Starting phenix.real_space_refine on Sun Jun 15 11:16:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hi4_34812/06_2025/8hi4_34812.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hi4_34812/06_2025/8hi4_34812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hi4_34812/06_2025/8hi4_34812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hi4_34812/06_2025/8hi4_34812.map" model { file = "/net/cci-nas-00/data/ceres_data/8hi4_34812/06_2025/8hi4_34812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hi4_34812/06_2025/8hi4_34812.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.181 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: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 10933 2.51 5 N 3197 2.21 5 O 3249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17432 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1181, 8661 Classifications: {'peptide': 1181} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 61, 'TRANS': 1119} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 422 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 330 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 19, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 23, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 301 Chain: "B" Number of atoms: 8771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1187, 8771 Classifications: {'peptide': 1187} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 61, 'TRANS': 1125} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 349 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 273 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 26, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 236 Time building chain proxies: 10.79, per 1000 atoms: 0.62 Number of scatterers: 17432 At special positions: 0 Unit cell: (97.37, 114.49, 170.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 3249 8.00 N 3197 7.00 C 10933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.81 Conformation dependent library (CDL) restraints added in 2.8 seconds 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4380 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 17 sheets defined 47.2% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 19 through 30 Processing helix chain 'A' and resid 41 through 45 removed outlier: 4.240A pdb=" N GLU A 44 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 88 Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 140 through 150 Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 184 through 197 Processing helix chain 'A' and resid 213 through 228 Processing helix chain 'A' and resid 232 through 241 removed outlier: 3.701A pdb=" N PHE A 238 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N MET A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 272 removed outlier: 3.594A pdb=" N VAL A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 335 Processing helix chain 'A' and resid 349 through 359 removed outlier: 3.905A pdb=" N GLU A 359 " --> pdb=" O VAL A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 403 Processing helix chain 'A' and resid 430 through 438 Processing helix chain 'A' and resid 439 through 456 Processing helix chain 'A' and resid 477 through 502 removed outlier: 3.769A pdb=" N GLN A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 531 through 543 removed outlier: 4.236A pdb=" N CYS A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 566 removed outlier: 3.654A pdb=" N GLY A 566 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 578 Processing helix chain 'A' and resid 595 through 608 Processing helix chain 'A' and resid 617 through 632 removed outlier: 4.283A pdb=" N LEU A 621 " --> pdb=" O ASN A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 669 Processing helix chain 'A' and resid 692 through 704 Processing helix chain 'A' and resid 704 through 722 removed outlier: 3.862A pdb=" N TYR A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) Proline residue: A 716 - end of helix removed outlier: 3.827A pdb=" N ALA A 720 " --> pdb=" O PRO A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 759 removed outlier: 3.798A pdb=" N LYS A 753 " --> pdb=" O TYR A 749 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG A 757 " --> pdb=" O LYS A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 768 removed outlier: 3.554A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 763 through 768' Processing helix chain 'A' and resid 795 through 822 removed outlier: 3.940A pdb=" N GLU A 822 " --> pdb=" O ALA A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 834 Processing helix chain 'A' and resid 848 through 861 removed outlier: 3.672A pdb=" N ARG A 852 " --> pdb=" O PRO A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 888 removed outlier: 3.594A pdb=" N ARG A 879 " --> pdb=" O ALA A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 924 removed outlier: 3.685A pdb=" N ARG A 915 " --> pdb=" O ALA A 911 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A 916 " --> pdb=" O GLN A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 947 removed outlier: 3.649A pdb=" N VAL A 939 " --> pdb=" O THR A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 987 removed outlier: 3.568A pdb=" N LEU A 986 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1012 Processing helix chain 'A' and resid 1024 through 1036 Processing helix chain 'A' and resid 1037 through 1039 No H-bonds generated for 'chain 'A' and resid 1037 through 1039' Processing helix chain 'A' and resid 1052 through 1064 removed outlier: 3.893A pdb=" N TYR A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1107 Processing helix chain 'A' and resid 1107 through 1120 Processing helix chain 'A' and resid 1140 through 1165 removed outlier: 3.613A pdb=" N ALA A1160 " --> pdb=" O ALA A1156 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A1161 " --> pdb=" O THR A1157 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU A1163 " --> pdb=" O GLY A1159 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG A1164 " --> pdb=" O ALA A1160 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A1165 " --> pdb=" O GLU A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1204 Processing helix chain 'B' and resid 20 through 26 Processing helix chain 'B' and resid 51 through 57 Processing helix chain 'B' and resid 74 through 78 removed outlier: 4.490A pdb=" N VAL B 77 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 96 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 131 through 149 removed outlier: 3.714A pdb=" N LEU B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ILE B 142 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 removed outlier: 4.018A pdb=" N ARG B 169 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 183 Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 184 through 197 removed outlier: 4.155A pdb=" N ARG B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.552A pdb=" N TYR B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 241 removed outlier: 3.550A pdb=" N MET B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 269 removed outlier: 4.093A pdb=" N LEU B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 removed outlier: 5.699A pdb=" N ASP B 273 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU B 274 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 277 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 336 removed outlier: 3.847A pdb=" N ALA B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 359 removed outlier: 4.302A pdb=" N GLU B 351 " --> pdb=" O PRO B 347 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU B 359 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 402 Processing helix chain 