A' and resid 838 through 856 Processing helix chain 'A' and resid 863 through 874 Processing helix chain 'A' and resid 888 through 905 Processing helix chain 'A' and resid 925 through 929 removed outlier: 4.171A pdb=" N SER A 928 " --> pdb=" O GLY A 925 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA A 929 " --> pdb=" O GLN A 926 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 925 through 929' Processing helix chain 'A' and resid 934 through 941 Processing helix chain 'A' and resid 941 through 958 Processing helix chain 'A' and resid 964 through 969 Processing helix chain 'A' and resid 971 through 976 removed outlier: 3.608A pdb=" N THR A 975 " --> pdb=" O VAL A 972 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 976 " --> pdb=" O PHE A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 999 Processing helix chain 'A' and resid 1012 through 1020 removed outlier: 3.583A pdb=" N TYR A1018 " --> pdb=" O TYR A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1043 removed outlier: 3.880A pdb=" N LEU A1043 " --> pdb=" O MET A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1064 Processing helix chain 'A' and resid 1089 through 1101 Processing helix chain 'A' and resid 1117 through 1122 removed outlier: 3.652A pdb=" N VAL A1120 " --> pdb=" O THR A1117 " (cutoff:3.500A) Proline residue: A1122 - end of helix Processing helix chain 'A' and resid 1123 through 1132 Processing helix chain 'A' and resid 1154 through 1159 removed outlier: 3.711A pdb=" N GLN A1159 " --> pdb=" O LYS A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1169 removed outlier: 4.038A pdb=" N THR A1164 " --> pdb=" O PRO A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1184 Processing helix chain 'A' and resid 1200 through 1210 removed outlier: 3.887A pdb=" N PHE A1204 " --> pdb=" O VAL A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1240 Processing helix chain 'A' and resid 1247 through 1256 removed outlier: 4.248A pdb=" N ASP A1251 " --> pdb=" O TYR A1248 " (cutoff:3.500A) Proline residue: A1253 - end of helix Processing helix chain 'B' and resid 19 through 29 removed outlier: 3.709A pdb=" N VAL B 23 " --> pdb=" O CYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 51 Proline residue: B 43 - end of helix Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 66 through 69 Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'B' and resid 80 through 102 removed outlier: 3.808A pdb=" N ALA B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 131 removed outlier: 3.561A pdb=" N VAL B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 137 through 163 Processing helix chain 'B' and resid 184 through 199 Processing helix chain 'B' and resid 223 through 234 removed outlier: 3.682A pdb=" N THR B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 234 " --> pdb=" O PHE B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 265 removed outlier: 3.500A pdb=" N VAL B 260 " --> pdb=" O THR B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 308 Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 344 through 351 Processing helix chain 'B' and resid 398 through 408 Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 462 through 466 Processing helix chain 'B' and resid 467 through 484 Processing helix chain 'B' and resid 528 through 530 No H-bonds generated for 'chain 'B' and resid 528 through 530' Processing helix chain 'B' and resid 531 through 540 Processing helix chain 'B' and resid 554 through 570 Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 660 through 676 Processing helix chain 'B' and resid 678 through 680 No H-bonds generated for 'chain 'B' and resid 678 through 680' Processing helix chain 'B' and resid 693 through 708 removed outlier: 3.990A pdb=" N SER B 697 " --> pdb=" O GLN B 693 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR B 700 " --> pdb=" O ASP B 696 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR B 701 " --> pdb=" O SER B 697 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 753 Processing helix chain 'B' and resid 772 through 776 removed outlier: 3.559A pdb=" N ASN B 776 " --> pdb=" O ALA B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 855 Processing helix chain 'B' and resid 863 through 873 Processing helix chain 'B' and resid 888 through 906 removed outlier: 4.050A pdb=" N GLY B 906 " --> pdb=" O ARG B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 941 Processing helix chain 'B' and resid 941 through 958 Processing helix chain 'B' and resid 964 through 968 Processing helix chain 'B' and resid 971 through 976 removed outlier: 3.647A pdb=" N SER B 974 " --> pdb=" O LYS B 971 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 976 " --> pdb=" O PHE B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 1000 removed outlier: 3.590A pdb=" N GLY B1000 " --> pdb=" O TRP B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1021 removed outlier: 4.159A pdb=" N ALA B1015 " --> pdb=" O LEU B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1043 removed outlier: 3.611A pdb=" N LEU B1043 " --> pdb=" O MET