Starting phenix.real_space_refine on Sat Aug 8 15:40:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24ip_69549/08_2026/24ip_69549.cif Found real_map, /net/cci-nas-00/data/ceres_data/24ip_69549/08_2026/24ip_69549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/24ip_69549/08_2026/24ip_69549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24ip_69549/08_2026/24ip_69549.map" model { file = "/net/cci-nas-00/data/ceres_data/24ip_69549/08_2026/24ip_69549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24ip_69549/08_2026/24ip_69549.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.272 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 172 5.16 5 C 17970 2.51 5 N 4863 2.21 5 O 5204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 188 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28209 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 8677 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1100, 8666 Classifications: {'peptide': 1100} Link IDs: {'PTRANS': 47, 'TRANS': 1052} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 1100, 8666 Classifications: {'peptide': 1100} Link IDs: {'PTRANS': 47, 'TRANS': 1052} Chain breaks: 6 bond proxies already assigned to first conformer: 8838 Chain: "C" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2466 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 6, 'TRANS': 301} Chain breaks: 5 Chain: "A" Number of atoms: 8728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1103, 8685 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 48, 'TRANS': 1054} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 1103, 8685 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 48, 'TRANS': 1054} Chain breaks: 6 bond proxies already assigned to first conformer: 8822 Chain: "B" Number of atoms: 2986 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 380, 2976 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 21, 'TRANS': 358} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 380, 2976 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 21, 'TRANS': 358} Chain breaks: 3 bond proxies already assigned to first conformer: 3030 Chain: "F" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2468 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 8, 'TRANS': 298} Chain breaks: 4 Chain: "E" Number of atoms: 2884 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 367, 2874 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 367, 2874 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 4 bond proxies already assigned to first conformer: 2923 Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N AARG D 129 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 129 " occ=0.50 residue: pdb=" N AARG A 129 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 129 " occ=0.50 residue: pdb=" N AARG A 351 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 351 " occ=0.50 residue: pdb=" N AHIS A 690 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 690 " occ=0.50 residue: pdb=" N AARG A1185 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A1185 " occ=0.50 residue: pdb=" N AHIS B 774 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 774 " occ=0.50 residue: pdb=" N AHIS E 774 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS E 774 " occ=0.50 Time building chain proxies: 10.13, per 1000 atoms: 0.36 Number of scatterers: 28209 At special positions: 0 Unit cell: (129.548, 123.024, 359.752, 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 172 16.00 O 5204 8.00 N 4863 7.00 C 17970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 39 " - pdb=" SG CYS C 153 " distance=2.03 Simple disulfide: pdb=" SG CYS F 39 " - pdb=" SG CYS F 153 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 2.3 seconds 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6754 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 40 sheets defined 36.3% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'D' and resid 20 through 24 removed outlier: 3.988A pdb=" N LYS D 24 " --> pdb=" O ALA D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 430 removed outlier: 4.077A pdb=" N SER D 426 " --> pdb=" O PRO D 423 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU D 427 " --> pdb=" O ASP D 424 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASP D 428 " --> pdb=" O LEU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 843 through 847 Processing helix chain 'D' and resid 848 through 861 Processing helix chain 'D' and resid 871 through 875 removed outlier: 3.693A pdb=" N VAL D 875 " --> pdb=" O ILE D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 893 Processing helix chain 'D' and resid 895 through 903 Processing helix chain 'D' and resid 908 through 921 Processing helix chain 'D' and resid 922 through 940 removed outlier: 3.506A pdb=" N SER D 940 " --> pdb=" O LEU D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 972 through 990 removed outlier: 3.605A pdb=" N PHE D 979 " --> pdb=" O TYR D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 993 through 1008 Processing helix chain 'D' and resid 1009 through 1019 removed outlier: 3.521A pdb=" N GLU D1019 " --> pdb=" O GLN D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1026 through 1038 Processing helix chain 'D' and resid 1044 through 1060 removed outlier: 3.738A pdb=" N SER D1048 " --> pdb=" O GLY D1044 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR D1049 " --> pdb=" O PRO D1045 " (cutoff:3.500A) Processing helix chain 'D' and resid 1062 through 1073 removed outlier: 3.576A pdb=" N GLY D1066 " --> pdb=" O LYS D1062 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D1072 " --> pdb=" O GLN D1068 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE D1073 " --> pdb=" O LEU D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1075 through 1086 Processing helix chain 'D' and resid 1088 through 1100 removed outlier: 3.607A pdb=" N VAL D1098 " --> pdb=" O TRP D1094 " (cutoff:3.500A) Processing helix chain 'D' and resid 1101 through 1117 Processing helix chain 'D' and resid 1123 through 1135 Processing helix chain 'D' and resid 1136 through 1147 Processing helix chain 'D' and resid 1149 through 1164 Processing helix chain 'D' and resid 1172 through 1190 Processing helix chain 'D' and resid 1192 through 1204 removed outlier: 3.589A pdb=" N PHE D1199 " --> pdb=" O GLY D1195 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS D1202 " --> pdb=" O LEU D1198 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY D1204 " --> pdb=" O ALA D1200 " (cutoff:3.500A) Processing helix chain 'D' and resid 1207 through 1215 Processing helix chain 'C' and resid 86 through 99 Processing helix chain 'C' and resid 158 through 165 removed outlier: 3.566A pdb=" N PHE C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 179 Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 205 through 213 removed outlier: 4.132A pdb=" N VAL C 209 " --> pdb=" O PRO C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 226 removed outlier: 3.890A pdb=" N LEU C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 251 Processing helix chain 'C' and resid 257 through 272 removed outlier: 3.820A pdb=" N MET C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR C 269 " --> pdb=" O CYS C 265 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 305 Processing helix chain 'C' and resid 311 through 341 removed outlier: 3.620A pdb=" N PHE C 315 " --> pdb=" O ASN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 358 removed outlier: 3.568A pdb=" N LEU C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY C 358 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 371 removed outlier: 3.713A pdb=" N LYS C 365 " --> pdb=" O ASP C 361 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 370 " --> pdb=" O ILE C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 394 Processing helix chain 'A' and resid 20 through 24 removed outlier: 3.508A pdb=" N LYS A 24 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.776A pdb=" N ASP A 246 " --> pdb=" O THR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 430 removed outlier: 4.101A pdb=" N SER A 426 " --> pdb=" O PRO A 423 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU A 427 " --> pdb=" O ASP A 424 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ASP A 428 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 847 Processing helix chain 'A' and resid 848 through 861 Processing helix chain 'A' and resid 871 through 875 removed outlier: 3.587A pdb=" N VAL A 875 " --> pdb=" O ILE A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 893 Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 908 through 921 Processing helix chain 'A' and resid 922 through 939 removed outlier: 3.523A pdb=" N LEU A 939 " --> pdb=" O TYR A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 990 removed outlier: 3.600A pdb=" N PHE A 979 " --> pdb=" O TYR A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1008 Processing helix chain 'A' and resid 1009 through 1018 Processing helix chain 'A' and resid 1026 through 1040 Processing helix chain 'A' and resid 1044 through 1060 removed outlier: 4.050A pdb=" N SER A1048 " --> pdb=" O GLY A1044 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR A1049 " --> pdb=" O PRO A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1071 Processing helix chain 'A' and resid 1072 through 1074 No H-bonds generated for 'chain 'A' and resid 1072 through 1074' Processing helix chain 'A' and resid 1075 through 1086 Processing helix chain 'A' and resid 1088 through 1100 Processing helix chain 'A' and resid 1101 through 1117 Processing helix chain 'A' and resid 1123 through 1135 Processing helix chain 'A' and resid 1136 through 1147 Processing helix chain 'A' and resid 1149 through 1164 Processing helix chain 'A' and resid 1172 through 1191 Processing helix chain 'A' and resid 1192 through 1204 Processing helix chain 'A' and resid 1207 through 1216 Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.889A pdb=" N THR B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 409 removed outlier: 3.820A pdb=" N LYS B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 416 through 426 removed outlier: 3.572A pdb=" N PHE B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B 426 " --> pdb=" O ILE B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 453 Processing helix chain 'B' and resid 479 through 484 Processing helix chain 'B' and resid 486 through 497 Processing helix chain 'B' and resid 526 through 530 Processing helix chain 'B' and resid 531 through 543 removed outlier: 3.706A pdb=" N LYS B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 595 removed outlier: 3.949A pdb=" N MET B 590 " --> pdb=" O ASN B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 647 Processing helix chain 'B' and resid 733 through 748 Processing helix chain 'B' and resid 751 through 777 removed outlier: 3.831A pdb=" N PHE B 776 " --> pdb=" O PHE B 772 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 98 removed outlier: 4.024A pdb=" N SER F 92 " --> pdb=" O PRO F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 163 removed outlier: 3.756A pdb=" N LEU F 162 " --> pdb=" O SER F 158 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU F 163 " --> pdb=" O GLU F 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 158 through 163' Processing helix chain 'F' and resid 165 through 179 Processing helix chain 'F' and resid 206 through 211 Processing helix chain 'F' and resid 216 through 226 removed outlier: 4.539A pdb=" N LEU F 220 " --> pdb=" O LYS F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 250 removed outlier: 3.646A pdb=" N LYS F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG F 241 " --> pdb=" O GLU F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 271 removed outlier: 3.663A pdb=" N THR F 262 " --> pdb=" O GLU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 306 removed outlier: 3.676A pdb=" N GLN F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA F 302 " --> pdb=" O ASP F 298 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE F 303 " --> pdb=" O TRP F 299 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU F 304 " --> pdb=" O MET F 300 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY F 306 " --> pdb=" O ALA F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 341 Processing helix chain 'F' and resid 343 through 357 removed outlier: 3.539A pdb=" N LEU F 347 " --> pdb=" O ASN F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 372 removed outlier: 4.068A pdb=" N VAL F 369 " --> pdb=" O LYS F 365 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU F 370 " --> pdb=" O ILE F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 394 removed outlier: 3.525A pdb=" N GLN F 394 " --> pdb=" O GLU F 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 391 removed outlier: 3.975A pdb=" N THR E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 409 Processing helix chain 'E' and resid 416 through 426 removed outlier: 3.582A pdb=" N PHE E 420 " --> pdb=" O SER E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 453 Processing helix chain 'E' and resid 479 through 483 removed outlier: 3.680A pdb=" N LEU E 483 " --> pdb=" O CYS E 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 479 through 483' Processing helix chain 'E' and resid 486 through 497 Processing helix chain 'E' and resid 526 through 530 Processing helix chain 'E' and resid 531 through 543 removed outlier: 3.694A pdb=" N LYS E 535 " --> pdb=" O SER E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 566 removed outlier: 4.166A pdb=" N SER E 566 " --> pdb=" O ASP E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 586 through 595 removed outlier: 3.890A pdb=" N MET E 590 " --> pdb=" O ASN E 586 " (cutoff:3.500A) Processing helix chain 'E' and resid 637 through 647 Processing helix chain 'E' and resid 733 through 748 Processing helix chain 'E' and resid 751 through 777 removed outlier: 3.980A pdb=" N ASN E 757 " --> pdb=" O GLU E 753 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE E 776 " --> pdb=" O PHE E 772 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 14 through 15 removed outlier: 7.584A pdb=" N LYS D 808 " --> pdb=" O TRP D 803 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TRP D 803 " --> pdb=" O LYS D 808 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE D 810 " --> pdb=" O VAL D 801 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL D 801 " --> pdb=" O ILE D 810 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA D 812 " --> pdb=" O LEU D 799 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 27 through 29 removed outlier: 6.038A pdb=" N VAL D 43 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL D 56 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL D 45 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 64 through 69 removed outlier: 4.116A pdb=" N LEU D 86 " --> pdb=" O TRP D 98 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS D 107 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASP D 99 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ALA D 105 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 119 through 121 removed outlier: 6.898A pdb=" N ILE D 141 " --> pdb=" O LYS D 154 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LYS D 154 " --> pdb=" O ILE D 141 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU D 143 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 163 through 166 Processing sheet with id=AA6, first strand: chain 'D' and resid 249 through 252 removed outlier: 3.690A pdb=" N GLN D 249 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP D 272 " --> pdb=" O THR D 278 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR D 278 " --> pdb=" O ASP D 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 291 through 296 removed outlier: 3.538A pdb=" N GLN D 293 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE D 312 " --> pdb=" O GLN D 346 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLN D 346 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU D 314 " --> pdb=" O ARG D 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 358 through 363 removed outlier: 3.876A pdb=" N SER D 360 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL D 380 " --> pdb=" O LEU D 459 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU D 459 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE D 382 " --> pdb=" O THR D 457 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 409 through 410 removed outlier: 3.614A pdb=" N ILE D 413 " --> pdb=" O PHE D 410 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 469 through 472 removed outlier: 6.199A pdb=" N HIS D 501 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LEU D 507 " --> pdb=" O HIS D 501 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 518 through 523 removed outlier: 4.026A pdb=" N GLY D 520 " --> pdb=" O PHE D 532 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE D 532 " --> pdb=" O GLY D 520 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 571 through 576 removed outlier: 7.023A pdb=" N VAL D 586 " --> pdb=" O GLU D 572 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE D 574 " --> pdb=" O ALA D 584 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA D 584 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL D 576 " --> pdb=" O TYR D 582 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TYR D 582 " --> pdb=" O VAL D 576 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU D 593 " --> pdb=" O VAL D 585 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU D 594 " --> pdb=" O LEU D 603 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 615 through 618 removed outlier: 4.006A pdb=" N ALA D 615 " --> pdb=" O THR D 682 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR D 682 " --> pdb=" O ALA D 615 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE D 681 " --> pdb=" O TYR D 689 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP D 683 " --> pdb=" O GLN D 687 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLN D 687 " --> pdb=" O ASP D 683 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL D 688 " --> pdb=" O ARG D 703 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ARG D 703 " --> pdb=" O VAL D 688 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N HIS D 690 " --> pdb=" O SER D 701 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 713 through 719 removed outlier: 3.523A pdb=" N CYS D 715 " --> pdb=" O GLY D 726 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 741 " --> pdb=" O ASP D 736 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 752 through 757 removed outlier: 6.672A pdb=" N MET D 769 " --> pdb=" O ARG D 753 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE D 755 " --> pdb=" O ILE D 767 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE D 767 " --> pdb=" O ILE D 755 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N PHE D 757 " --> pdb=" O LYS D 765 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LYS D 765 " --> pdb=" O PHE D 757 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY D 773 " --> pdb=" O TYR D 770 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASP D 778 " --> pdb=" O MET D 784 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N MET D 784 " --> pdb=" O ASP D 778 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 109 through 111 Processing sheet with id=AB8, first strand: chain 'C' and resid 230 through 232 removed outlier: 3.622A pdb=" N GLU C 231 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE C 278 " --> pdb=" O GLU C 231 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 277 " --> pdb=" O CYS C 288 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 14 through 15 removed outlier: 7.384A pdb=" N LYS A 808 " --> pdb=" O TRP A 803 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TRP A 803 " --> pdb=" O LYS A 808 