Starting phenix.real_space_refine on Fri Mar 6 22:41:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c97_30307/03_2026/7c97_30307.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c97_30307/03_2026/7c97_30307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7c97_30307/03_2026/7c97_30307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c97_30307/03_2026/7c97_30307.map" model { file = "/net/cci-nas-00/data/ceres_data/7c97_30307/03_2026/7c97_30307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c97_30307/03_2026/7c97_30307.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 111 5.49 5 Mg 1 5.21 5 S 147 5.16 5 C 21672 2.51 5 N 6173 2.21 5 O 6943 1.98 5 H 532 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35581 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1312 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain: "I" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1663 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 190} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1629 Classifications: {'peptide': 201} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 185} Chain: "K" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1050 Classifications: {'peptide': 67} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 62} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1787 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "B" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1755 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 216} Chain breaks: 1 Chain: "C" Number of atoms: 10569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10569 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "D" Number of atoms: 10368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1343, 10368 Classifications: {'peptide': 1343} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1287} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3845 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 14, 'TRANS': 457} Chain breaks: 2 Chain: "G" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 973 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain breaks: 2 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20230 SG CYS D 70 111.100 84.467 62.617 1.00 14.03 S ATOM 20244 SG CYS D 72 111.997 83.736 59.315 1.00 18.97 S ATOM 20352 SG CYS D 85 114.539 84.803 62.251 1.00 19.52 S ATOM 20376 SG CYS D 88 111.467 87.575 61.109 1.00 24.48 S ATOM 26586 SG CYS D 888 84.673 99.016 120.932 1.00 18.36 S ATOM 26637 SG CYS D 895 83.190 95.803 122.142 1.00 12.88 S ATOM 26658 SG CYS D 898 81.593 98.760 122.911 1.00 10.20 S Time building chain proxies: 7.59, per 1000 atoms: 0.21 Number of scatterers: 35581 At special positions: 0 Unit cell: (172.524, 193.436, 159.454, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 147 16.00 P 111 15.00 Mg 1 11.99 O 6943 8.00 N 6173 7.00 C 21672 6.00 H 532 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 70 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 88 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 85 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 72 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 898 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 888 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 895 " Number of angles added : 6 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7754 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 50 sheets defined 39.3% alpha, 8.6% beta 21 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'I' and resid 19 through 32 removed outlier: 3.520A pdb=" N HIS I 23 " --> pdb=" O ASP I 19 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE I 27 " --> pdb=" O HIS I 23 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS I 32 " --> pdb=" O VAL I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 53 removed outlier: 3.528A pdb=" N ILE I 51 " --> pdb=" O PRO I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 83 removed outlier: 3.850A pdb=" N ASP I 80 " --> pdb=" O MET I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 108 removed outlier: 3.653A pdb=" N GLU I 98 " --> pdb=" O VAL I 94 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET I 103 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS I 104 " --> pdb=" O ARG I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 120 Processing helix chain 'I' and resid 121 through 139 removed outlier: 3.547A pdb=" N ASP I 126 " --> pdb=" O ALA I 122 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU I 135 " --> pdb=" O GLN I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 146 removed outlier: 4.432A pdb=" N GLN I 145 " --> pdb=" O PRO I 141 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS I 146 " --> pdb=" O VAL I 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 141 through 146' Processing helix chain 'I' and resid 155 through 160 removed outlier: 3.523A pdb=" N CYS I 159 " --> pdb=" O SER I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 167 removed outlier: 3.587A pdb=" N ARG I 167 " --> pdb=" O PRO I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 172 removed outlier: 3.802A pdb=" N LEU I 171 " --> pdb=" O LEU I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 191 removed outlier: 3.971A pdb=" N LEU I 183 " --> pdb=" O GLY I 179 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG I 189 " --> pdb=" O GLY I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 198 Processing helix chain 'I' and resid 201 through 206 removed outlier: 3.519A pdb=" N GLU I 206 " --> pdb=" O GLU I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 209 No H-bonds generated for 'chain 'I' and resid 207 through 209' Processing helix chain 'J' and resid 19 through 33 Processing helix chain 'J' and resid 47 through 52 removed outlier: 3.858A pdb=" N LEU J 50 " --> pdb=" O