'B' and resid 427 through 435 removed outlier: 4.002A pdb=" N VAL B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 456 removed outlier: 3.593A pdb=" N TYR B 456 " --> pdb=" O PHE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 501 removed outlier: 3.695A pdb=" N LEU B 483 " --> pdb=" O TYR B 479 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 498 " --> pdb=" O TRP B 494 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU B 499 " --> pdb=" O ARG B 495 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR B 500 " --> pdb=" O HIS B 496 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP B 501 " --> pdb=" O GLU B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 531 through 546 Processing helix chain 'B' and resid 572 through 578 Processing helix chain 'B' and resid 595 through 608 Processing helix chain 'B' and resid 618 through 634 Processing helix chain 'B' and resid 657 through 669 removed outlier: 3.840A pdb=" N LEU B 661 " --> pdb=" O GLY B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 691 Processing helix chain 'B' and resid 692 through 704 Processing helix chain 'B' and resid 704 through 720 removed outlier: 3.985A pdb=" N TYR B 708 " --> pdb=" O LEU B 704 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 710 " --> pdb=" O SER B 706 " (cutoff:3.500A) Proline residue: B 716 - end of helix removed outlier: 4.249A pdb=" N ALA B 720 " --> pdb=" O PRO B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 735 Processing helix chain 'B' and resid 746 through 768 removed outlier: 3.895A pdb=" N LYS B 753 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN B 756 " --> pdb=" O SER B 752 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG B 757 " --> pdb=" O LYS B 753 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ARG B 765 " --> pdb=" O GLU B 761 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N PHE B 766 " --> pdb=" O SER B 762 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY B 768 " --> pdb=" O ALA B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 821 Processing helix chain 'B' and resid 825 through 830 removed outlier: 3.551A pdb=" N LEU B 829 " --> pdb=" O THR B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 836 removed outlier: 3.595A pdb=" N ALA B 835 " --> pdb=" O ASP B 832 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN B 836 " --> pdb=" O LEU B 833 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 832 through 836' Processing helix chain 'B' and resid 837 through 845 removed outlier: 3.688A pdb=" N ALA B 845 " --> pdb=" O ILE B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 862 removed outlier: 3.763A pdb=" N ARG B 852 " --> pdb=" O PRO B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 870 Processing helix chain 'B' and resid 876 through 889 removed outlier: 3.554A pdb=" N LEU B 881 " --> pdb=" O ILE B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 926 Processing helix chain 'B' and resid 935 through 947 removed outlier: 3.549A pdb=" N VAL B 939 " --> pdb=" O THR B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1012 removed outlier: 4.006A pdb=" N GLU B1012 " --> pdb=" O THR B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1036 Processing helix chain 'B' and resid 1052 through 1063 Processing helix chain 'B' and resid 1095 through 1107 Processing helix chain 'B' and resid 1107 through 1117 Processing helix chain 'B' and resid 1138 through 1141 Processing helix chain 'B' and resid 1142 through 1165 removed outlier: 3.540A pdb=" N GLU B1163 " --> pdb=" O GLY B1159 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG B1164 " --> pdb=" O ALA B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1191 through 1207 removed outlier: 3.674A pdb=" N VAL B1199 " --> pdb=" O LEU B1195 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 163 removed outlier: 7.394A pdb=" N VAL A 160 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ILE A 206 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASN A 162 " --> pdb=" O ILE A 206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 298 removed outlier: 6.380A pdb=" N THR A 297 " --> pdb=" O TYR A 556 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 378 through 382 removed outlier: 6.985A pdb=" N VAL A 340 " --> pdb=" O ARG A 379 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL A 381 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE A 342 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS A 407 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366 removed outlier: 4.260A pdb=" N ALA A 365 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 463 through 465 removed outlier: 5.625A pdb=" N HIS A 463 " --> pdb=" O TRP A 518 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 610 through 614 removed outlier: 6.946A pdb=" N ALA A 724 " --> pdb=" O GLN A 772 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 775 through 776 removed outlier: 6.863A pdb=" N ALA A 775 " --> pdb=" O PHE A 957 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 990 through 994 removed outlier: 3.946A pdb=" N ILE A1047 " --> pdb=" O LEU A1020 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1070 through 1071 removed outlier: 7.035A pdb=" N VAL A1070 " --> pdb=" O THR A1126 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL A1128 " --> pdb=" O VAL A1070 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A1125 " --> pdb=" O ASN A1172 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL A1174 " --> pdb=" O VAL A1125 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A1127 " --> pdb=" O VAL A1174 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 163 removed outlier: 6.426A pdb=" N VAL B 160 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE B 206 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ASN B 162 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N PHE B 283 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N THR B 205 " --> pdb=" O PHE B 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 314 through 319 removed outlier: 7.527A pdb=" N VAL B 340 " --> pdb=" O ARG B 379 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N VAL B 381 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE B 342 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 463 through 464 removed outlier: 5.785A pdb=" N HIS B 463 " --> pdb=" O TRP B 518 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 521 through 523 removed outlier: 6.461A pdb=" N GLN B 521 " --> pdb=" O LEU B 555 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 646 through 647 removed outlier: 8.948A pdb=" N PHE B 647 " --> pdb=" O VAL B 611 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU B 613 " --> pdb=" O PHE B 647 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR B 590 " --> pdb=" O ILE B 676 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA B 724 " --> pdb=" O GLN B 772 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ASN B 774 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 726 " --> pdb=" O ASN B 774 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE B 776 " --> pdb=" O VAL B 726 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN B 728 " --> pdb=" O ILE B 776 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N PHE B 957 " --> pdb=" O ILE B 773 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA B 775 " --> pdb=" O PHE B 957 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 990 through 994 removed outlier: 3.768A pdb=" N VAL B1045 " --> pdb=" O VAL B1018 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE B1047 " --> pdb=" O LEU B1020 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1071 through 1072 729 hydrogen bonds defined for protein. 