B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1063 Processing helix chain 'B' and resid 1089 through 1102 Processing helix chain 'B' and resid 1117 through 1122 removed outlier: 3.589A pdb=" N VAL B1120 " --> pdb=" O THR B1117 " (cutoff:3.500A) Proline residue: B1122 - end of helix Processing helix chain 'B' and resid 1123 through 1133 removed outlier: 3.910A pdb=" N ALA B1133 " --> pdb=" O GLN B1129 " (cutoff:3.500A) Processing helix chain 'B' and resid 1154 through 1158 removed outlier: 3.641A pdb=" N ASP B1157 " --> pdb=" O SER B1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 1159 through 1169 removed outlier: 4.096A pdb=" N PHE B1163 " --> pdb=" O GLN B1159 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR B1164 " --> pdb=" O PRO B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1173 through 1183 Processing helix chain 'B' and resid 1200 through 1210 Processing helix chain 'B' and resid 1224 through 1240 removed outlier: 4.025A pdb=" N LEU B1228 " --> pdb=" O ASP B1224 " (cutoff:3.500A) Processing helix chain 'B' and resid 1244 through 1250 removed outlier: 3.620A pdb=" N TYR B1248 " --> pdb=" O GLU B1244 " (cutoff:3.500A) Processing helix chain 'B' and resid 1252 through 1256 Processing helix chain 'C' and resid 12 through 27 Processing helix chain 'C' and resid 38 through 43 Processing helix chain 'C' and resid 45 through 60 Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 75 through 85 removed outlier: 3.569A pdb=" N LEU C 79 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY C 85 " --> pdb=" O LYS C 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 116 removed outlier: 6.472A pdb=" N MET A 7 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 181 removed outlier: 6.729A pdb=" N SER A 221 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU A 209 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 311 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AA4, first strand: chain 'A' and resid 500 through 503 removed outlier: 4.391A pdb=" N GLY A 578 " --> pdb=" O TRP A 502 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A 622 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA A 389 " --> pdb=" O THR A 622 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE A 624 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 384 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 640 " --> pdb=" O ILE A 386 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 450 through 451 Processing sheet with id=AA6, first strand: chain 'A' and resid 644 through 646 removed outlier: 3.882A pdb=" N GLY A 644 " --> pdb=" O VAL A 811 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 796 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 684 through 686 removed outlier: 6.107A pdb=" N CYS A 685 " --> pdb=" O GLY A 725 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 754 through 755 Processing sheet with id=AA9, first strand: chain 'A' and resid 830 through 836 Processing sheet with id=AB1, first strand: chain 'A' and resid 919 through 920 Processing sheet with id=AB2, first strand: chain 'A' and resid 1006 through 1007 removed outlier: 6.678A pdb=" N VAL A1006 " --> pdb=" O ILE A1144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1106 through 1109 removed outlier: 4.327A pdb=" N MET A1050 " --> pdb=" O LEU A1109 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLY A1086 " --> pdb=" O PHE A1074 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N PHE A1074 " --> pdb=" O GLY A1086 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL A1171 " --> pdb=" O GLU A1073 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N SER A1075 " --> pdb=" O VAL A1171 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 113 through 116 removed outlier: 6.840A pdb=" N MET B 7 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N SER B 335 " --> pdb=" O MET B 7 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 9 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE B 337 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA B 11 " --> pdb=" O ILE B 337 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 208 through 214 removed outlier: 7.081A pdb=" N SER B 219 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA B 212 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLN B 217 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 280 through 281 Processing sheet with id=AB7, first strand: chain 'B' and resid 389 through 390 removed outlier: 9.030A pdb=" N TYR B 547 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 501 " --> pdb=" O TYR B 547 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 389 through 390 removed outlier: 3.862A pdb=" N ALA B 640 " --> pdb=" O ILE B 386 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ILE B 642 " --> pdb=" O GLU B 813 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLU B 813 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY B 644 " --> pdb=" O VAL B 811 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 796 " --> pdb=" O LEU B 812 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU B 