PRO J 47 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE J 51 " --> pdb=" O GLN J 48 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP J 52 " --> pdb=" O ASP J 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 47 through 52' Processing helix chain 'J' and resid 72 through 83 removed outlier: 3.747A pdb=" N GLU J 77 " --> pdb=" O ARG J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 107 removed outlier: 3.721A pdb=" N ARG J 96 " --> pdb=" O TYR J 92 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY J 97 " --> pdb=" O PRO J 93 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU J 98 " --> pdb=" O VAL J 94 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS J 104 " --> pdb=" O ARG J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 114 Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 121 through 139 removed outlier: 3.706A pdb=" N ASP J 126 " --> pdb=" O ALA J 122 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA J 127 " --> pdb=" O SER J 123 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS J 130 " --> pdb=" O ASP J 126 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN J 131 " --> pdb=" O ALA J 127 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU J 135 " --> pdb=" O GLN J 131 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE J 139 " --> pdb=" O GLU J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 145 Processing helix chain 'J' and resid 155 through 160 removed outlier: 3.715A pdb=" N TYR J 160 " --> pdb=" O VAL J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 166 Processing helix chain 'J' and resid 167 through 172 Processing helix chain 'J' and resid 180 through 191 removed outlier: 3.943A pdb=" N GLY J 185 " --> pdb=" O LYS J 181 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR J 186 " --> pdb=" O GLU J 182 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET J 187 " --> pdb=" O LEU J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 198 Processing helix chain 'J' and resid 201 through 206 removed outlier: 4.016A pdb=" N GLU J 206 " --> pdb=" O GLU J 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 261 removed outlier: 4.055A pdb=" N LEU K 260 " --> pdb=" O VAL K 257 " (cutoff:3.500A) Processing helix chain 'K' and resid 263 through 273 removed outlier: 4.039A pdb=" N LEU K 270 " --> pdb=" O SER K 266 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 281 removed outlier: 3.521A pdb=" N ASP K 280 " --> pdb=" O TYR K 277 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 289 removed outlier: 3.512A pdb=" N LEU K 289 " --> pdb=" O GLU K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 299 through 311 removed outlier: 3.802A pdb=" N ILE K 303 " --> pdb=" O SER K 299 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS K 304 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL K 306 " --> pdb=" O GLU K 302 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU K 307 " --> pdb=" O ILE K 303 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG K 310 " --> pdb=" O VAL K 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 51 removed outlier: 3.565A pdb=" N ASN A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 removed outlier: 3.831A pdb=" N LEU A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.624A pdb=" N HIS A 160 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 removed outlier: 4.119A pdb=" N THR A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'B' and resid 34 through 48 removed outlier: 4.028A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 removed outlier: 3.855A pdb=" N LEU B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.734A pdb=" N ILE B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 160' Processing helix chain 'B' and resid 212 through 228 removed outlier: 4.009A pdb=" N ILE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.539A pdb=" N LYS C 9 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 33 removed outlier: 3.542A pdb=" N ASP C 33 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 54 removed outlier: 3.676A pdb=" N ARG C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.973A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 removed outlier: 3.930A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.994A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.500A pdb=" N LEU C 277 " --> pdb=" O HIS C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.825A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 removed outlier: 3.657A pdb=" N GLN C 327 " --> pdb=" O ALA C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.501A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR C 350 " --> pdb=" O TYR C 346 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C 352 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 371 removed outlier: 3.549A pdb=" N VAL C 364 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.989A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.689A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.678A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN C 462 " --> pdb=" O GLU C 458 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.166A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 502 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 820 through 825 removed outlier: 3.717A pdb=" N GLU C 825 " --> pdb=" O ARG C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 removed outlier: 3.833A pdb=" N ALA C 904 " --> pdb=" O LYS C 900 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 977 removed outlier: 3.505A pdb=" N GLU C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET C 951 " --> pdb=" O GLU C 947 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN C 952 " --> pdb=" O ILE C 948 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS C 957 " --> pdb=" O