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE A 810 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL A 801 " --> pdb=" O ILE A 810 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA A 812 " --> pdb=" O LEU A 799 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 27 through 29 removed outlier: 6.389A pdb=" N ASP A 47 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR A 53 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 64 through 69 removed outlier: 4.508A pdb=" N LYS A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS A 107 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ASP A 99 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ALA A 105 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 119 through 121 removed outlier: 6.854A pdb=" N ILE A 141 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LYS A 154 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU A 143 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 163 through 166 Processing sheet with id=AC5, first strand: chain 'A' and resid 249 through 252 removed outlier: 3.668A pdb=" N GLN A 249 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP A 272 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N THR A 278 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 291 through 296 removed outlier: 6.733A pdb=" N ILE A 312 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLN A 346 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 314 " --> pdb=" O ARG A 344 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 358 through 363 removed outlier: 3.705A pdb=" N SER A 360 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL A 380 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU A 459 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 382 " --> pdb=" O THR A 457 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 409 through 410 removed outlier: 3.660A pdb=" N ILE A 413 " --> pdb=" O PHE A 410 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 469 through 472 removed outlier: 6.240A pdb=" N HIS A 501 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU A 507 " --> pdb=" O HIS A 501 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 521 through 523 Processing sheet with id=AD2, first strand: chain 'A' and resid 571 through 576 removed outlier: 6.914A pdb=" N VAL A 586 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE A 574 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA A 584 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N VAL A 576 " --> pdb=" O TYR A 582 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TYR A 582 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU A 594 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 615 through 618 removed outlier: 3.661A pdb=" N ALA A 615 " --> pdb=" O THR A 682 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A 688 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG A 703 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N AHIS A 690 " --> pdb=" O SER A 701 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 697 " --> pdb=" O GLU A 694 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 713 through 719 removed outlier: 3.515A pdb=" N ARG A 743 " --> pdb=" O PHE A 734 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 741 " --> pdb=" O ASP A 736 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 754 through 757 removed outlier: 6.894A pdb=" N ASP A 778 " --> pdb=" O MET A 784 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N MET A 784 " --> pdb=" O ASP A 778 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 411 through 412 removed outlier: 7.697A pdb=" N ARG B 377 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 501 " --> pdb=" O ARG B 377 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA B 379 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N SER B 503 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU B 381 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE B 522 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU B 501 " --> pdb=" O ILE B 522 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 580 through 583 removed outlier: 6.693A pdb=" N ARG B 569 " --> pdb=" O HIS B 605 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 612 through 617 removed outlier: 6.911A pdb=" N TYR B 655 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU B 725 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR B 657 " --> pdb=" O LEU B 723 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 109 through 110 Processing sheet with id=AE1, first strand: chain 'F' and resid 277 through 278 removed outlier: 3.504A pdb=" N VAL F 277 " --> pdb=" O CYS F 288 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 411 through 412 removed outlier: 6.053A pdb=" N ILE E 378 " --> pdb=" O ASP E 475 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU E 477 " --> pdb=" O ILE E 378 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N PHE E 380 " --> pdb=" O LEU E 477 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ARG E 377 " --> pdb=" O THR E 499 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU E 501 " --> pdb=" O ARG E 377 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA E 379 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N SER E 503 " --> pdb=" O ALA E 379 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU E 381 " --> pdb=" O SER E 503 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 579 through 583 removed outlier: 6.778A pdb=" N ARG E 569 " --> pdb=" O HIS E 605 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL E 600 " --> pdb=" O LEU E 551 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 612 through 616 removed outlier: 6.717A pdb=" N TYR E 655 " --> pdb=" O LEU E 725 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU E 725 " --> pdb=" O TYR E 655 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR E 657 " --> pdb=" O LEU E 723 " (cutoff:3.500A) 1199 hydrogen bonds defined for protein. 3445 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: 7.28 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9221 1.34 - 1.46: 5908 1.46 - 1.58: 13432 1.58 - 1.69: 0 1.69 - 1.81: 242 Bond restraints: 28803 Sorted by residual: bond pdb=" C PRO A 137 " pdb=" N PRO A 138 " ideal model delta sigma weight residual 1.334 1.361 -0.028 2.34e-02 1.83e+03 1.38e+00 bond pdb=" C PRO D 137 " pdb=" N PRO D 138 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.13e+00 bond pdb=" CB PRO C 205 " pdb=" CG PRO C 205 " ideal model delta sigma weight residual 1.492 1.540 -0.048 5.00e-02 4.00e+02 9.29e-01 bond pdb=" N CYS D 843 " pdb=" CA CYS D 843 " ideal model delta sigma weight residual 1.463 1.455 0.008 8.80e-03 1.29e+04 8.40e-01 bond pdb=" C ASN F 146 " pdb=" N PRO F 147 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.21e-01 ... (remaining 28798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 38770 2.01 - 4.02: 239 4.02 - 6.04: 19 6.04 - 8.05: 1 8.05 - 10.06: 3 Bond angle restraints: 39032 Sorted by residual: angle pdb=" CA LEU E 395 " pdb=" CB LEU E 395 " pdb=" CG LEU E 395 " ideal model delta sigma weight residual 116.30 126.36 -10.06 3.50e+00 8.16e-02 8.26e+00 angle pdb=" CA LEU D 86 " pdb=" CB LEU D 86 " pdb=" CG LEU D 86 " ideal model delta sigma weight residual 116.30 125.05 -8.75 3.50e+00 8.16e-02 6.25e+00 angle pdb=" CA LEU E 483 " pdb=" CB LEU E 483 " pdb=" CG LEU E 483 " ideal model delta sigma weight residual 116.30 124.41 -8.11 3.50e+00 8.16e-02 5.37e+00 angle pdb=" CA LEU D 737 " pdb=" CB LEU D 737 " pdb=" CG LEU D 737 " ideal model delta sigma weight residual 116.30 123.96 -7.66 3.50e+00 8.16e-02 4.79e+00 angle pdb=" N PHE E 618 " pdb=" CA PHE E 618 " pdb=" C PHE E 618 " ideal model delta sigma weight residual 109.81 114.58 -4.77 2.21e+00 2.05e-01 4.66e+00 ... (remaining 39027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 16689 17.54 - 35.07: 561 35.07 - 52.61: 73 52.61 - 70.14: 14 70.14 - 87.68: 2 Dihedral angle restraints: 17339 sinusoidal: 6939 harmonic: 10400 Sorted by residual: dihedral pdb=" CB GLU F 370 " pdb=" CG GLU F 370 " pdb=" CD GLU F 370 " pdb=" OE1 GLU F 370 " ideal model delta sinusoidal sigma weight residual 0.00 87.68 -87.68 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA ASN A 139 " pdb=" C ASN A 139 " pdb=" N TYR A 140 " pdb=" CA TYR A 140 " ideal model delta harmonic sigma weight residual 180.00 -164.22 -15.78 0 5.00e+00 4.00e-02 9.96e+00 dihedral pdb=" N PHE C 303 " pdb=" CA PHE C 303 " pdb=" CB PHE C 303 " pdb=" CG PHE C 303 " ideal model delta sinusoidal sigma weight residual -60.00 -116.09 56.09 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 17336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3103 0.033 - 0.066: 976 0.066 - 0.100: 222 0.100 - 0.133: 144 0.133 - 0.166: 3 Chirality restraints: 4448 Sorted by residual: chirality pdb=" CG LEU E 395 " pdb=" CB LEU E 395 " pdb=" CD1 LEU E 395 " pdb=" CD2 LEU E 395 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CG LEU D 86 " pdb=" CB LEU D 86 " pdb=" CD1 LEU D 86 " pdb=" CD2 LEU D 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA PHE E 618 " pdb=" N PHE E 618 " pdb=" C PHE E 618 " pdb=" CB PHE E 618 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 4445 not shown) Planarity restraints: 4970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 463 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO D 464 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 464 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 464 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 465 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO D 466 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 466 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 466 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 618 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO E 619 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO E 619 