797 " --> pdb=" O SER B 683 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N CYS B 685 " --> pdb=" O LEU B 797 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASN B 799 " --> pdb=" O CYS B 685 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N MET B 687 " --> pdb=" O ASN B 799 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N SER B 683 " --> pdb=" O TYR B 723 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N GLY B 725 " --> pdb=" O SER B 683 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N CYS B 685 " --> pdb=" O GLY B 725 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 450 through 451 Processing sheet with id=AC1, first strand: chain 'B' and resid 830 through 836 removed outlier: 3.878A pdb=" N ALA B 882 " --> pdb=" O LEU B 834 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1150 through 1152 removed outlier: 3.552A pdb=" N SER B1145 " --> pdb=" O LYS B1150 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE B1144 " --> pdb=" O LYS B1004 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL B1006 " --> pdb=" O ILE B1144 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N PHE B 919 " --> pdb=" O LYS B1004 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL B1006 " --> pdb=" O PHE B 919 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU B 921 " --> pdb=" O VAL B1006 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 920 " --> pdb=" O LEU B1193 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE B1195 " --> pdb=" O VAL B 920 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA B 922 " --> pdb=" O ILE B1195 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N SER B1218 " --> pdb=" O GLY B1192 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N GLU B1194 " --> pdb=" O SER B1218 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1106 through 1109 removed outlier: 4.766A pdb=" N MET B1050 " --> pdb=" O LEU B1109 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS B1076 " --> pdb=" O VAL B1084 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY B1086 " --> pdb=" O PHE B1074 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N PHE B1074 " --> pdb=" O GLY B1086 " (cutoff:3.500A) 870 hydrogen bonds defined for protein. 2463 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: 8.56 Time building geometry restraints manager: 4.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18699 1.03 - 1.23: 53 1.23 - 1.42: 7953 1.42 - 1.62: 11277 1.62 - 1.82: 130 Bond restraints: 38112 Sorted by residual: bond pdb=" C22 42X C2000 " pdb=" N24 42X C2000 " ideal model delta sigma weight residual 1.335 1.448 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C44 42X C2000 " pdb=" N42 42X C2000 " ideal model delta sigma weight residual 1.342 1.452 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C32 42X C2000 " pdb=" N34 42X C2000 " ideal model delta sigma weight residual 1.340 1.448 -0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" C22 42X C2000 " pdb=" O23 42X C2000 " ideal model delta sigma weight residual 1.238 1.183 0.055 2.00e-02 2.50e+03 7.52e+00 bond pdb=" C32 42X C2000 " pdb=" O33 42X C2000 " ideal model delta sigma weight residual 1.238 1.183 0.055 2.00e-02 2.50e+03 7.46e+00 ... (remaining 38107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 68580 2.51 - 5.02: 309 5.02 - 7.54: 18 7.54 - 10.05: 3 10.05 - 12.56: 2 Bond angle restraints: 68912 Sorted by residual: angle pdb=" CA PRO A 378 " pdb=" N PRO A 378 " pdb=" CD PRO A 378 " ideal model delta sigma weight residual 112.00 100.70 11.30 1.40e+00 5.10e-01 6.51e+01 angle pdb=" CA PRO A 709 " pdb=" N PRO A 709 " pdb=" CD PRO A 709 " ideal model delta sigma weight residual 112.00 104.99 7.01 1.40e+00 5.10e-01 2.51e+01 angle pdb=" CA PRO B 709 " pdb=" N PRO B 709 " pdb=" CD PRO B 709 " ideal model delta sigma weight residual 112.00 106.04 5.96 1.40e+00 5.10e-01 1.81e+01 angle pdb=" N PRO B 709 " pdb=" CD PRO B 709 " pdb=" CG PRO B 709 " ideal model delta sigma weight residual 103.20 97.11 6.09 1.50e+00 4.44e-01 1.65e+01 angle pdb=" CA PRO B 709 " pdb=" CB PRO B 709 " pdb=" CG PRO B 709 " ideal model delta sigma weight residual 104.50 96.92 7.58 1.90e+00 2.77e-01 1.59e+01 ... (remaining 68907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.81: 16684 24.81 - 49.62: 1140 49.62 - 74.43: 196 74.43 - 99.24: 40 99.24 - 124.05: 2 Dihedral angle restraints: 18062 sinusoidal: 9909 harmonic: 8153 Sorted by residual: dihedral pdb=" CA THR A 364 " pdb=" C THR A 364 " pdb=" N SER A 365 " pdb=" CA SER A 365 " ideal model delta harmonic sigma weight residual 180.00 154.40 25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" C18 42X C2000 " pdb=" C06 42X C2000 " pdb=" C09 42X C2000 " pdb=" O05 42X C2000 " ideal model delta sinusoidal sigma weight residual 71.00 -164.95 -124.05 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" CA GLY B 121 " pdb=" C GLY B 121 " pdb=" N ALA B 122 " pdb=" CA ALA B 122 " ideal model delta harmonic sigma weight residual 180.00 160.14 19.86 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 18059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2295 