2109 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: 6.49 Time building geometry restraints manager: 5.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5525 1.34 - 1.46: 2419 1.46 - 1.58: 9714 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 17756 Sorted by residual: bond pdb=" N ILE A 247 " pdb=" CA ILE A 247 " ideal model delta sigma weight residual 1.459 1.493 -0.035 9.10e-03 1.21e+04 1.44e+01 bond pdb=" N LYS B 977 " pdb=" CA LYS B 977 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.38e+01 bond pdb=" N SER A 867 " pdb=" CA SER A 867 " ideal model delta sigma weight residual 1.458 1.490 -0.031 9.00e-03 1.23e+04 1.22e+01 bond pdb=" N VAL A 567 " pdb=" CA VAL A 567 " ideal model delta sigma weight residual 1.458 1.500 -0.041 1.19e-02 7.06e+03 1.21e+01 bond pdb=" N VAL B1046 " pdb=" CA VAL B1046 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.18e-02 7.18e+03 1.08e+01 ... (remaining 17751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 22954 2.09 - 4.19: 1179 4.19 - 6.28: 59 6.28 - 8.37: 9 8.37 - 10.46: 2 Bond angle restraints: 24203 Sorted by residual: angle pdb=" C PHE A1141 " pdb=" CA PHE A1141 " pdb=" CB PHE A1141 " ideal model delta sigma weight residual 110.92 102.62 8.30 1.59e+00 3.96e-01 2.72e+01 angle pdb=" C ALA B 679 " pdb=" N GLY B 680 " pdb=" CA GLY B 680 " ideal model delta sigma weight residual 121.65 118.34 3.31 6.80e-01 2.16e+00 2.36e+01 angle pdb=" C TYR B 369 " pdb=" CA TYR B 369 " pdb=" CB TYR B 369 " ideal model delta sigma weight residual 117.23 110.63 6.60 1.36e+00 5.41e-01 2.36e+01 angle pdb=" CA GLY B 683 " pdb=" C GLY B 683 " pdb=" O GLY B 683 " ideal model delta sigma weight residual 122.56 118.10 4.46 1.03e+00 9.43e-01 1.87e+01 angle pdb=" C GLU B1163 " pdb=" N ARG B1164 " pdb=" CA ARG B1164 " ideal model delta sigma weight residual 120.44 115.13 5.31 1.30e+00 5.92e-01 1.67e+01 ... (remaining 24198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 9386 17.80 - 35.59: 991 35.59 - 53.39: 256 53.39 - 71.18: 36 71.18 - 88.98: 20 Dihedral angle restraints: 10689 sinusoidal: 3899 harmonic: 6790 Sorted by residual: dihedral pdb=" CA ASP B 367 " pdb=" CB ASP B 367 " pdb=" CG ASP B 367 " pdb=" OD1 ASP B 367 " ideal model delta sinusoidal sigma weight residual -30.00 -89.96 59.96 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CB GLU B 902 " pdb=" CG GLU B 902 " pdb=" CD GLU B 902 " pdb=" OE1 GLU B 902 " ideal model delta sinusoidal sigma weight residual 0.00 88.98 -88.98 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CG ARG A 932 " pdb=" CD ARG A 932 " pdb=" NE ARG A 932 " pdb=" CZ ARG A 932 " ideal model delta sinusoidal sigma weight residual 90.00 134.47 -44.47 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 10686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2062 0.056 - 0.113: 554 0.113 - 0.169: 173 0.169 - 0.226: 40 0.226 - 0.282: 3 Chirality restraints: 2832 Sorted by residual: chirality pdb=" CA VAL B 562 " pdb=" N VAL B 562 " pdb=" C VAL B 562 " pdb=" CB VAL B 562 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ILE A 776 " pdb=" N ILE A 776 " pdb=" C ILE A 776 " pdb=" CB ILE A 776 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB VAL A 426 " pdb=" CA VAL A 426 " pdb=" CG1 VAL A 426 " pdb=" CG2 VAL A 426 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2829 not shown) Planarity restraints: 3213 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 811 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" CD GLU B 811 " -0.059 2.00e-02 2.50e+03 pdb=" OE1 GLU B 811 " 0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU B 811 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 874 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" CG ASN B 874 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN B 874 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN B 874 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 547 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C ASP A 547 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP A 547 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG A 548 " -0.014 2.00e-02 2.50e+03 ... (remaining 3210 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2776 2.77 - 3.30: 17962 3.30 - 3.83: 28193 3.83 - 4.37: 31982 4.37 - 4.90: 54469 Nonbonded interactions: 135382 Sorted by model distance: nonbonded pdb=" O LEU B 858 " pdb=" OG SER B 862 " model vdw 2.231 3.040 nonbonded pdb=" O GLU B 438 " pdb=" OG1 THR B 442 " model vdw 2.281 3.040 nonbonded pdb=" OG SER B 129 " pdb=" OE2 GLU B 130 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR A1095 " pdb=" OE1 GLU A1098 " model vdw 2.302 3.040 nonbonded pdb=" O SER A1092 " pdb=" OG SER A1092 " model vdw 2.303 3.040 ... (remaining 135377 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 19 through 51 or (resid 52 through 66 and (name N or name \ CA or name C or name O or name CB )) or resid 67 through 80 or (resid 81 through \ 82 and (name N or name CA or name C or name O or name CB )) or resid 83 or (res \ id 84 and (name N or name CA or name C or name O or name CB )) or resid 85 throu \ gh 246 or (resid 247 and (name N or name CA or name C or name O or name CB )) or \ resid 248 through 251 or (resid 252 and (name N or name CA or name C or name O \ or name CB )) or resid 253 through 269 or (resid 270 through 271 and (name N or \ name CA or name C or name O or name CB )) or resid 272 or (resid 273 and (name N \ or name CA or name C or name O or name CB )) or resid 274 through 322 or (resid \ 323 and (name N or name CA or name C or name O or name CB )) or resid 324 throu \ gh 332 or (resid 333 and (name N or name CA or name C or name O or name CB )) or \ resid 334 through 363 or (resid 364 through 366 and (name N or name CA or name \ C or name O or name CB )) or resid 367 through 374 or (resid 375 through 376 and \ (name N or name CA or name C or name O or name CB )) or resid 377 through 490 o \ r (resid 491 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 92 through 509 or (resid 510 and (name N or name CA or name C or name O or name \ CB )) or resid 511 or (resid 512 and (name N or name CA or name C or name O or n \ ame CB )) or resid 513 through 551 or (resid 552 and (name N or name CA or name \ C or name O or name CB )) or resid 553 through 558 or (resid 559 through 560 and \ (name N or name CA or name C or name O or name CB )) or resid 561 through 706 o \ r (resid 707 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 08 through 783 or (resid 794 through 796 and (name N or name CA or name C or nam \ e O or name CB )) or resid 797 through 806 or (resid 807 through 808 and (name N \ or name CA or name C or name O or name CB )) or resid 809 through 816 or (resid \ 817 through 819 and (name N or name CA or name C or name O or name CB )) or res \ id 820 through 842 or (resid 843 and (name N or name CA or name C or name O or n \ ame CB )) or resid 844 through 856 or (resid 857 and (name N or name CA or name \ C or name O or name CB )) or resid 858 through 889 or (resid 890 through 893 and \ (name N or name CA or name C or name O or name CB )) or resid 894 through 965 o \ r (resid 966 through 967 and (name N or name CA or name C or name O or name CB ) \ ) or resid 968 through 969 or (resid 970 and (name N or name CA or name C or nam \ e O or name CB )) or resid 971 through 972 or (resid 973 through 974 and (name N \ or name CA or name C or name O or name CB )) or resid 975 through 979 or (resid \ 980 through 981 and (name N or name CA or name C or name O or name CB )) or res \ id 982 through 995 or (resid 996 and (name N or name CA or name C or name O or n \ ame CB )) or resid 997 through 1017 or (resid 1018 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1019 