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 619 " 0.020 5.00e-02 4.00e+02 ... (remaining 4967 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4140 2.76 - 3.30: 26176 3.30 - 3.83: 46698 3.83 - 4.37: 55039 4.37 - 4.90: 96650 Nonbonded interactions: 228703 Sorted by model distance: nonbonded pdb=" NH1 ARG A 344 " pdb=" O SER A 402 " model vdw 2.228 3.120 nonbonded pdb=" OG SER D 786 " pdb=" O MET D 823 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR A 935 " pdb=" O LEU A 970 " model vdw 2.251 3.040 nonbonded pdb=" O SER D1139 " pdb=" OG1 THR D1143 " model vdw 2.254 3.040 nonbonded pdb=" O SER A1139 " pdb=" OG1 THR A1143 " model vdw 2.264 3.040 ... (remaining 228698 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 7 through 128 or resid 130 through 236 or resid 243 throug \ h 350 or resid 352 through 625 or resid 675 through 689 or resid 691 through 118 \ 4 or resid 1186 through 1216)) selection = (chain 'D' and (resid 7 through 128 or resid 130 through 206 or resid 233 throug \ h 350 or resid 352 through 689 or resid 691 through 1184 or resid 1186 through 1 \ 216)) } ncs_group { reference = (chain 'B' and (resid 375 through 429 or resid 435 through 460 or resid 471 thro \ ugh 773 or resid 775 through 826)) selection = (chain 'E' and (resid 375 through 773 or resid 775 through 826)) } ncs_group { reference = (chain 'C' and (resid 34 through 44 or resid 73 through 98 or resid 108 through \ 394)) selection = (chain 'F' and (resid 34 through 82 or resid 85 through 115 or resid 120 through \ 130 or resid 148 through 184 or resid 188 through 394)) } 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=0.50 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: 19.460 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: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 33.880 Find NCS groups from input model: 0.570 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: 0.000 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 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 : 0.002 0.048 28805 Z= 0.077 Angle : 0.404 10.061 39036 Z= 0.220 Chirality : 0.038 0.166 4448 Planarity : 0.003 0.036 4970 Dihedral : 8.541 87.678 10579 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.41 % Allowed : 4.42 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.13), residues: 3518 helix: -0.16 (0.13), residues: 1233 sheet: -1.35 (0.17), residues: 776 loop : -2.58 (0.13), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 763 TYR 0.007 0.001 TYR D 935 PHE 0.014 0.001 PHE E 618 TRP 0.009 0.001 TRP C 299 HIS 0.002 0.000 HIS B 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00154 / 0.08 (28803) covalent geometry : angle 0.40403 / 0.22 (39032) SS BOND : bond 0.00085 / 0.04 ( 2) SS BOND : angle 0.50504 / 0.39 ( 4) hydrogen bonds : bond 0.16443 / 10.83 ( 1199) hydrogen bonds : angle 6.36380 / 4.33 ( 3445) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 549 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 487 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8444 (mt) REVERT: D 573 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7462 (pp-130) REVERT: D 727 ASP cc_start: 0.7465 (m-30) cc_final: 0.7141 (m-30) REVERT: D 745 ILE cc_start: 0.6512 (OUTLIER) cc_final: 0.5813 (pt) REVERT: C 41 TYR cc_start: 0.5539 (m-80) cc_final: 0.5193 (m-10) REVERT: C 93 PHE cc_start: 0.9065 (t80) cc_final: 0.8765 (t80) REVERT: C 120 TYR cc_start: 0.5249 (OUTLIER) cc_final: 0.4862 (t80) REVERT: C 124 CYS cc_start: 0.4958 (t) cc_final: 0.4441 (t) REVERT: C 180 MET cc_start: -0.1612 (tpt) cc_final: -0.1891 (tpt) REVERT: C 216 LYS cc_start: 0.7568 (mttt) cc_final: 0.6978 (mmmt) REVERT: C 227 TYR cc_start: 0.8678 (m-10) cc_final: 0.8205 (m-80) REVERT: C 242 ASP cc_start: 0.6124 (m-30) cc_final: 0.5394 (m-30) REVERT: C 321 ASN cc_start: 0.7916 (m-40) cc_final: 0.7576 (m-40) REVERT: B 504 MET cc_start: 0.8234 (ptm) cc_final: 0.7970 (ptm) REVERT: B 518 THR cc_start: 0.7379 (OUTLIER) cc_final: 0.7153 (p) REVERT: F 200 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8612 (tp30) REVERT: F 238 LYS cc_start: 0.8131 (tptm) cc_final: 0.7238 (tmtt) REVERT: F 300 MET cc_start: 0.7138 (ttp) cc_final: 0.6642 (ttp) REVERT: F 314 LEU cc_start: 0.8502 (tm) cc_final: 0.8112 (pt) REVERT: E 402 HIS cc_start: 0.6229 (m170) cc_final: 0.5940 (m170) outliers start: 76 outliers final: 24 residues processed: 617 average time/residue: 0.2336 time to fit residues: 215.0312 Evaluate side-chains 425 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 396 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 573 MET Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 745 ILE Chi-restraints excluded: chain D residue 820 VAL Chi-restraints excluded: chain D residue 981 LEU Chi-restraints excluded: chain D residue 1143 THR Chi-restraints excluded: chain C residue 43 TYR Chi-restraints excluded: chain C residue 120 TYR Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 464 GLN Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 274 LYS Chi-restraints excluded: chain F residue 308 LYS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 483 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 23 ASN D 52 GLN D 73 ASN D 77 ASN D 106 GLN D 117 GLN D 120 GLN D 125 GLN D 337 GLN D 429 ASN ** D 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 514 HIS D 548 GLN D 581 GLN D 690 HIS D 763 ASN D 835 GLN ** D 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 888 GLN D1015 GLN D1024 ASN D1047 GLN D1068 GLN D1101 ASN D1145 HIS C 222 HIS C 253 GLN C 272 GLN C 284 GLN C 293 ASN A 23 ASN A 73 ASN A 75 HIS A 106 GLN A 120 GLN A 125 GLN A 277 GLN A 337 GLN A 429 ASN A 467 GLN A 485 GLN A 501 HIS A 514 HIS A 548 GLN A 581 GLN ** A 690 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN A 783 GLN A 835 GLN A 861 HIS A 862 GLN A 885 ASN A 888 GLN A 937 HIS A 941 GLN A1003 GLN A1101 ASN A1145 HIS B 436 GLN B 461 GLN B 464 GLN B 592 ASN B 645 ASN F 81 ASN F 207 GLN F 222 HIS F 253 GLN F 284 GLN F 293 ASN F 311 ASN F 343 ASN F 371 HIS E 447 ASN E 454 HIS E 592 ASN E 605 HIS E 664 GLN E 756 GLN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.067418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.044783 restraints weight = 180494.325| |-----------------------------------------------------------------------------| r_work (start): 0.2453 rms_B_bonded: 3.76 r_work: 0.2333 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2335 r_free = 0.2335 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2335 r_free = 0.2335 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.2335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 28805 Z= 0.232 Angle : 0.656 10.455 39036 Z= 0.334 Chirality : 0.045 0.195 4448 Planarity : 0.005 0.069 4970 Dihedral : 5.148 53.796 3887 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.57 % Allowed : 8.29 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.13), residues: 3518 helix: 0.58 (0.14), residues: 1264 sheet: -0.66 (0.18), residues: 771 loop : -2.10 (0.14), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 286 TYR 0.016 0.002 TYR C 227 PHE 0.026 0.002 PHE A1199 TRP 0.034 0.002 TRP F 198 HIS 0.008 0.001 HIS B 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.23 (28803) covalent geometry : angle 0.65544 / 0.33 (39032) SS BOND : bond 0.00065 / 0.03 ( 2) SS BOND : angle 1.51125 / 1.13 ( 4) hydrogen bonds : bond 0.04690 / 3.12 ( 1199) hydrogen bonds : angle 4.70799 / 3.19 ( 3445) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 396 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 487 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8693 (mt) REVERT: D 573 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.7246 (pp-130) REVERT: D 783 GLN cc_start: 0.8027 (mm110) cc_final: 0.7528 (mm110) REVERT: D 888 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8745 (mm-40) REVERT: D 981 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8873 (tt) REVERT: C 93 PHE cc_start: 0.8840 (t80) cc_final: 0.8560 (t80) REVERT: C 120 TYR cc_start: 0.5665 (OUTLIER) cc_final: 0.5187 (t80) REVERT: C 180 MET cc_start: -0.1215 (tpt) cc_final: -0.1647 (tpt) REVERT: C 238 LYS cc_start: 0.8003 (ptpp) cc_final: 0.7579 (ptpp) REVERT: A 440 GLU cc_start: 0.8622 (mp0) cc_final: 0.8419 (mp0) REVERT: A 721 ASP cc_start: 0.8626 (p0) cc_final: 0.8405 (t0) REVERT: A 764 GLN cc_start: 0.8802 (mt0) cc_final: 0.8308 (mp10) REVERT: A 906 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8886 (mm-30) REVERT: F 41 TYR cc_start: 0.5531 (m-80) cc_final: 0.4955 (m-10) REVERT: F 154 PHE cc_start: 0.6424 (m-80) cc_final: 0.5782 (m-80) REVERT: F 314 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8231 (pt) REVERT: E 395 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.5330 (tp) REVERT: E 453 ARG cc_start: 0.7945 (ttt180) cc_final: 0.7645 (ttt180) outliers start: 81 outliers final: 49 residues processed: 459 average time/residue: 0.2248 time to fit residues: 154.5395 Evaluate side-chains 426 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 370 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 443 ARG Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 516 CYS Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 573 MET Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 712 SER Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 820 VAL Chi-restraints excluded: chain D residue 888 GLN Chi-restraints excluded: chain D residue 981 LEU Chi-restraints excluded: chain D residue 1171 ASP Chi-restraints excluded: chain D residue 1192 PHE Chi-restraints excluded: chain C residue 43 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 120 TYR Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1171 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 288 CYS Chi-restraints excluded: chain F residue 308 LYS Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 350 CYS Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 483 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 