0.039 - 0.079: 518 0.079 - 0.118: 193 0.118 - 0.157: 23 0.157 - 0.197: 2 Chirality restraints: 3031 Sorted by residual: chirality pdb=" C18 42X C2000 " pdb=" C09 42X C2000 " pdb=" C22 42X C2000 " pdb=" O20 42X C2000 " both_signs ideal model delta sigma weight residual False 2.30 2.50 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CB THR B 196 " pdb=" CA THR B 196 " pdb=" OG1 THR B 196 " pdb=" CG2 THR B 196 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ILE B 576 " pdb=" N ILE B 576 " pdb=" C ILE B 576 " pdb=" CB ILE B 576 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 3028 not shown) Planarity restraints: 5803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 377 " -0.091 5.00e-02 4.00e+02 1.30e-01 2.72e+01 pdb=" N PRO A 378 " 0.225 5.00e-02 4.00e+02 pdb=" CA PRO A 378 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 378 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 708 " 0.082 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO A 709 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO A 709 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 709 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 377 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO B 378 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 378 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 378 " 0.036 5.00e-02 4.00e+02 ... (remaining 5800 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.01: 422 2.01 - 2.66: 53555 2.66 - 3.31: 109958 3.31 - 3.95: 137822 3.95 - 4.60: 215553 Nonbonded interactions: 517310 Sorted by model distance: nonbonded pdb=" OE2 GLU A 157 " pdb=" HE ARG B 950 " model vdw 1.368 2.450 nonbonded pdb=" O LYS B1102 " pdb=" HZ2 LYS B1102 " model vdw 1.468 2.450 nonbonded pdb=" OE1 GLU B 823 " pdb=" H GLU B 823 " model vdw 1.476 2.450 nonbonded pdb=" O ASP A1138 " pdb="HH21 ARG B 167 " model vdw 1.504 2.450 nonbonded pdb=" O GLY A 346 " pdb="HD22 ASN A 350 " model vdw 1.518 2.450 ... (remaining 517305 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 420 or resid 440 through 508 or resid 530 throug \ h 1272)) selection = (chain 'B' and (resid 5 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 120 through 508 or (resid 530 and (name N or name CA or name C or nam \ e O or name CB or name HA or name HB1 or name HB2 or name HB3)) or resid 531 thr \ ough 586 or resid 600 through 650 or (resid 651 and (name N or name CA or name C \ or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or resid \ 664 through 1272)) } 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: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 32.090 Find NCS groups from input model: 0.480 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: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 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 : 0.003 0.123 19375 Z= 0.152 Angle : 0.593 12.559 26376 Z= 0.297 Chirality : 0.040 0.197 3031 Planarity : 0.005 0.130 3455 Dihedral : 17.181 124.054 7045 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.47 % Favored : 94.45 % Rotamer: Outliers : 0.20 % Allowed : 22.45 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.06 (0.18), residues: 2486 helix: 1.56 (0.17), residues: 1081 sheet: -1.57 (0.31), residues: 263 loop : -1.25 (0.19), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 950 TYR 0.012 0.001 TYR B 951 PHE 0.022 0.001 PHE A 607 TRP 0.014 0.001 TRP B 156 HIS 0.006 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00338 (19373) covalent geometry : angle 0.59279 (26376) hydrogen bonds : bond 0.17204 ( 868) hydrogen bonds : angle 6.29933 ( 2463) Misc. bond : bond 0.03974 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 153 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1054 ARG cc_start: 0.8777 (mtp-110) cc_final: 0.8523 (mtp85) outliers start: 4 outliers final: 3 residues processed: 155 average time/residue: 0.2828 time to fit residues: 67.4143 Evaluate side-chains 147 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1251 ASP Chi-restraints excluded: chain B residue 705 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.4980 chunk 247 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1078 ASN A1140 GLN A1227 GLN B1078 ASN B1091 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.092775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.071185 restraints weight = 161509.576| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 4.07 r_work: 0.3131 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19375 Z= 0.180 Angle : 0.580 6.344 26376 Z= 0.301 Chirality : 0.040 0.144 3031 Planarity : 0.005 0.065 3455 Dihedral : 7.219 103.960 2722 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.36 % Favored : 93.60 % Rotamer: Outliers : 1.98 % Allowed : 20.43 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.19 (0.18), residues: 2486 helix: 1.50 (0.16), residues: 1086 sheet: -1.51 (0.31), residues: 274 loop : -1.41 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 950 TYR 0.010 0.001 TYR A1248 PHE 0.020 0.001 PHE A 341 TRP 0.008 0.001 TRP