through 1034 or (resid 1035 through 10 \ 41 and (name N or name CA or name C or name O or name CB )) or resid 1042 throug \ h 1132 or (resid 1133 through 1136 and (name N or name CA or name C or name O or \ name CB )) or resid 1137 through 1183 or (resid 1184 and (name N or name CA or \ name C or name O or name CB )) or resid 1185 through 1186 or (resid 1187 through \ 1189 and (name N or name CA or name C or name O or name CB )) or resid 1190 or \ (resid 1191 through 1193 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1194 through 1203 or (resid 1204 and (name N or name CA or name C or \ name O or name CB )) or resid 1205 through 1208)) selection = (chain 'B' and (resid 19 or (resid 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 31 or (resid 32 and (name N or name CA or nam \ e C or name O or name CB )) or resid 33 through 36 or (resid 37 and (name N or n \ ame CA or name C or name O or name CB )) or resid 38 through 40 or (resid 41 thr \ ough 49 and (name N or name CA or name C or name O or name CB )) or resid 50 thr \ ough 53 or (resid 54 through 66 and (name N or name CA or name C or name O or na \ me CB )) or resid 67 or (resid 68 through 69 and (name N or name CA or name C or \ name O or name CB )) or resid 70 through 73 or (resid 74 through 75 and (name N \ or name CA or name C or name O or name CB )) or resid 76 through 77 or (resid 7 \ 8 through 79 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 0 through 85 or (resid 86 and (name N or name CA or name C or name O or name CB \ )) or resid 87 through 89 or (resid 90 and (name N or name CA or name C or name \ O or name CB )) or resid 91 through 92 or (resid 93 and (name N or name CA or na \ me C or name O or name CB )) or resid 94 or (resid 95 through 97 and (name N or \ name CA or name C or name O or name CB )) or resid 98 or (resid 99 through 102 a \ nd (name N or name CA or name C or name O or name CB )) or resid 103 or (resid 1 \ 04 through 105 and (name N or name CA or name C or name O or name CB )) or resid \ 106 through 129 or (resid 130 and (name N or name CA or name C or name O or nam \ e CB )) or resid 131 through 142 or (resid 143 and (name N or name CA or name C \ or name O or name CB )) or resid 144 through 158 or (resid 159 and (name N or na \ me CA or name C or name O or name CB )) or resid 160 through 212 or (resid 213 t \ hrough 214 and (name N or name CA or name C or name O or name CB )) or resid 215 \ or (resid 216 through 217 and (name N or name CA or name C or name O or name CB \ )) or resid 218 through 223 or (resid 224 through 225 and (name N or name CA or \ name C or name O or name CB )) or resid 226 or (resid 227 and (name N or name C \ A or name C or name O or name CB )) or resid 228 through 243 or (resid 244 and ( \ name N or name CA or name C or name O or name CB )) or resid 245 through 278 or \ (resid 279 and (name N or name CA or name C or name O or name CB )) or resid 280 \ through 293 or (resid 294 and (name N or name CA or name C or name O or name CB \ )) or resid 295 through 436 or (resid 437 and (name N or name CA or name C or n \ ame O or name CB )) or resid 438 through 459 or (resid 460 through 461 and (name \ N or name CA or name C or name O or name CB )) or resid 462 through 472 or (res \ id 473 and (name N or name CA or name C or name O or name CB )) or resid 474 or \ (resid 475 and (name N or name CA or name C or name O or name CB )) or resid 476 \ through 488 or (resid 489 and (name N or name CA or name C or name O or name CB \ )) or resid 490 through 507 or (resid 508 through 510 and (name N or name CA or \ name C or name O or name CB )) or resid 511 through 529 or (resid 530 through 5 \ 31 and (name N or name CA or name C or name O or name CB )) or resid 532 through \ 630 or (resid 631 and (name N or name CA or name C or name O or name CB )) or r \ esid 632 through 635 or (resid 636 and (name N or name CA or name C or name O or \ name CB )) or resid 637 through 638 or (resid 639 through 640 and (name N or na \ me CA or name C or name O or name CB )) or resid 641 through 794 or (resid 795 t \ hrough 796 and (name N or name CA or name C or name O or name CB )) or resid 797 \ or (resid 798 and (name N or name CA or name C or name O or name CB )) or resid \ 799 through 810 or (resid 811 and (name N or name CA or name C or name O or nam \ e CB )) or resid 812 through 828 or (resid 829 and (name N or name CA or name C \ or name O or name CB )) or resid 830 through 833 or (resid 834 through 843 and ( \ name N or name CA or name C or name O or name CB )) or resid 844 through 858 or \ (resid 859 through 860 and (name N or name CA or name C or name O or name CB )) \ or resid 861 through 920 or (resid 921 and (name N or name CA or name C or name \ O or name CB )) or resid 922 through 923 or (resid 924 and (name N or name CA or \ name C or name O or name CB )) or resid 925 through 976 or (resid 977 and (name \ N or name CA or name C or name O or name CB )) or resid 978 through 984 or (res \ id 985 and (name N or name CA or name C or name O or name CB )) or resid 986 thr \ ough 1029 or (resid 1030 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1031 through 1051 or (resid 1052 and (name N or name CA or name C or \ name O or name CB )) or resid 1053 through 1056 or (resid 1057 and (name N or na \ me CA or name C or name O or name CB )) or resid 1058 through 1062 or (resid 106 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 1064 through \ 1079 or (resid 1080 through 1082 and (name N or name CA or name C or name O or \ name CB )) or resid 1083 through 1085 or (resid 1086 through 1087 and (name N or \ name CA or name C or name O or name CB )) or resid 1088 through 1138 or (resid \ 1139 and (name N or name CA or name C or name O or name CB )) or resid 1140 thro \ ugh 1176 or (resid 1177 and (name N or name CA or name C or name O or name CB )) \ or resid 1178 through 1180 or (resid 1181 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1182 through 1208)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 43.310 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.080 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: 0.020 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 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 : 0.006 0.041 17756 Z= 0.454 Angle : 0.871 10.465 24203 Z= 0.616 Chirality : 0.061 0.282 2832 Planarity : 0.004 0.047 3213 Dihedral : 15.951 88.976 6309 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.35 % Allowed : 25.93 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.17), residues: 2360 helix: -0.07 (0.17), residues: 982 sheet: -2.10 (0.34), residues: 230 loop : -2.49 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 539 HIS 0.005 0.001 HIS B 417 PHE 0.012 0.001 PHE A 299 TYR 0.018 0.001 TYR A 732 ARG 0.007 0.000 ARG B 853 Details of bonding type rmsd hydrogen bonds : bond 0.15780 ( 729) hydrogen bonds : angle 6.55793 ( 2109) covalent geometry : bond 0.00605 (17756) covalent geometry : angle 0.87135 (24203) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 244 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASN cc_start: 0.5247 (p0) cc_final: 0.4930 (m110) REVERT: A 677 ASN cc_start: 0.5802 (m-40) cc_final: 0.5475 (m110) outliers start: 6 outliers final: 1 residues processed: 249 average time/residue: 0.4668 time to fit residues: 169.6603 Evaluate side-chains 183 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1129 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 120 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 71 optimal weight: 0.0270 chunk 112 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 chunk 214 optimal weight: 2.