269 optimal weight: 0.0770 chunk 90 optimal weight: 0.0870 chunk 138 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 187 optimal weight: 0.0770 chunk 311 optimal weight: 2.9990 chunk 325 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 262 optimal weight: 0.5980 chunk 336 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 690 HIS D 888 GLN C 317 GLN C 321 ASN A 106 GLN ** A 690 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN A 783 GLN A 888 GLN F 253 GLN F 293 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.069004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.046180 restraints weight = 211216.784| |-----------------------------------------------------------------------------| r_work (start): 0.2502 rms_B_bonded: 4.17 r_work: 0.2375 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2378 r_free = 0.2378 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2378 r_free = 0.2378 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28805 Z= 0.118 Angle : 0.545 10.517 39036 Z= 0.274 Chirality : 0.041 0.171 4448 Planarity : 0.004 0.078 4970 Dihedral : 4.734 53.743 3875 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.16 % Allowed : 9.82 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.14), residues: 3518 helix: 1.07 (0.15), residues: 1263 sheet: -0.39 (0.19), residues: 757 loop : -1.88 (0.15), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 751 TYR 0.010 0.001 TYR A 157 PHE 0.026 0.001 PHE E 439 TRP 0.040 0.001 TRP F 198 HIS 0.009 0.001 HIS C 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (28803) covalent geometry : angle 0.54441 / 0.27 (39032) SS BOND : bond 0.00398 / 0.21 ( 2) SS BOND : angle 1.76087 / 1.09 ( 4) hydrogen bonds : bond 0.03601 / 2.41 ( 1199) hydrogen bonds : angle 4.37241 / 2.97 ( 3445) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 385 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 487 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8562 (mt) REVERT: D 573 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7337 (pp-130) REVERT: D 687 GLN cc_start: 0.8617 (tp40) cc_final: 0.8384 (tp40) REVERT: D 689 TYR cc_start: 0.8893 (m-80) cc_final: 0.8603 (m-80) REVERT: D 735 TRP cc_start: 0.7340 (t-100) cc_final: 0.6794 (t-100) REVERT: D 745 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7097 (pt) REVERT: D 783 GLN cc_start: 0.7810 (mm110) cc_final: 0.7519 (mm-40) REVERT: D 888 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8837 (tp40) REVERT: D 981 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8840 (tt) REVERT: C 93 PHE cc_start: 0.8869 (t80) cc_final: 0.8604 (t80) REVERT: C 120 TYR cc_start: 0.5683 (OUTLIER) cc_final: 0.5252 (t80) REVERT: C 180 MET cc_start: -0.1441 (tpt) cc_final: -0.1760 (tpt) REVERT: C 208 ARG cc_start: 0.6732 (mtp180) cc_final: 0.6060 (mtp180) REVERT: C 214 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7284 (mm-40) REVERT: C 216 LYS cc_start: 0.8151 (mtpt) cc_final: 0.7915 (mtpt) REVERT: C 238 LYS cc_start: 0.8044 (ptpp) cc_final: 0.7502 (ptpp) REVERT: C 242 ASP cc_start: 0.5807 (m-30) cc_final: 0.5010 (m-30) REVERT: C 268 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.5954 (mtt) REVERT: C 316 ARG cc_start: 0.8157 (mmm-85) cc_final: 0.7911 (tpt90) REVERT: C 321 ASN cc_start: 0.8118 (m-40) cc_final: 0.7895 (m110) REVERT: A 260 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8945 (mtp) REVERT: A 764 GLN cc_start: 0.8842 (mt0) cc_final: 0.8337 (mp10) REVERT: A 906 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8893 (mm-30) REVERT: B 390 LEU cc_start: 0.9271 (mt) cc_final: 0.9043 (mt) REVERT: B 499 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8643 (p) REVERT: F 41 TYR cc_start: 0.5508 (m-80) cc_final: 0.4961 (m-10) REVERT: F 154 PHE cc_start: 0.5936 (m-80) cc_final: 0.5518 (m-80) REVERT: F 261 MET cc_start: 0.7967 (mmm) cc_final: 0.7200 (mmm) REVERT: F 314 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8180 (pt) REVERT: E 395 LEU cc_start: 0.6305 (OUTLIER) cc_final: 0.5345 (tp) REVERT: E 453 ARG cc_start: 0.7999 (ttt180) cc_final: 0.7737 (ttt180) outliers start: 67 outliers final: 38 residues processed: 435 average time/residue: 0.2082 time to fit residues: 136.0398 Evaluate side-chains 405 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 356 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 443 ARG Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 573 MET Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 745 ILE Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain D residue 820 VAL Chi-restraints excluded: chain D residue 888 GLN Chi-restraints excluded: chain D residue 981 LEU Chi-restraints excluded: chain D residue 1074 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 120 TYR Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 735 TRP Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 308 LYS Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 350 CYS Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 483 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 237 optimal weight: 0.9980 chunk 238 optimal weight: 0.1980 chunk 154 optimal weight: 1.9990 chunk 328 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 291 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 344 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 243 optimal weight: 0.3980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 HIS D 690 HIS ** D 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 888 GLN ** A 690 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 ASN ** E 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 HIS E 455 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.065474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.043215 restraints weight = 165158.173| |-----------------------------------------------------------------------------| r_work (start): 0.2408 rms_B_bonded: 3.56 r_work: 0.2289 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2289 r_free = 0.2289 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2289 r_free = 0.2289 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 28805 Z= 0.241 Angle : 0.657 10.336 39036 Z= 0.335 Chirality : 0.045 0.222 4448 Planarity : 0.005 0.085 4970 Dihedral : 5.331 58.610 3873 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.29 % Allowed : 10.07 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.14), residues: 3518 helix: 0.96 (0.14), residues: 1262 sheet: -0.28 (0.19), residues: 765 loop : -1.74 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 751 TYR 0.020 0.002 TYR E 438 PHE 0.029 0.002 PHE A1199 TRP 0.037 0.002 TRP F 198 HIS 0.008 0.002 HIS C 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.24 (28803) covalent geometry : angle 0.65654 / 0.34 (39032) SS BOND : bond 0.00855 / 0.45 ( 2) SS BOND : angle 1.78106 / 1.12 ( 4) hydrogen bonds : bond 0.04603 / 3.08 ( 1199) hydrogen bonds : angle 4.56459 / 3.10 ( 3445) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 363 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 487 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8682 (mt) REVERT: D 573 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.7392 (pp-130) REVERT: D 687 GLN cc_start: 0.8651 (tp40) cc_final: 0.8447 (tp40) REVERT: D 783 GLN cc_start: 0.8129 (mm110) cc_final: 0.7770 (mm-40) REVERT: D 888 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8656 (tp-100) REVERT: D 981 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8784 (tt) REVERT: C 93 PHE cc_start: 0.8838 (t80) cc_final: 0.8481 (t80) REVERT: C 120 TYR cc_start: 0.5890 (OUTLIER) cc_final: 0.5469 (t80) REVERT: C 124 CYS cc_start: 0.6077 (t) cc_final: 0.5578 (t) REVERT: C 180 MET cc_start: -0.1132 (tpt) cc_final: -0.1506 (tpt) REVERT: C 208 ARG cc_start: 0.6938 (mtp180) cc_final: 0.5841 (mtp180) REVERT: C 216 LYS cc_start: 0.8309 (mtpt) cc_final: 0.8060 (mtpt) REVERT: C 238 LYS cc_start: 0.8145 (ptpp) cc_final: 0.7917 (ptmm) REVERT: C 242 ASP cc_start: 0.5968 (m-30) cc_final: 0.5046 (m-30) REVERT: C 268 MET cc_start: 0.6649 (ttm) cc_final: 0.5930 (mtt) REVERT: C 300 MET cc_start: 0.8588 (ttp) cc_final: 0.8374 (ttp) REVERT: C 316 ARG cc_start: 0.8340 (mmm-85) cc_final: 0.8044 (tpt90) REVERT: A 260 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.9005 (mtp) REVERT: A 906 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8917 (mm-30) REVERT: A 1002 ASP cc_start: 0.8338 (m-30) cc_final: 0.7925 (m-30) REVERT: B 390 LEU cc_start: 0.9285 (mt) cc_final: 0.9056 (mt) REVERT: B 499 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8737 (p) REVERT: F 41 TYR cc_start: 0.5474 (m-80) cc_final: 0.4752 (m-10) REVERT: F 154 PHE cc_start: 0.6222 (m-80) cc_final: 0.5682 (m-80) REVERT: F 261 MET cc_start: 0.8304 (mmm) cc_final: 0.7825 (mmm) REVERT: F 342 MET cc_start: 0.8672 (mmm) cc_final: 0.8206 (mmm) REVERT: F 351 TYR cc_start: 0.8706 (t80) cc_final: 0.8307 (t80) REVERT: E 395 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.5601 (tp) REVERT: E 453 ARG cc_start: 0.7984 (ttt180) cc_final: 0.7705 (ttt180) REVERT: E 803 MET cc_start: 0.7365 (tmm) cc_final: 0.7085 (tpt) outliers start: 71 outliers final: 45 residues processed: 415 average time/residue: 0.2076 time to fit residues: 128.6674 Evaluate side-chains 404 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 351 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 516 CYS Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 573 MET Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 712 SER Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 888 GLN Chi-restraints excluded: chain D residue 981 LEU Chi-restraints excluded: chain D residue 1074 ASP Chi-restraints excluded: chain D residue 1192 PHE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 120 TYR Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1171 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain F residue 308 LYS Chi-restraints excluded: chain F residue 350 