B1226 HIS 0.005 0.001 HIS B1249 Details of bonding type rmsd covalent geometry : bond 0.00391 (19373) covalent geometry : angle 0.57959 (26376) hydrogen bonds : bond 0.04358 ( 868) hydrogen bonds : angle 5.03764 ( 2463) Misc. bond : bond 0.00243 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1042 HIS cc_start: 0.7688 (OUTLIER) cc_final: 0.7408 (m-70) REVERT: A 1054 ARG cc_start: 0.8880 (mtp-110) cc_final: 0.8644 (mtp85) REVERT: B 157 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8312 (tm-30) REVERT: B 550 ASP cc_start: 0.6669 (OUTLIER) cc_final: 0.5952 (p0) REVERT: B 705 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8164 (tp30) REVERT: C 45 ASP cc_start: 0.6995 (m-30) cc_final: 0.6702 (m-30) outliers start: 40 outliers final: 18 residues processed: 182 average time/residue: 0.2958 time to fit residues: 84.5689 Evaluate side-chains 162 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1140 GLN Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 749 MET Chi-restraints excluded: chain C residue 70 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 132 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 180 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN A1140 GLN B 665 GLN B 897 GLN B1078 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.091638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.070069 restraints weight = 162767.770| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 4.05 r_work: 0.3118 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19375 Z= 0.188 Angle : 0.557 6.175 26376 Z= 0.290 Chirality : 0.040 0.153 3031 Planarity : 0.004 0.052 3455 Dihedral : 6.890 103.187 2720 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.68 % Favored : 93.28 % Rotamer: Outliers : 1.63 % Allowed : 21.17 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.19 (0.17), residues: 2486 helix: 1.55 (0.16), residues: 1075 sheet: -1.44 (0.31), residues: 274 loop : -1.47 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1168 TYR 0.011 0.001 TYR B1018 PHE 0.017 0.001 PHE A 607 TRP 0.009 0.001 TRP B1226 HIS 0.004 0.001 HIS B 540 Details of bonding type rmsd covalent geometry : bond 0.00414 (19373) covalent geometry : angle 0.55737 (26376) hydrogen bonds : bond 0.04224 ( 868) hydrogen bonds : angle 4.83521 ( 2463) Misc. bond : bond 0.00096 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1027 ASP cc_start: 0.8184 (m-30) cc_final: 0.7733 (m-30) REVERT: A 1042 HIS cc_start: 0.7728 (OUTLIER) cc_final: 0.7413 (m-70) REVERT: A 1054 ARG cc_start: 0.8860 (mtp-110) cc_final: 0.8617 (mtp85) REVERT: A 1140 GLN cc_start: 0.8831 (mm110) cc_final: 0.8437 (mm110) REVERT: B 157 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8352 (tm-30) REVERT: B 550 ASP cc_start: 0.6793 (OUTLIER) cc_final: 0.6054 (p0) outliers start: 33 outliers final: 24 residues processed: 170 average time/residue: 0.2854 time to fit residues: 75.8667 Evaluate side-chains 169 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1251 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 730 ASN Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1169 SER Chi-restraints excluded: chain C residue 70 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 178 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 224 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN ** A 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 ASN B 92 GLN B 497 ASN B1078 ASN B1093 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.089714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.068373 restraints weight = 163161.625| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.98 r_work: 0.3076 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19375 Z= 0.247 Angle : 0.595 6.342 26376 Z= 0.313 Chirality : 0.041 0.147 3031 Planarity : 0.005 0.047 3455 Dihedral : 6.425 100.796 2717 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.05 % Favored : 91.91 % Rotamer: Outliers : 2.67 % Allowed : 20.52 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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 (0.17), residues: 2486 helix: 1.33 (0.16), residues: 1070 sheet: -1.42 (0.31), residues: 273 loop : -1.67 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1168 TYR 0.013 0.002 TYR B1018 PHE 0.017 0.002 PHE A 607 TRP 0.009 0.001 TRP A1226 HIS 0.006 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00538 (19373) covalent geometry : angle 0.59518 (26376) hydrogen bonds : bond 0.04153 ( 868) hydrogen bonds : angle 4.82010 ( 2463) Misc. bond : bond 0.00114 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 144 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ARG cc_start: 0.8011 (tpm170) cc_final: 0.7642 (tpm170) REVERT: A 1054 ARG cc_start: 0.8870 (mtp-110) cc_final: 0.8634 (mtp85) REVERT: A 1140 GLN cc_start: 0.8746 (mm110) cc_final: 0.8404 (mm110) REVERT: B 7 MET cc_start: 0.8579 (ttp) cc_final: 0.8360 (ptm) REVERT: B 497 ASN cc_start: 0.9425 (OUTLIER) cc_final: 0.9187 (p0) REVERT: B 550 ASP cc_start: 0.7043 (OUTLIER) cc_final: 0.6315 (p0) outliers start: 54 outliers final: 39 