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 287 HIS ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 ASN ** A 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 GLN A 756 GLN A 774 ASN A1109 HIS A1110 HIS A1152 HIS A1196 GLN B 96 HIS B 125 GLN B 138 ASN B 281 HIS B 474 GLN ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 ASN B 509 GLN B 620 GLN B 717 GLN B 756 GLN B1109 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.241941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.211158 restraints weight = 21985.879| |-----------------------------------------------------------------------------| r_work (start): 0.4419 rms_B_bonded: 2.77 r_work: 0.4077 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17756 Z= 0.130 Angle : 0.595 11.013 24203 Z= 0.302 Chirality : 0.042 0.158 2832 Planarity : 0.004 0.042 3213 Dihedral : 3.943 19.311 2584 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.17 % Allowed : 24.93 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.17), residues: 2360 helix: 0.54 (0.17), residues: 1004 sheet: -1.97 (0.33), residues: 241 loop : -2.20 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 144 HIS 0.005 0.001 HIS A 496 PHE 0.018 0.001 PHE A1146 TYR 0.018 0.001 TYR B1064 ARG 0.006 0.000 ARG B1081 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 729) hydrogen bonds : angle 4.75768 ( 2109) covalent geometry : bond 0.00281 (17756) covalent geometry : angle 0.59539 (24203) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 206 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.6341 (OUTLIER) cc_final: 0.5392 (t80) REVERT: A 204 ASN cc_start: 0.4698 (p0) cc_final: 0.4248 (m110) REVERT: A 242 MET cc_start: 0.5671 (tmm) cc_final: 0.5400 (tmm) REVERT: A 808 ARG cc_start: 0.7548 (mmm160) cc_final: 0.7120 (mtp85) REVERT: B 76 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7367 (pt0) REVERT: B 224 ASP cc_start: 0.6883 (p0) cc_final: 0.6681 (p0) REVERT: B 284 GLU cc_start: 0.6078 (OUTLIER) cc_final: 0.5584 (pt0) REVERT: B 369 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.5939 (t80) REVERT: B 624 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6491 (ttm) REVERT: B 767 LEU cc_start: 0.7046 (mt) cc_final: 0.6625 (mt) REVERT: B 897 ARG cc_start: 0.7906 (ptt180) cc_final: 0.7385 (pmt170) REVERT: B 1161 GLU cc_start: 0.6589 (mt-10) cc_final: 0.6347 (mt-10) outliers start: 71 outliers final: 36 residues processed: 262 average time/residue: 0.3295 time to fit residues: 127.8836 Evaluate side-chains 225 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 759 MET Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 624 MET Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 717 GLN Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1057 ILE Chi-restraints excluded: chain B residue 1070 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 194 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 178 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 223 optimal weight: 8.9990 chunk 144 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 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 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 HIS ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN B 678 ASN B 774 ASN B 894 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.235603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.203796 restraints weight = 21776.054| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 2.98 r_work: 0.3979 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17756 Z= 0.197 Angle : 0.661 11.775 24203 Z= 0.336 Chirality : 0.044 0.306 2832 Planarity : 0.005 0.042 3213 Dihedral : 4.412 21.486 2583 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 4.70 % Allowed : 25.34 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.17), residues: 2360 helix: 0.36 (0.17), residues: 997 sheet: -2.24 (0.31), residues: 256 loop : -2.15 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 494 HIS 0.016 0.002 HIS B 436 PHE 0.026 0.002 PHE A1146 TYR 0.027 0.002 TYR B 207 ARG 0.006 0.000 ARG B1164 Details of bonding type rmsd hydrogen bonds : bond 0.04740 ( 729) hydrogen bonds : angle 4.82748 ( 2109) covalent geometry : bond 0.00464 (17756) covalent geometry : angle 0.66115 (24203) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 193 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.6587 (OUTLIER) cc_final: 0.5410 (t80) REVERT: A 204 ASN cc_start: 0.4701 (p0) cc_final: 0.4256 (m110) REVERT: A 438 GLU cc_start: 0.5065 (OUTLIER) cc_final: 0.4635 (tt0) REVERT: A 472 ASP cc_start: 0.4940 (OUTLIER) cc_final: 0.3837 (t70) REVERT: A 808 ARG cc_start: 0.7385 (mmm160) cc_final: 0.6922 (mtp85) REVERT: B 223 MET cc_start: 0.7277 (tpt) cc_final: 0.6664 (tpt) REVERT: B 284 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.5858 (pt0) REVERT: B 369 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.5860 (t80) REVERT: B 433 ARG cc_start: 0.5718 (tmm160) cc_final: 0.5450 (tmm160) REVERT: B 624 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6451 (ttm) REVERT: B 1049 THR cc_start: 0.8898 (m) cc_final: 0.8503 (t) outliers start: 80 outliers final: 57 residues processed: 257 average time/residue: 0.3257 time to fit residues: 124.1117 Evaluate side-chains 239 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 176 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 759 MET Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1100 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 496 HIS Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 624 MET Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1057 ILE Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1197 ARG Chi-restraints excluded: chain B residue 1205 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 187 optimal weight: 3.9990 chunk 93 optimal weight: 0.0870 chunk 13 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 21 optimal weight: 30.0000 chunk 214 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 86 optimal weight: 8.9990 overall best weight: 1.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN B 717 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.236419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.204064 restraints weight = 22014.894| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 2.88 r_work: 0.4010 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17756 Z= 0.140 Angle : 0.599 13.584 24203 Z= 0.302 Chirality : 0.042 0.237 2832 Planarity : 0.004 0.043 3213 Dihedral : 4.215 20.673 2583 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 5.29 % Allowed : 25.98 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.17), residues: 2360 helix: 0.52 (0.17), residues: 998 sheet: -2.17 (0.31), residues: 251 loop : -2.10 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 696 HIS 0.005 0.001 HIS A 406 PHE 0.019 0.001 PHE A1146 TYR 0.018 0.002 TYR A 525 ARG 0.005 0.000 ARG B 447 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 729) hydrogen bonds : angle 4.55430 ( 2109) covalent geometry : bond 0.00320 (17756) covalent geometry : angle 0.59869 (24203) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 191 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: A 172 TYR cc_start: 0.6503 (OUTLIER) cc_final: 0.5039 (t80) REVERT: A 204 ASN cc_start: 0.4151 (p0) cc_final: 0.3783 (m110) REVERT: A 438 GLU cc_start: 0.5069 (OUTLIER) cc_final: 0.4660 (tt0) REVERT: A 808 ARG cc_start: 0.7408 (mmm160) cc_final: 0.6990 (mtp85) REVERT: A 918 ILE cc_start: 0.7837 (mm) cc_final: 0.7607 (mm) REVERT: A 1169 VAL cc_start: 0.7346 (OUTLIER) cc_final: 0.7142 (m) REVERT: B 76 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7444 (pt0) REVERT: B 172 TYR cc_start: 0.6092 (OUTLIER) cc_final: 0.5294 (t80) REVERT: B 223 MET cc_start: 0.7231 (tpt) cc_final: 0.6717 (tpt) REVERT: B 284 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.5848 (pt0) REVERT: B 329 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.5943 (mt) REVERT: B 369 TYR cc_start: 0.7389 (OUTLIER) cc_final: 0.5823 (t80) REVERT: B 624 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6332 (ttm) REVERT: B 999 ARG cc_start: 0.4050 (OUTLIER) cc_final: 0.3761 (ptm-80) REVERT: B 1049 THR cc_start: 0.8844 (m) cc_final: 0.8473 (t) REVERT: B 1161 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6685 (mt-10) outliers start: 90 outliers final: 61 residues processed: 265 average time/residue: 0.3065 time to fit residues: 121.9137 Evaluate side-chains 250 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 179 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 759 MET Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1100 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1152 HIS Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 624 MET Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 717 GLN Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 933 MET Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 999 ARG Chi-restraints excluded: chain B residue 1057 ILE Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1197 ARG Chi-restraints excluded: chain B residue 1205 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 132 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 229 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 227 optimal weight: 6.9990 chunk 202 optimal weight: 30.0000 chunk 180 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.230909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.198471 restraints weight = 22037.326| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 3.13 r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 17756 Z= 0.258 Angle : 0.736 14.279 24203 Z= 0.376 Chirality : 0.046 0.305 2832 Planarity : 0.006 0.044 3213 Dihedral : 4.989 27.191 2583 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 6.53 % Allowed : 25.75 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.17), residues: 2360 helix: 0.08 (0.16), residues: 998 sheet: -2.45 (0.31), residues: 256 loop : -2.27 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 494 HIS 0.011 0.001 HIS A 406 PHE 0.023 0.002 PHE A1146 TYR 0.031 0.003 TYR B 207 ARG 0.005 0.001 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.05362 ( 729) hydrogen bonds : angle 4.95299 ( 2109) covalent geometry : bond 0.00616 (17756) covalent geometry : angle 0.73589 (24203) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 194 time to evaluate : 1.947 Fit side-chains revert: symmetry clash REVERT: A 172 TYR cc_start: 0.6506 (OUTLIER) cc_final: 0.5215 (t80) REVERT: A 438 GLU cc_start: 0.5052 (OUTLIER) cc_final: 0.4620 (tt0) REVERT: A 472 ASP cc_start: 0.5066 (OUTLIER) cc_final: 0.3897 (t0) REVERT: A 736 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6770 (tp30) REVERT: A 847 MET cc_start: 0.5002 (mpp) cc_final: 0.4641 (mpp) REVERT: A 918 ILE cc_start: 0.8033 (mm) cc_final: 0.7791 (mm) REVERT: A 1152 HIS cc_start: 0.5948 (OUTLIER) cc_final: 0.5630 (m90) REVERT: B 111 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6837 (ptp-110) REVERT: B 148 ARG cc_start: 0.6948 (OUTLIER) cc_final: 0.6615 (mpp80) REVERT: B 172 TYR cc_start: 0.6001 (OUTLIER) cc_final: 0.5161 (t80) REVERT: B 284 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.5898 (pt0) REVERT: B 329 LEU cc_start: 0.6173 (OUTLIER) cc_final: 0.5797 (mt) REVERT: B 369 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.6389 (t80) REVERT: B 572 PHE cc_start: 0.6225 (OUTLIER) cc_final: 0.5807 (m-10) REVERT: B 624 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6558 (ttm) REVERT: B 696 TRP cc_start: 0.7042 (t-100) cc_final: 0.6459 (t-100) outliers start: 111 outliers final: 76 residues processed: 283 average time/residue: 0.3111 time to fit residues: 133.0118 Evaluate side-chains 269 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 180 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 759 MET Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1100 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1152 HIS Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 572 PHE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 624 MET Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 752 SER Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 993 LEU Chi-restraints excluded: chain B residue 1057 ILE Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1080 ASP Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain B residue 1197 ARG Chi-restraints excluded: chain B residue 1205 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 168 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 120 optimal weight: 30.0000 chunk 140 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 117 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 ASN ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 HIS B 874 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.230593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.197503 restraints weight = 22313.604| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 3.14 r_work: 0.3927 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 17756 Z= 0.230 Angle : 0.712 12.781 24203 Z= 0.362 Chirality : 0.046 0.259 2832 Planarity : 0.005 0.055 3213 Dihedral : 4.989 26.769 2583 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 6.94 % Allowed : 25.51 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.17), residues: 2360 helix: 0.03 (0.16), residues: 1002 sheet: -2.60 (0.31), residues: 251 loop : -2.27 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 494 HIS 0.008 0.001 HIS A 406 PHE 0.022 0.002 PHE A1146 TYR 0.028 0.002 TYR B 525 ARG 0.007 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.05009 ( 729) hydrogen bonds : angle 4.89607 ( 2109) covalent geometry : bond 0.00547 (17756) covalent geometry : angle 0.71169 (24203) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 182 time to evaluate : 1.851 Fit side-chains REVERT: A 172 TYR cc_start: 0.6634 (OUTLIER) cc_final: 0.5199 (t80) REVERT: A 402 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6069 (mt) REVERT: A 438 GLU cc_start: 0.5152 (OUTLIER) cc_final: 0.4682 (tt0) REVERT: A 472 ASP cc_start: 0.5120 (OUTLIER) cc_final: 0.4085 (t0) REVERT: A 696 TRP cc_start: 0.6946 (t-100) cc_final: 0.5983 (t-100) REVERT: A 847 MET cc_start: 0.4716 (mpp) cc_final: 0.4258 (mpp) REVERT: A 918 ILE cc_start: 0.7866 (mm) cc_final: 0.7619 (mm) REVERT: B 76 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7457 (pt0) REVERT: B 148 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.6418 (mpp80) REVERT: B 172 TYR cc_start: 0.6424 (OUTLIER) cc_final: 0.5378 (t80) REVERT: B 223 MET cc_start: 0.7024 (tpt) cc_final: 0.6674 (tpt) REVERT: B 284 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6230 (pt0) REVERT: B 329 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6108 (mt) REVERT: B 342 ILE cc_start: 0.8026 (mp) cc_final: 0.7636 (mt) REVERT: B 369 TYR cc_start: 0.7677 (OUTLIER) cc_final: 0.6591 (t80) REVERT: B 532 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8298 (p0) REVERT: B 624 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6491 (ttm) outliers start: 118 outliers final: 86 residues processed: 278 average time/residue: 0.3000 time to fit residues: 125.1484 Evaluate side-chains 276 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 178 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 759 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1100 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1152 