CYS Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 483 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 329 optimal weight: 0.3980 chunk 263 optimal weight: 0.7980 chunk 228 optimal weight: 1.9990 chunk 258 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 291 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 342 optimal weight: 0.9980 chunk 326 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 136 HIS D 299 GLN ** D 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 HIS ** A 690 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN ** E 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 509 ASN E 608 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.066246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.043922 restraints weight = 178734.856| |-----------------------------------------------------------------------------| r_work (start): 0.2432 rms_B_bonded: 3.72 r_work: 0.2311 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2313 r_free = 0.2313 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2313 r_free = 0.2313 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 28805 Z= 0.176 Angle : 0.597 10.497 39036 Z= 0.303 Chirality : 0.043 0.224 4448 Planarity : 0.005 0.089 4970 Dihedral : 5.154 59.700 3867 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.10 % Allowed : 10.99 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 3518 helix: 1.12 (0.15), residues: 1261 sheet: -0.15 (0.19), residues: 733 loop : -1.67 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 792 TYR 0.022 0.001 TYR E 438 PHE 0.023 0.002 PHE E 439 TRP 0.022 0.002 TRP F 198 HIS 0.007 0.001 HIS E 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (28803) covalent geometry : angle 0.59631 / 0.30 (39032) SS BOND : bond 0.00169 / 0.08 ( 2) SS BOND : angle 1.83172 / 1.10 ( 4) hydrogen bonds : bond 0.04042 / 2.70 ( 1199) hydrogen bonds : angle 4.44524 / 3.01 ( 3445) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 362 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 487 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8615 (mt) REVERT: D 573 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.7416 (pp-130) REVERT: D 721 ASP cc_start: 0.8100 (t0) cc_final: 0.7817 (t0) REVERT: D 783 GLN cc_start: 0.8136 (mm110) cc_final: 0.7738 (mm-40) REVERT: D 981 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8754 (tt) REVERT: C 93 PHE cc_start: 0.8855 (t80) cc_final: 0.8596 (t80) REVERT: C 120 TYR cc_start: 0.5867 (OUTLIER) cc_final: 0.5423 (t80) REVERT: C 159 GLU cc_start: 0.8122 (tp30) cc_final: 0.7918 (pm20) REVERT: C 180 MET cc_start: -0.0980 (tpt) cc_final: -0.1291 (tpt) REVERT: C 208 ARG cc_start: 0.7064 (mtp180) cc_final: 0.6591 (mtp180) REVERT: C 216 LYS cc_start: 0.8279 (mtpt) cc_final: 0.8006 (mtpt) REVERT: C 227 TYR cc_start: 0.8924 (m-80) cc_final: 0.8553 (m-80) REVERT: C 238 LYS cc_start: 0.8140 (ptpp) cc_final: 0.7605 (ptpp) REVERT: C 242 ASP cc_start: 0.5986 (m-30) cc_final: 0.5139 (m-30) REVERT: C 268 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.6122 (mtt) REVERT: A 19 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8995 (mt) REVERT: A 260 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.9005 (mtp) REVERT: A 617 GLU cc_start: 0.8147 (tp30) cc_final: 0.7879 (tp30) REVERT: A 764 GLN cc_start: 0.8873 (mt0) cc_final: 0.8429 (mp10) REVERT: A 906 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8912 (mm-30) REVERT: A 1002 ASP cc_start: 0.8327 (m-30) cc_final: 0.7890 (m-30) REVERT: B 390 LEU cc_start: 0.9308 (mt) cc_final: 0.9079 (mt) REVERT: F 41 TYR cc_start: 0.5520 (m-80) cc_final: 0.4827 (m-10) REVERT: F 154 PHE cc_start: 0.6155 (m-80) cc_final: 0.5599 (m-80) REVERT: F 214 GLN cc_start: 0.8019 (mm110) cc_final: 0.7678 (mm-40) REVERT: F 218 THR cc_start: 0.7273 (OUTLIER) cc_final: 0.6947 (m) REVERT: F 261 MET cc_start: 0.8444 (mmm) cc_final: 0.8113 (mmm) REVERT: F 342 MET cc_start: 0.8659 (mmm) cc_final: 0.8224 (mmm) REVERT: F 351 TYR cc_start: 0.8731 (t80) cc_final: 0.8400 (t80) REVERT: E 436 GLN cc_start: 0.8728 (tp40) cc_final: 0.8351 (tp40) outliers start: 65 outliers final: 44 residues processed: 407 average time/residue: 0.2136 time to fit residues: 129.7017 Evaluate side-chains 402 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 350 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 516 CYS Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 573 MET Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 981 LEU Chi-restraints excluded: chain D residue 1074 ASP Chi-restraints excluded: chain D residue 1192 PHE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 120 TYR Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 735 TRP Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1171 ASP Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain F residue 288 CYS Chi-restraints excluded: chain F residue 308 LYS Chi-restraints excluded: chain F residue 350 CYS Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 483 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 81 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 265 optimal weight: 0.9980 chunk 352 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 221 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 306 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 888 GLN C 222 HIS C 321 ASN ** A 690 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN B 603 GLN F 253 GLN ** E 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 509 ASN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.065141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.042655 restraints weight = 211351.621| |-----------------------------------------------------------------------------| r_work (start): 0.2394 rms_B_bonded: 4.05 r_work: 0.2266 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2266 r_free = 0.2266 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2266 r_free = 0.2266 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 28805 Z= 0.214 Angle : 0.642 11.187 39036 Z= 0.325 Chirality : 0.044 0.225 4448 Planarity : 0.005 0.089 4970 Dihedral : 5.345 57.605 3867 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.13 % Allowed : 11.15 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3518 helix: 1.10 (0.14), residues: 1263 sheet: -0.16 (0.19), residues: 755 loop : -1.61 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 792 TYR 0.021 0.002 TYR E 438 PHE 0.028 0.002 PHE E 439 TRP 0.040 0.002 TRP F 198 HIS 0.009 0.001 HIS C 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 (28803) covalent geometry : angle 0.64155 / 0.33 (39032) SS BOND : bond 0.00366 / 0.19 ( 2) SS BOND : angle 1.75644 / 1.06 ( 4) hydrogen bonds : bond 0.04349 / 2.91 ( 1199) hydrogen bonds : angle 4.51809 / 3.07 ( 3445) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 354 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 487 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8676 (mt) REVERT: D 573 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.7482 (pp-130) REVERT: D 721 ASP cc_start: 0.8171 (t0) cc_final: 0.7831 (t0) REVERT: D 783 GLN cc_start: 0.8251 (mm110) cc_final: 0.7880 (mm-40) REVERT: C 91 ARG cc_start: 0.8023 (ttm110) cc_final: 0.7479 (mtt90) REVERT: C 93 PHE cc_start: 0.8866 (t80) cc_final: 0.8486 (t80) REVERT: C 159 GLU cc_start: 0.8164 (tp30) cc_final: 0.7878 (pm20) REVERT: C 180 MET cc_start: -0.0872 (tpt) cc_final: -0.1190 (tpt) REVERT: C 208 ARG cc_start: 0.7180 (mtp180) cc_final: 0.6742 (mtp180) REVERT: C 216 LYS cc_start: 0.8344 (mtpt) cc_final: 0.8079 (mtpt) REVERT: C 238 LYS cc_start: 0.8110 (ptpp) cc_final: 0.7639 (ptpp) REVERT: C 242 ASP cc_start: 0.6005 (m-30) cc_final: 0.5228 (m-30) REVERT: A 19 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8998 (mt) REVERT: A 260 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.9008 (mtp) REVERT: A 617 GLU cc_start: 0.8270 (tp30) cc_final: 0.7983 (tp30) REVERT: A 764 GLN cc_start: 0.8898 (mt0) cc_final: 0.8452 (mp10) REVERT: A 906 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8953 (mm-30) REVERT: A 1002 ASP cc_start: 0.8339 (m-30) cc_final: 0.7915 (m-30) REVERT: B 390 LEU cc_start: 0.9317 (mt) cc_final: 0.9095 (mt) REVERT: F 41 TYR cc_start: 0.5496 (m-80) cc_final: 0.4889 (m-80) REVERT: F 154 PHE cc_start: 0.6233 (m-80) cc_final: 0.5609 (m-80) REVERT: F 163 GLU cc_start: 0.8503 (tp30) cc_final: 0.8294 (tp30) REVERT: F 198 TRP cc_start: 0.6918 (p-90) cc_final: 0.6498 (p-90) REVERT: F 261 MET cc_start: 0.8494 (mmm) cc_final: 0.8059 (mmm) REVERT: F 351 TYR cc_start: 0.8764 (t80) cc_final: 0.8257 (t80) REVERT: E 439 PHE cc_start: 0.8806 (t80) cc_final: 0.8434 (t80) outliers start: 66 outliers final: 53 residues processed: 399 average time/residue: 0.2178 time to fit residues: 130.2546 Evaluate side-chains 404 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 347 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 516 CYS Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 573 MET Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 712 SER Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 823 MET Chi-restraints excluded: chain D residue 1074 ASP Chi-restraints excluded: chain D residue 1192 PHE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 735 TRP Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1171 ASP Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 288 CYS Chi-restraints excluded: chain F residue 308 LYS Chi-restraints excluded: chain F residue 350 CYS Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 522 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 36 optimal weight: 0.7980 chunk 202 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 185 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 321 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 292 optimal weight: 6.9990 chunk 171 optimal weight: 0.0770 chunk 129 optimal weight: 0.4980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 888 GLN ** A 690 