residues processed: 184 average time/residue: 0.2875 time to fit residues: 83.6490 Evaluate side-chains 178 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1251 ASP Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 497 ASN Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 749 MET Chi-restraints excluded: chain B residue 1169 SER Chi-restraints excluded: chain B residue 1179 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 70 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 25 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 176 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN B1078 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.090513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.069104 restraints weight = 162153.300| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 4.00 r_work: 0.3092 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19375 Z= 0.160 Angle : 0.548 6.470 26376 Z= 0.282 Chirality : 0.040 0.148 3031 Planarity : 0.004 0.042 3455 Dihedral : 6.025 98.515 2717 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.98 % Allowed : 21.51 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.25 (0.17), residues: 2486 helix: 1.54 (0.16), residues: 1070 sheet: -1.34 (0.31), residues: 268 loop : -1.57 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 55 TYR 0.011 0.001 TYR B1018 PHE 0.017 0.001 PHE A 607 TRP 0.010 0.001 TRP A1226 HIS 0.004 0.001 HIS B 540 Details of bonding type rmsd covalent geometry : bond 0.00356 (19373) covalent geometry : angle 0.54822 (26376) hydrogen bonds : bond 0.03823 ( 868) hydrogen bonds : angle 4.58724 ( 2463) Misc. bond : bond 0.00087 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1054 ARG cc_start: 0.8864 (mtp-110) cc_final: 0.8627 (mtp85) REVERT: A 1140 GLN cc_start: 0.8776 (mm110) cc_final: 0.8281 (mm-40) REVERT: B 550 ASP cc_start: 0.6856 (OUTLIER) cc_final: 0.6183 (p0) REVERT: B 822 GLN cc_start: 0.8820 (mm110) cc_final: 0.8534 (mp10) outliers start: 40 outliers final: 32 residues processed: 170 average time/residue: 0.2750 time to fit residues: 73.6588 Evaluate side-chains 171 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1251 ASP Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 749 MET Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1169 SER Chi-restraints excluded: chain C residue 70 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 117 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 191 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 244 optimal weight: 20.0000 chunk 178 optimal weight: 0.0040 chunk 200 optimal weight: 0.7980 chunk 197 optimal weight: 0.6980 chunk 206 optimal weight: 1.9990 overall best weight: 1.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1078 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.091149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.069699 restraints weight = 161679.692| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 4.02 r_work: 0.3105 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19375 Z= 0.126 Angle : 0.525 6.230 26376 Z= 0.267 Chirality : 0.039 0.147 3031 Planarity : 0.004 0.042 3455 Dihedral : 5.534 95.779 2717 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.73 % Allowed : 21.66 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.02 (0.18), residues: 2486 helix: 1.72 (0.16), residues: 1079 sheet: -1.25 (0.31), residues: 274 loop : -1.45 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 63 TYR 0.011 0.001 TYR A1018 PHE 0.016 0.001 PHE A 607 TRP 0.009 0.001 TRP A1226 HIS 0.004 0.001 HIS B 540 Details of bonding type rmsd covalent geometry : bond 0.00281 (19373) covalent geometry : angle 0.52542 (26376) hydrogen bonds : bond 0.03510 ( 868) hydrogen bonds : angle 4.39256 ( 2463) Misc. bond : bond 0.00132 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ARG cc_start: 0.7969 (tpm170) cc_final: 0.7609 (tpm170) REVERT: A 823 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7450 (tm-30) REVERT: A 1054 ARG cc_start: 0.8857 (mtp-110) cc_final: 0.8623 (mtp85) REVERT: A 1140 GLN cc_start: 0.8725 (mm110) cc_final: 0.8236 (mm-40) REVERT: B 550 ASP cc_start: 0.6826 (OUTLIER) cc_final: 0.6013 (p0) REVERT: B 822 GLN cc_start: 0.8763 (mm110) cc_final: 0.8536 (mp10) outliers start: 35 outliers final: 28 residues processed: 168 average time/residue: 0.2968 time to fit residues: 77.9849 Evaluate side-chains 168 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1251 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1169 SER Chi-restraints excluded: chain C residue 70 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 229 optimal weight: 3.9990 chunk 157 optimal weight: 0.0010 chunk 40 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 69 optimal weight: 0.0770 chunk 209 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 overall best weight: 2.2150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 844 ASN B1078 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.090256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.068827 restraints weight = 