HIS Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 496 HIS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 624 MET Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 717 GLN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 752 SER Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 933 MET Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 993 LEU Chi-restraints excluded: chain B residue 1057 ILE Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1197 ARG Chi-restraints excluded: chain B residue 1205 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 176 optimal weight: 0.8980 chunk 121 optimal weight: 40.0000 chunk 125 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 136 optimal weight: 0.1980 chunk 110 optimal weight: 0.0020 chunk 170 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 chunk 153 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 678 ASN ** A 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.238679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.207857 restraints weight = 22077.254| |-----------------------------------------------------------------------------| r_work (start): 0.4393 rms_B_bonded: 2.73 r_work: 0.4042 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17756 Z= 0.110 Angle : 0.591 13.236 24203 Z= 0.299 Chirality : 0.041 0.164 2832 Planarity : 0.005 0.065 3213 Dihedral : 4.193 20.763 2583 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.76 % Allowed : 29.16 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.17), residues: 2360 helix: 0.59 (0.17), residues: 997 sheet: -2.33 (0.32), residues: 241 loop : -2.09 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 696 HIS 0.016 0.001 HIS B 496 PHE 0.011 0.001 PHE B 299 TYR 0.015 0.001 TYR B 708 ARG 0.014 0.000 ARG A 348 Details of bonding type rmsd hydrogen bonds : bond 0.03388 ( 729) hydrogen bonds : angle 4.40426 ( 2109) covalent geometry : bond 0.00236 (17756) covalent geometry : angle 0.59089 (24203) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 193 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.6496 (OUTLIER) cc_final: 0.4839 (t80) REVERT: A 223 MET cc_start: 0.7769 (tpt) cc_final: 0.7125 (tpt) REVERT: A 289 MET cc_start: 0.7852 (tpp) cc_final: 0.7528 (tpp) REVERT: A 383 LEU cc_start: 0.5929 (OUTLIER) cc_final: 0.5194 (mt) REVERT: A 438 GLU cc_start: 0.4852 (OUTLIER) cc_final: 0.4379 (tt0) REVERT: A 464 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7479 (mtt180) REVERT: A 474 GLN cc_start: 0.6975 (pm20) cc_final: 0.6671 (pm20) REVERT: A 847 MET cc_start: 0.5031 (mpp) cc_final: 0.4613 (mpp) REVERT: A 1102 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6574 (tp) REVERT: B 148 ARG cc_start: 0.6195 (OUTLIER) cc_final: 0.5953 (mpp80) REVERT: B 172 TYR cc_start: 0.6066 (OUTLIER) cc_final: 0.5177 (t80) REVERT: B 223 MET cc_start: 0.6880 (tpt) cc_final: 0.6613 (tpt) REVERT: B 369 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.6120 (t80) REVERT: B 456 TYR cc_start: 0.7955 (m-10) cc_final: 0.7715 (m-10) REVERT: B 624 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.6301 (ttm) REVERT: B 1124 ASN cc_start: 0.7513 (m-40) cc_final: 0.7305 (m-40) REVERT: B 1161 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6560 (mt-10) outliers start: 64 outliers final: 43 residues processed: 242 average time/residue: 0.3256 time to fit residues: 117.0472 Evaluate side-chains 231 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 179 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 996 GLU Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1152 HIS Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 624 MET Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 933 MET Chi-restraints excluded: chain B residue 993 LEU Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain B residue 1197 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 12 optimal weight: 9.9990 chunk 89 optimal weight: 0.0570 chunk 115 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 121 optimal weight: 40.0000 chunk 67 optimal weight: 0.5980 chunk 118 optimal weight: 40.0000 chunk 203 optimal weight: 10.0000 overall best weight: 1.2900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.236933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.205869 restraints weight = 21978.990| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 2.63 r_work: 0.4026 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17756 Z= 0.121 Angle : 0.603 13.623 24203 Z= 0.302 Chirality : 0.042 0.170 2832 Planarity : 0.004 0.043 3213 Dihedral : 4.124 20.292 2583 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.06 % Allowed : 29.22 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.17), residues: 2360 helix: 0.63 (0.17), residues: 998 sheet: -2.29 (0.32), residues: 241 loop : -2.05 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 696 HIS 0.006 0.001 HIS A 997 PHE 0.014 0.001 PHE A1146 TYR 0.015 0.001 TYR A 525 ARG 0.005 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 729) hydrogen bonds : angle 4.35335 ( 2109) covalent geometry : bond 0.00274 (17756) covalent geometry : angle 0.60266 (24203) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 183 time to evaluate : 1.862 Fit side-chains revert: symmetry clash REVERT: A 172 TYR cc_start: 0.6645 (OUTLIER) cc_final: 0.5022 (t80) REVERT: A 223 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7211 (tpt) REVERT: A 289 MET cc_start: 0.7906 (tpp) cc_final: 0.7576 (tpp) REVERT: A 383 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5270 (mt) REVERT: A 402 LEU cc_start: 0.6047 (OUTLIER) cc_final: 0.5541 (mt) REVERT: A 438 GLU cc_start: 0.4743 (OUTLIER) cc_final: 0.4217 (tt0) REVERT: A 474 GLN cc_start: 0.6952 (pm20) cc_final: 0.6673 (pm20) REVERT: A 847 MET cc_start: 0.5094 (mpp) cc_final: 0.4651 (mpp) REVERT: A 1102 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6749 (tp) REVERT: B 76 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7195 (pt0) REVERT: B 148 ARG cc_start: 0.6432 (mpp80) cc_final: 0.6219 (mpp80) REVERT: B 172 TYR cc_start: 0.5851 (OUTLIER) cc_final: 0.5040 (t80) REVERT: B 205 THR cc_start: 0.5164 (OUTLIER) cc_final: 0.4919 (m) REVERT: B 223 MET cc_start: 0.6848 (tpt) cc_final: 0.6583 (tpt) REVERT: B 329 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6477 (mt) REVERT: B 369 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.6062 (t80) REVERT: B 456 TYR cc_start: 0.7839 (m-10) cc_final: 0.7579 (m-10) REVERT: B 624 MET cc_start: 0.6936 (OUTLIER) cc_final: 0.6404 (ttm) REVERT: B 853 ARG cc_start: 0.7701 (mtt90) cc_final: 0.7161 (mtm180) outliers start: 69 outliers final: 49 residues processed: 241 average time/residue: 0.3113 time to fit residues: 113.1316 Evaluate side-chains 240 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 179 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 HIS Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1100 GLU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1152 HIS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 624 MET Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 933 MET Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain B residue 1197 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 139 optimal weight: 9.9990 chunk 165 optimal weight: 0.7980 chunk 145 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 HIS ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.234805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.203369 restraints weight = 21926.642| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 2.83 r_work: 0.3999 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17756 Z= 0.164 Angle : 0.644 13.846 24203 Z= 0.326 Chirality : 0.043 0.206 