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 ASN F 253 GLN E 509 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.066353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.044029 restraints weight = 192948.777| |-----------------------------------------------------------------------------| r_work (start): 0.2438 rms_B_bonded: 3.88 r_work: 0.2313 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2314 r_free = 0.2314 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2314 r_free = 0.2314 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 28805 Z= 0.149 Angle : 0.588 11.068 39036 Z= 0.296 Chirality : 0.042 0.252 4448 Planarity : 0.004 0.094 4970 Dihedral : 5.020 49.370 3863 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.78 % Allowed : 11.69 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3518 helix: 1.28 (0.14), residues: 1268 sheet: -0.09 (0.19), residues: 736 loop : -1.60 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 751 TYR 0.012 0.001 TYR D 935 PHE 0.037 0.002 PHE E 389 TRP 0.024 0.002 TRP F 198 HIS 0.006 0.001 HIS A 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (28803) covalent geometry : angle 0.58785 / 0.30 (39032) SS BOND : bond 0.00167 / 0.09 ( 2) SS BOND : angle 1.85974 / 1.11 ( 4) hydrogen bonds : bond 0.03788 / 2.54 ( 1199) hydrogen bonds : angle 4.39071 / 2.98 ( 3445) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 358 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 448 ARG cc_start: 0.8540 (ttp80) cc_final: 0.8308 (ttp80) REVERT: D 487 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8589 (mt) REVERT: D 573 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.7497 (pp-130) REVERT: D 604 ARG cc_start: 0.8250 (mtp85) cc_final: 0.7967 (mmm-85) REVERT: D 721 ASP cc_start: 0.8092 (t0) cc_final: 0.7605 (t0) REVERT: D 783 GLN cc_start: 0.8139 (mm110) cc_final: 0.7809 (mm-40) REVERT: C 91 ARG cc_start: 0.7970 (ttm110) cc_final: 0.7475 (mtt90) REVERT: C 120 TYR cc_start: 0.5759 (OUTLIER) cc_final: 0.5359 (t80) REVERT: C 180 MET cc_start: -0.1017 (tpt) cc_final: -0.1295 (tpt) REVERT: C 208 ARG cc_start: 0.7107 (mtp180) cc_final: 0.6703 (mtp180) REVERT: C 216 LYS cc_start: 0.8265 (mtpt) cc_final: 0.8009 (mtpt) REVERT: C 227 TYR cc_start: 0.8688 (m-80) cc_final: 0.8196 (m-10) REVERT: C 238 LYS cc_start: 0.8042 (ptpp) cc_final: 0.7613 (ptpp) REVERT: C 242 ASP cc_start: 0.5909 (m-30) cc_final: 0.5199 (m-30) REVERT: C 265 CYS cc_start: 0.8636 (p) cc_final: 0.8042 (m) REVERT: A 19 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8990 (mt) REVERT: A 260 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8997 (mtp) REVERT: A 617 GLU cc_start: 0.8156 (tp30) cc_final: 0.7893 (tp30) REVERT: A 764 GLN cc_start: 0.8934 (mt0) cc_final: 0.8700 (mp10) REVERT: A 906 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8912 (mm-30) REVERT: A 1002 ASP cc_start: 0.8316 (m-30) cc_final: 0.7870 (m-30) REVERT: B 390 LEU cc_start: 0.9313 (mt) cc_final: 0.9094 (mt) REVERT: F 41 TYR cc_start: 0.5538 (m-80) cc_final: 0.5327 (m-10) REVERT: F 154 PHE cc_start: 0.6235 (m-80) cc_final: 0.5912 (m-80) REVERT: F 214 GLN cc_start: 0.8003 (mm110) cc_final: 0.7711 (mm-40) REVERT: F 253 GLN cc_start: 0.8677 (mm110) cc_final: 0.8445 (mm-40) REVERT: F 261 MET cc_start: 0.8456 (mmm) cc_final: 0.8075 (mmm) REVERT: F 351 TYR cc_start: 0.8759 (t80) cc_final: 0.8354 (t80) REVERT: E 439 PHE cc_start: 0.8675 (t80) cc_final: 0.8194 (t80) REVERT: E 453 ARG cc_start: 0.7893 (ttt180) cc_final: 0.7455 (ttm-80) outliers start: 55 outliers final: 44 residues processed: 397 average time/residue: 0.2110 time to fit residues: 125.4737 Evaluate side-chains 399 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 350 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 573 MET Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 1074 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 120 TYR Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 735 TRP Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1171 ASP Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 308 LYS Chi-restraints excluded: chain F residue 350 CYS Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 522 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 131 optimal weight: 0.9990 chunk 84 optimal weight: 0.2980 chunk 175 optimal weight: 0.5980 chunk 176 optimal weight: 0.4980 chunk 126 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 171 optimal weight: 0.0970 chunk 254 optimal weight: 0.9980 chunk 342 optimal weight: 0.0670 chunk 162 optimal weight: 0.5980 chunk 184 optimal weight: 1.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 862 GLN D 892 ASN C 321 ASN ** A 690 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 HIS A F 339 GLN ** E 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 ASN E 509 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.067247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.044896 restraints weight = 213875.451| |-----------------------------------------------------------------------------| r_work (start): 0.2464 rms_B_bonded: 4.09 r_work: 0.2337 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2339 r_free = 0.2339 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2339 r_free = 0.2339 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 28805 Z= 0.123 Angle : 0.574 11.066 39036 Z= 0.286 Chirality : 0.041 0.253 4448 Planarity : 0.004 0.096 4970 Dihedral : 4.839 52.152 3861 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.84 % Allowed : 11.57 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.14), residues: 3518 helix: 1.49 (0.15), residues: 1262 sheet: -0.09 (0.19), residues: 733 loop : -1.49 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 751 TYR 0.017 0.001 TYR F 125 PHE 0.027 0.001 PHE E 439 TRP 0.026 0.001 TRP C 198 HIS 0.006 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (28803) covalent geometry : angle 0.57337 / 0.29 (39032) SS BOND : bond 0.00192 / 0.10 ( 2) SS BOND : angle 1.95051 / 1.14 ( 4) hydrogen bonds : bond 0.03483 / 2.34 ( 1199) hydrogen bonds : angle 4.28369 / 2.91 ( 3445) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 359 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 448 ARG cc_start: 0.8566 (ttp80) cc_final: 0.8331 (ttp80) REVERT: D 487 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8570 (mt) REVERT: D 573 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7426 (pp-130) REVERT: D 604 ARG cc_start: 0.8239 (mtp85) cc_final: 0.7977 (mmm-85) REVERT: D 721 ASP cc_start: 0.8079 (t0) cc_final: 0.7694 (t0) REVERT: D 783 GLN cc_start: 0.8008 (mm110) cc_final: 0.7678 (mm-40) REVERT: C 91 ARG cc_start: 0.7989 (ttm110) cc_final: 0.7489 (mtt90) REVERT: C 120 TYR cc_start: 0.5720 (OUTLIER) cc_final: 0.5284 (t80) REVERT: C 180 MET cc_start: -0.0990 (tpt) cc_final: -0.1265 (tpt) REVERT: C 208 ARG cc_start: 0.7129 (mtp180) cc_final: 0.6717 (mtp180) REVERT: C 216 LYS cc_start: 0.8236 (mtpt) cc_final: 0.7983 (mtpt) REVERT: C 238 LYS cc_start: 0.8037 (ptpp) cc_final: 0.7630 (ptpp) REVERT: C 242 ASP cc_start: 0.6137 (m-30) cc_final: 0.5371 (m-30) REVERT: C 268 MET cc_start: 0.6561 (ptm) cc_final: 0.6282 (ptm) REVERT: C 278 ILE cc_start: 0.7545 (mt) cc_final: 0.7138 (mt) REVERT: A 19 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8932 (mt) REVERT: A 260 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8975 (mtp) REVERT: A 764 GLN cc_start: 0.8909 (mt0) cc_final: 0.8664 (mp10) REVERT: A 906 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8888 (mm-30) REVERT: A 1002 ASP cc_start: 0.8328 (m-30) cc_final: 0.7879 (m-30) REVERT: B 390 LEU cc_start: 0.9296 (mt) cc_final: 0.9074 (mt) REVERT: F 154 PHE cc_start: 0.6397 (m-80) cc_final: 0.5855 (m-80) REVERT: F 214 GLN cc_start: 0.7918 (mm110) cc_final: 0.7639 (mm-40) REVERT: F 245 ARG cc_start: 0.8020 (tpp-160) cc_final: 0.7741 (ttp-170) REVERT: F 261 MET cc_start: 0.8446 (mmm) cc_final: 0.8122 (mmm) REVERT: F 339 GLN cc_start: 0.8458 (mt0) cc_final: 0.8230 (mt0) REVERT: F 351 TYR cc_start: 0.8781 (t80) cc_final: 0.8357 (t80) REVERT: E 453 ARG cc_start: 0.7922 (ttt180) cc_final: 0.7490 (ttm-80) outliers start: 57 outliers final: 48 residues processed: 399 average time/residue: 0.2107 time to fit residues: 125.8404 Evaluate side-chains 398 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 345 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 573 MET Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 1074 ASP Chi-restraints excluded: chain D residue 1192 PHE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 120 TYR Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 735 TRP Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1171 ASP Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 288 CYS Chi-restraints excluded: chain F residue 308 LYS Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 350 CYS Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 522 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 126 optimal weight: 0.1980 chunk 231 optimal weight: 0.7980 chunk 163 optimal weight: 0.5980 chunk 230 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 349 optimal weight: 0.8980 chunk 274 optimal weight: 0.0870 chunk 92 optimal weight: 0.0870 chunk 121 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 221 optimal weight: 0.7980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 257 HIS C 321 ASN ** A 690 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 GLN ** E 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 509 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.067560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.045246 restraints weight = 185479.934| |-----------------------------------------------------------------------------| r_work (start): 0.2477 rms_B_bonded: 3.78 r_work: 0.2357 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2358 r_free = 0.2358 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2358 r_free = 0.2358 