162568.800| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 4.01 r_work: 0.3086 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19375 Z= 0.182 Angle : 0.545 6.257 26376 Z= 0.280 Chirality : 0.040 0.144 3031 Planarity : 0.004 0.042 3455 Dihedral : 5.366 95.726 2717 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.88 % Allowed : 21.51 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.09 (0.18), residues: 2486 helix: 1.68 (0.16), residues: 1078 sheet: -1.27 (0.31), residues: 275 loop : -1.51 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1168 TYR 0.013 0.001 TYR A1018 PHE 0.016 0.001 PHE A 607 TRP 0.009 0.001 TRP B1226 HIS 0.004 0.001 HIS B 540 Details of bonding type rmsd covalent geometry : bond 0.00402 (19373) covalent geometry : angle 0.54504 (26376) hydrogen bonds : bond 0.03625 ( 868) hydrogen bonds : angle 4.45288 ( 2463) Misc. bond : bond 0.00111 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 823 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7549 (tm-30) REVERT: A 1054 ARG cc_start: 0.8862 (mtp-110) cc_final: 0.8607 (mtp85) REVERT: A 1140 GLN cc_start: 0.8719 (mm110) cc_final: 0.8390 (mm-40) REVERT: B 550 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.6093 (p0) REVERT: B 822 GLN cc_start: 0.8771 (mm110) cc_final: 0.8517 (mp10) outliers start: 38 outliers final: 30 residues processed: 167 average time/residue: 0.2914 time to fit residues: 76.5915 Evaluate side-chains 171 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1251 ASP Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 749 MET Chi-restraints excluded: chain B residue 989 GLN Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1169 SER Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 70 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 155 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 116 optimal weight: 0.0970 chunk 214 optimal weight: 3.9990 chunk 125 optimal weight: 0.0870 chunk 194 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1078 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.091387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.069946 restraints weight = 160554.583| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 4.02 r_work: 0.3111 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19375 Z= 0.109 Angle : 0.516 6.338 26376 Z= 0.260 Chirality : 0.039 0.147 3031 Planarity : 0.004 0.042 3455 Dihedral : 5.136 97.024 2717 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.63 % Allowed : 21.71 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 0.13 (0.18), residues: 2486 helix: 1.89 (0.16), residues: 1072 sheet: -1.23 (0.31), residues: 278 loop : -1.38 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 55 TYR 0.009 0.001 TYR B1018 PHE 0.016 0.001 PHE A 607 TRP 0.010 0.001 TRP A 403 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00248 (19373) covalent geometry : angle 0.51594 (26376) hydrogen bonds : bond 0.03324 ( 868) hydrogen bonds : angle 4.24781 ( 2463) Misc. bond : bond 0.00081 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ARG cc_start: 0.7967 (tpm170) cc_final: 0.7611 (tpm170) REVERT: A 823 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7431 (tm-30) REVERT: A 1054 ARG cc_start: 0.8870 (mtp-110) cc_final: 0.8560 (mtp85) REVERT: A 1140 GLN cc_start: 0.8696 (mm110) cc_final: 0.8360 (mm-40) REVERT: B 550 ASP cc_start: 0.6772 (OUTLIER) cc_final: 0.6023 (p0) REVERT: B 634 ASP cc_start: 0.8834 (t0) cc_final: 0.8568 (t0) REVERT: B 822 GLN cc_start: 0.8732 (mm110) cc_final: 0.8520 (mp10) outliers start: 33 outliers final: 27 residues processed: 173 average time/residue: 0.2682 time to fit residues: 73.4058 Evaluate side-chains 174 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1251 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 989 GLN Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1169 SER Chi-restraints excluded: chain B residue 1179 SER Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 70 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 33 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 234 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1078 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.091859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.070443 restraints weight = 161723.096| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 4.04 r_work: 0.3124 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19375 Z= 0.103 Angle : 0.508 6.138 26376 Z= 0.255 Chirality : 0.039 0.144 3031 Planarity : 0.004 0.042 3455 Dihedral : 4.853 97.662 2715 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.34 % Allowed : 21.91 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 0.25 (0.18), residues: 2486 helix: 1.98 (0.16), residues: 1079 sheet: -1.18 (0.31), residues: 278 loop : -1.32 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 55 TYR 0.010 0.001 TYR A1018 PHE 0.015 0.001 PHE A 607 TRP 0.010 0.001 TRP A 403 HIS 0.003 0.001 HIS B 540 Details of bonding type rmsd covalent geometry : bond 0.00236 (19373) covalent geometry : angle 0.50780 (26376) hydrogen bonds : bond 