2832 Planarity : 0.005 0.051 3213 Dihedral : 4.383 22.590 2583 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 4.64 % Allowed : 28.57 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.17), residues: 2360 helix: 0.45 (0.17), residues: 997 sheet: -2.38 (0.32), residues: 237 loop : -2.11 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 539 HIS 0.007 0.001 HIS A 406 PHE 0.020 0.002 PHE A1146 TYR 0.022 0.002 TYR B 525 ARG 0.008 0.000 ARG A 348 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 729) hydrogen bonds : angle 4.50402 ( 2109) covalent geometry : bond 0.00385 (17756) covalent geometry : angle 0.64440 (24203) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 186 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.6660 (OUTLIER) cc_final: 0.4947 (t80) REVERT: A 223 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7222 (tpt) REVERT: A 289 MET cc_start: 0.7942 (tpp) cc_final: 0.7593 (tpp) REVERT: A 383 LEU cc_start: 0.6165 (OUTLIER) cc_final: 0.5442 (mt) REVERT: A 402 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5596 (mt) REVERT: A 438 GLU cc_start: 0.4941 (OUTLIER) cc_final: 0.4394 (tt0) REVERT: A 474 GLN cc_start: 0.7040 (pm20) cc_final: 0.6768 (pm20) REVERT: A 736 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6472 (tp30) REVERT: A 847 MET cc_start: 0.5024 (mpp) cc_final: 0.4606 (mpp) REVERT: A 1102 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6627 (tp) REVERT: B 76 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7121 (pt0) REVERT: B 148 ARG cc_start: 0.6536 (OUTLIER) cc_final: 0.6287 (mpp80) REVERT: B 172 TYR cc_start: 0.5913 (OUTLIER) cc_final: 0.5040 (t80) REVERT: B 329 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6055 (mt) REVERT: B 369 TYR cc_start: 0.7586 (OUTLIER) cc_final: 0.6380 (t80) REVERT: B 456 TYR cc_start: 0.7816 (m-10) cc_final: 0.7555 (m-10) REVERT: B 624 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6433 (ttm) REVERT: B 696 TRP cc_start: 0.7062 (t-100) cc_final: 0.5985 (t-100) outliers start: 79 outliers final: 57 residues processed: 247 average time/residue: 0.3079 time to fit residues: 114.4105 Evaluate side-chains 251 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 181 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 996 GLU Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1100 GLU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1152 HIS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 624 MET Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 933 MET Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1197 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 65 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 204 optimal weight: 0.0870 chunk 228 optimal weight: 6.9990 chunk 229 optimal weight: 4.9990 chunk 218 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 166 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 overall best weight: 1.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 HIS A 698 HIS ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.235510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.204150 restraints weight = 22076.444| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 2.88 r_work: 0.4010 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17756 Z= 0.139 Angle : 0.636 15.054 24203 Z= 0.317 Chirality : 0.042 0.177 2832 Planarity : 0.005 0.042 3213 Dihedral : 4.296 21.574 2583 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 4.23 % Allowed : 28.57 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.17), residues: 2360 helix: 0.52 (0.17), residues: 996 sheet: -2.34 (0.32), residues: 241 loop : -2.09 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 539 HIS 0.007 0.001 HIS A 997 PHE 0.017 0.001 PHE A1146 TYR 0.018 0.002 TYR B 525 ARG 0.008 0.000 ARG B 853 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 729) hydrogen bonds : angle 4.42032 ( 2109) covalent geometry : bond 0.00319 (17756) covalent geometry : angle 0.63605 (24203) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 184 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.6658 (OUTLIER) cc_final: 0.4928 (t80) REVERT: A 223 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7306 (tpt) REVERT: A 289 MET cc_start: 0.7862 (tpp) cc_final: 0.7518 (tpp) REVERT: A 383 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.5424 (mt) REVERT: A 402 LEU cc_start: 0.6018 (OUTLIER) cc_final: 0.5551 (mt) REVERT: A 438 GLU cc_start: 0.4900 (OUTLIER) cc_final: 0.4371 (tt0) REVERT: A 474 GLN cc_start: 0.7002 (pm20) cc_final: 0.6748 (pm20) REVERT: A 736 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6461 (tp30) REVERT: A 847 MET cc_start: 0.5016 (mpp) cc_final: 0.4596 (mpp) REVERT: A 1102 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6744 (tp) REVERT: B 76 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7018 (pt0) REVERT: B 148 ARG cc_start: 0.6513 (OUTLIER) cc_final: 0.6270 (mpp80) REVERT: B 172 TYR cc_start: 0.5863 (OUTLIER) cc_final: 0.4914 (t80) REVERT: B 223 MET cc_start: 0.6731 (tpt) cc_final: 0.6390 (tpt) REVERT: B 329 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6176 (mt) REVERT: B 369 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.6338 (t80) REVERT: B 456 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.7564 (m-10) REVERT: B 624 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6405 (ttm) REVERT: B 696 TRP cc_start: 0.6948 (t-100) cc_final: 0.5932 (t-100) REVERT: B 853 ARG cc_start: 0.7813 (mtt90) cc_final: 0.7445 (mtm180) outliers start: 72 outliers final: 53 residues processed: 239 average time/residue: 0.3191 time to fit residues: 112.9178 Evaluate side-chains 249 residues out of total 1903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 182 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 406 HIS Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 572 PHE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1100 GLU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1152 HIS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 172 TYR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 624 MET Chi-restraints excluded: chain B residue 643 ARG Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 933 MET Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1083 LEU Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain B residue 1197 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 117 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 chunk 31 optimal weight: 10.0000 chunk 209 optimal weight: 0.7980 chunk 131 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 HIS B 496 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.237491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.206145 restraints weight = 22090.063| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 2.72 r_work: 0.4034 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17756 Z= 0.120 Angle : 0.621 18.855 24203 Z= 0.307 Chirality : 0.042 0.178 2832 Planarity : 0.004 0.043 3213 Dihedral : 4.092 19.907 2583 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.47 % Allowed : 28.34 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2360 helix: 0.64 (0.17), residues: 997 sheet: -2.24 (0.32), residues: 242 loop : -2.06 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 696 HIS 0.008 0.001 HIS A 997 PHE 0.015 0.001 PHE A 278 TYR 0.016 0.001 TYR A 525 ARG 0.005 0.000 ARG B 853 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 729) hydrogen bonds : angle 4.31683 ( 2109) covalent geometry : bond 0.00268 (17756) covalent geometry : angle 0.62066 (24203) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8236.54 seconds wall clock time: 144 minutes 3.35 seconds (8643.35 seconds total)