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 28805 Z= 0.122 Angle : 0.577 10.556 39036 Z= 0.288 Chirality : 0.041 0.238 4448 Planarity : 0.004 0.097 4970 Dihedral : 4.759 54.503 3859 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.72 % Allowed : 11.76 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3518 helix: 1.59 (0.15), residues: 1258 sheet: -0.04 (0.19), residues: 734 loop : -1.44 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 751 TYR 0.013 0.001 TYR F 125 PHE 0.025 0.001 PHE E 439 TRP 0.027 0.001 TRP C 198 HIS 0.004 0.001 HIS A 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (28803) covalent geometry : angle 0.57686 / 0.29 (39032) SS BOND : bond 0.00184 / 0.09 ( 2) SS BOND : angle 2.04147 / 1.22 ( 4) hydrogen bonds : bond 0.03459 / 2.33 ( 1199) hydrogen bonds : angle 4.22189 / 2.87 ( 3445) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 347 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 448 ARG cc_start: 0.8586 (ttp80) cc_final: 0.8342 (ttp80) REVERT: D 487 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8600 (mt) REVERT: D 573 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7411 (pp-130) REVERT: D 604 ARG cc_start: 0.8184 (mtp85) cc_final: 0.7928 (mmm-85) REVERT: D 721 ASP cc_start: 0.7896 (t0) cc_final: 0.7466 (t0) REVERT: C 120 TYR cc_start: 0.5647 (OUTLIER) cc_final: 0.5233 (t80) REVERT: C 159 GLU cc_start: 0.8212 (tp30) cc_final: 0.7880 (tp30) REVERT: C 180 MET cc_start: -0.0755 (tpt) cc_final: -0.1005 (tpt) REVERT: C 208 ARG cc_start: 0.7149 (mtp180) cc_final: 0.6721 (mtp180) REVERT: C 216 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7963 (mtpt) REVERT: C 238 LYS cc_start: 0.8012 (ptpp) cc_final: 0.7601 (ptpp) REVERT: C 242 ASP cc_start: 0.6175 (m-30) cc_final: 0.5269 (m-30) REVERT: C 265 CYS cc_start: 0.8693 (p) cc_final: 0.8006 (m) REVERT: C 268 MET cc_start: 0.6725 (ptm) cc_final: 0.6357 (ptm) REVERT: C 321 ASN cc_start: 0.7948 (m-40) cc_final: 0.7683 (m110) REVERT: A 19 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8917 (mt) REVERT: A 764 GLN cc_start: 0.8893 (mt0) cc_final: 0.8633 (mp10) REVERT: A 906 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8867 (mm-30) REVERT: A 1002 ASP cc_start: 0.8299 (m-30) cc_final: 0.7859 (m-30) REVERT: B 390 LEU cc_start: 0.9308 (mt) cc_final: 0.9090 (mt) REVERT: F 154 PHE cc_start: 0.6417 (m-80) cc_final: 0.5921 (m-80) REVERT: F 215 GLU cc_start: 0.7884 (mp0) cc_final: 0.7646 (pm20) REVERT: F 261 MET cc_start: 0.8406 (mmm) cc_final: 0.8068 (mmm) REVERT: F 339 GLN cc_start: 0.8429 (mt0) cc_final: 0.8199 (mt0) REVERT: F 342 MET cc_start: 0.8640 (mmm) cc_final: 0.8363 (mmm) REVERT: F 351 TYR cc_start: 0.8783 (t80) cc_final: 0.8358 (t80) REVERT: E 453 ARG cc_start: 0.7959 (ttt180) cc_final: 0.7559 (ttm-80) outliers start: 53 outliers final: 45 residues processed: 385 average time/residue: 0.2406 time to fit residues: 138.7261 Evaluate side-chains 393 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 344 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 573 MET Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 1074 ASP Chi-restraints excluded: chain D residue 1192 PHE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 120 TYR Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 735 TRP Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1171 ASP Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain F residue 288 CYS Chi-restraints excluded: chain F residue 308 LYS Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 350 CYS Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 522 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 123 optimal weight: 0.0770 chunk 107 optimal weight: 0.0170 chunk 310 optimal weight: 1.9990 chunk 171 optimal weight: 0.0980 chunk 132 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 263 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 320 optimal weight: 0.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 690 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 509 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.067255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.045034 restraints weight = 187077.679| |-----------------------------------------------------------------------------| r_work (start): 0.2467 rms_B_bonded: 3.81 r_work: 0.2345 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2347 r_free = 0.2347 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2347 r_free = 0.2347 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 28805 Z= 0.132 Angle : 0.586 10.218 39036 Z= 0.293 Chirality : 0.041 0.266 4448 Planarity : 0.004 0.095 4970 Dihedral : 4.793 56.337 3859 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.59 % Allowed : 11.92 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 3518 helix: 1.57 (0.15), residues: 1260 sheet: -0.02 (0.19), residues: 735 loop : -1.43 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 751 TYR 0.012 0.001 TYR F 125 PHE 0.024 0.002 PHE E 389 TRP 0.027 0.001 TRP C 198 HIS 0.005 0.001 HIS A 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (28803) covalent geometry : angle 0.58543 / 0.29 (39032) SS BOND : bond 0.00156 / 0.07 ( 2) SS BOND : angle 2.06984 / 1.23 ( 4) hydrogen bonds : bond 0.03552 / 2.39 ( 1199) hydrogen bonds : angle 4.23229 / 2.88 ( 3445) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7036 Ramachandran restraints generated. 3518 Oldfield, 0 Emsley, 3518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 345 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 448 ARG cc_start: 0.8604 (ttp80) cc_final: 0.8356 (ttp80) REVERT: D 487 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8583 (mt) REVERT: D 573 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7431 (pp-130) REVERT: D 604 ARG cc_start: 0.8203 (mtp85) cc_final: 0.7956 (mmm-85) REVERT: D 721 ASP cc_start: 0.7915 (t0) cc_final: 0.7535 (t0) REVERT: C 120 TYR cc_start: 0.5693 (OUTLIER) cc_final: 0.5275 (t80) REVERT: C 159 GLU cc_start: 0.8233 (tp30) cc_final: 0.7870 (tp30) REVERT: C 180 MET cc_start: -0.0767 (tpt) cc_final: -0.1030 (tpt) REVERT: C 208 ARG cc_start: 0.7196 (mtp180) cc_final: 0.6780 (mtp180) REVERT: C 216 LYS cc_start: 0.8229 (mtpt) cc_final: 0.7879 (mmmt) REVERT: C 238 LYS cc_start: 0.8054 (ptpp) cc_final: 0.7641 (ptpp) REVERT: C 242 ASP cc_start: 0.6052 (m-30) cc_final: 0.5230 (m-30) REVERT: C 265 CYS cc_start: 0.8677 (p) cc_final: 0.8046 (m) REVERT: C 278 ILE cc_start: 0.7554 (mt) cc_final: 0.7197 (mt) REVERT: A 764 GLN cc_start: 0.8895 (mt0) cc_final: 0.8626 (mp10) REVERT: A 906 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8887 (mm-30) REVERT: A 1002 ASP cc_start: 0.8320 (m-30) cc_final: 0.7880 (m-30) REVERT: B 390 LEU cc_start: 0.9287 (mt) cc_final: 0.9066 (mt) REVERT: F 154 PHE cc_start: 0.6397 (m-80) cc_final: 0.5879 (m-80) REVERT: F 214 GLN cc_start: 0.7824 (mm110) cc_final: 0.7502 (mm-40) REVERT: F 215 GLU cc_start: 0.7869 (mp0) cc_final: 0.7640 (pm20) REVERT: F 240 LYS cc_start: 0.8483 (mptt) cc_final: 0.8228 (mmtm) REVERT: F 261 MET cc_start: 0.8433 (mmm) cc_final: 0.8085 (mmm) REVERT: F 339 GLN cc_start: 0.8425 (mt0) cc_final: 0.8191 (mt0) REVERT: F 351 TYR cc_start: 0.8791 (t80) cc_final: 0.8288 (t80) REVERT: E 439 PHE cc_start: 0.8696 (t80) cc_final: 0.8145 (t80) REVERT: E 453 ARG cc_start: 0.7984 (ttt180) cc_final: 0.7554 (ttm-80) outliers start: 49 outliers final: 45 residues processed: 381 average time/residue: 0.2445 time to fit residues: 139.0296 Evaluate side-chains 389 residues out of total 3133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 341 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 573 MET Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 1074 ASP Chi-restraints excluded: chain D residue 1192 PHE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 120 TYR Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 735 TRP Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1171 ASP Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain F residue 288 CYS Chi-restraints excluded: chain F residue 308 LYS Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 350 CYS Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 522 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 202 optimal weight: 0.9980 chunk 320 optimal weight: 0.5980 chunk 339 optimal weight: 1.9990 chunk 329 optimal weight: 0.7980 chunk 273 optimal weight: 0.9980 chunk 161 optimal weight: 0.0010 chunk 44 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 GLN ** E 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 509 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.066147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.043737 restraints weight = 191821.517| |-----------------------------------------------------------------------------| r_work (start): 0.2427 rms_B_bonded: 3.87 r_work: 0.2305 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2308 r_free = 0.2308 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2308 r_free = 0.2308 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 28805 Z= 0.173 Angle : 0.625 9.998 39036 Z= 0.314 Chirality : 0.042 0.273 4448 Planarity : 0.005 0.095 4970 Dihedral : 4.999 58.011 3859 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.68 % Allowed : 12.01 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.14), residues: 3518 helix: 1.44 (0.15), residues: 1256 sheet: -0.06 (0.19), residues: 750 loop : -1.43 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 751 TYR 0.012 0.001 TYR D 935 PHE 0.025 0.002 PHE E 389 TRP 0.026 0.002 TRP C 198 HIS 0.007 0.001 HIS A 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (28803) covalent geometry : angle 0.62480 / 0.31 (39032) SS BOND : bond 0.00198 / 0.10 ( 2) SS BOND : angle 2.01333 / 1.21 ( 4) hydrogen bonds : bond 0.03973 / 2.67 ( 1199) hydrogen bonds : angle 4.35558 / 2.96 ( 3445) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9055.96 seconds wall clock time: 155 minutes 31.14 seconds (9331.14 seconds total)