0.03105 ( 868) hydrogen bonds : angle 4.13557 ( 2463) Misc. bond : bond 0.00077 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ARG cc_start: 0.7967 (tpm170) cc_final: 0.7626 (tpm170) REVERT: A 503 TYR cc_start: 0.8195 (m-80) cc_final: 0.7973 (m-80) REVERT: A 823 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7473 (tm-30) REVERT: A 1054 ARG cc_start: 0.8863 (mtp-110) cc_final: 0.8611 (mtp85) REVERT: A 1082 ARG cc_start: 0.8112 (ttp-110) cc_final: 0.7760 (ttp-110) REVERT: A 1140 GLN cc_start: 0.8677 (mm110) cc_final: 0.8330 (mm-40) REVERT: B 550 ASP cc_start: 0.6676 (OUTLIER) cc_final: 0.6000 (p0) REVERT: B 634 ASP cc_start: 0.8844 (t0) cc_final: 0.8604 (t0) REVERT: B 822 GLN cc_start: 0.8694 (mm110) cc_final: 0.8444 (mp10) outliers start: 27 outliers final: 23 residues processed: 171 average time/residue: 0.2709 time to fit residues: 73.5026 Evaluate side-chains 173 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 443 CYS Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 989 GLN Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1169 SER Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 70 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 149 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 72 optimal weight: 0.2980 chunk 89 optimal weight: 0.0980 chunk 68 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 0.0040 chunk 35 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1078 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.091959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.070638 restraints weight = 160793.503| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 4.03 r_work: 0.3129 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19375 Z= 0.102 Angle : 0.504 6.682 26376 Z= 0.252 Chirality : 0.039 0.145 3031 Planarity : 0.004 0.043 3455 Dihedral : 4.741 96.951 2715 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.14 % Allowed : 22.06 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 0.33 (0.18), residues: 2486 helix: 2.05 (0.16), residues: 1079 sheet: -1.15 (0.31), residues: 278 loop : -1.29 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 55 TYR 0.009 0.001 TYR B1018 PHE 0.015 0.001 PHE A 607 TRP 0.010 0.001 TRP A 403 HIS 0.003 0.001 HIS A1042 Details of bonding type rmsd covalent geometry : bond 0.00234 (19373) covalent geometry : angle 0.50434 (26376) hydrogen bonds : bond 0.03027 ( 868) hydrogen bonds : angle 4.07589 ( 2463) Misc. bond : bond 0.00071 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 ARG cc_start: 0.7984 (tpm170) cc_final: 0.7637 (tpm170) REVERT: A 503 TYR cc_start: 0.8240 (m-80) cc_final: 0.7957 (m-80) REVERT: A 997 LYS cc_start: 0.9126 (tppp) cc_final: 0.8788 (tppt) REVERT: A 1054 ARG cc_start: 0.8852 (mtp-110) cc_final: 0.8585 (mtp85) REVERT: A 1140 GLN cc_start: 0.8678 (mm110) cc_final: 0.8326 (mm-40) REVERT: B 550 ASP cc_start: 0.6620 (OUTLIER) cc_final: 0.5952 (p0) REVERT: B 634 ASP cc_start: 0.8798 (t0) cc_final: 0.8560 (t0) REVERT: B 686 GLU cc_start: 0.7753 (tp30) cc_final: 0.7452 (tp30) REVERT: B 822 GLN cc_start: 0.8684 (mm110) cc_final: 0.8430 (mp10) outliers start: 23 outliers final: 22 residues processed: 169 average time/residue: 0.2840 time to fit residues: 75.7390 Evaluate side-chains 173 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 443 CYS Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 989 GLN Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1169 SER Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 70 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 175 optimal weight: 20.0000 chunk 226 optimal weight: 8.9990 chunk 228 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 115 optimal weight: 0.0870 chunk 146 optimal weight: 0.0870 chunk 171 optimal weight: 8.9990 overall best weight: 1.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 693 GLN B1078 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.091427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.070136 restraints weight = 161596.992| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 4.00 r_work: 0.3118 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19375 Z= 0.127 Angle : 0.515 6.736 26376 Z= 0.258 Chirality : 0.039 0.143 3031 Planarity : 0.004 0.042 3455 Dihedral : 4.735 95.741 2715 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.34 % Allowed : 21.76 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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 (0.18), residues: 2486 helix: 2.05 (0.16), residues: 1078 sheet: -1.19 (0.31), residues: 279 loop : -1.30 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 55 TYR 0.009 0.001 TYR B1018 PHE 0.020 0.001 PHE A 539 TRP 0.009 0.001 TRP B1226 HIS 0.003 0.001 HIS B 540 Details of bonding type rmsd covalent geometry : bond 0.00289 (19373) covalent geometry : angle 0.51468 (26376) hydrogen bonds : bond 0.03102 ( 868) hydrogen bonds : angle 4.10390 ( 2463) Misc. bond : bond 0.00063 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6236.82 seconds wall clock time: 106 minutes 55.14 seconds (6415.14 seconds total)