LEU C 953 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA C 969 " --> pdb=" O GLN C 965 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 973 " --> pdb=" O ALA C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1010 Processing helix chain 'C' and resid 1010 through 1038 removed outlier: 3.926A pdb=" N GLN C1017 " --> pdb=" O GLN C1013 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C1036 " --> pdb=" O LYS C1032 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR C1037 " --> pdb=" O ARG C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1132 removed outlier: 3.573A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS C1116 " --> pdb=" O ILE C1112 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET C1119 " --> pdb=" O THR C1115 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS C1122 " --> pdb=" O GLY C1118 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP C1126 " --> pdb=" O LYS C1122 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA C1130 " --> pdb=" O ASP C1126 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET C1131 " --> pdb=" O LYS C1127 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1151 removed outlier: 3.572A pdb=" N GLN C1146 " --> pdb=" O ARG C1142 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR C1149 " --> pdb=" O ILE C1145 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP C1150 " --> pdb=" O GLN C1146 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1168 through 1173 Processing helix chain 'C' and resid 1175 through 1179 removed outlier: 4.170A pdb=" N LYS C1178 " --> pdb=" O ASN C1175 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1200 removed outlier: 3.540A pdb=" N LEU C1198 " --> pdb=" O GLU C1194 " (cutoff:3.500A) Processing helix chain 'C' and resid 1201 through 1203 No H-bonds generated for 'chain 'C' and resid 1201 through 1203' Processing helix chain 'C' and resid 1238 through 1242 removed outlier: 3.739A pdb=" N ASP C1241 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1274 Processing helix chain 'C' and resid 1275 through 1280 Processing helix chain 'C' and resid 1285 through 1290 Processing helix chain 'C' and resid 1303 through 1309 removed outlier: 3.700A pdb=" N ILE C1308 " --> pdb=" O MET C1304 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.780A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL C1325 " --> pdb=" O GLU C1321 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU C1326 " --> pdb=" O SER C1322 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE C1330 " --> pdb=" O LEU C1326 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 removed outlier: 3.517A pdb=" N ARG D 31 " --> pdb=" O PRO D 27 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER D 32 " --> pdb=" O ASP D 28 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 34 " --> pdb=" O ILE D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.693A pdb=" N GLU D 100 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.619A pdb=" N LEU D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 161 through 170 removed outlier: 3.523A pdb=" N LEU D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.749A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 208 removed outlier: 3.537A pdb=" N GLU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 225 removed outlier: 4.411A pdb=" N THR D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS D 222 " --> pdb=" O THR D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 230 removed outlier: 4.450A pdb=" N GLN D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 removed outlier: 4.024A pdb=" N TRP D 236 " --> pdb=" O LYS D 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 268 through 286 removed outlier: 3.703A pdb=" N ARG D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG D 281 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 308 removed outlier: 3.828A pdb=" N ARG D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU D 301 " --> pdb=" O ARG D 297 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 removed outlier: 3.848A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 327 through 332' Processing helix chain 'D' and resid 370 through 377 removed outlier: 4.284A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 removed outlier: 3.633A pdb=" N GLY D 383 " --> pdb=" O PRO D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 403 removed outlier: 3.666A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 416 removed outlier: 4.086A pdb=" N ASP D 413 " --> pdb=" O TRP D 409 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 456 removed outlier: 3.852A pdb=" N ALA D 455 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.560A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.520A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.589A pdb=" N VAL D 592 " --> pdb=" O TYR D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 613 removed outlier: 3.556A pdb=" N ASN D 606 " --> pdb=" O SER D 602 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS D 608 " --> pdb=" O MET D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 634 removed outlier: 3.904A pdb=" N ASP D 622 " --> pdb=" O VAL D 618 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN D 623 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE D 624 " --> pdb=" O PHE D 620 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N MET D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA D 630 " --> pdb=" O TYR D 626 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 663 removed outlier: 4.010A pdb=" N ALA D 657 " --> pdb=" O ILE D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 670 Processing helix chain 'D' and resid 675 through 702 removed outlier: 4.200A pdb=" N LYS D 681 " --> pdb=" O GLU D 677 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA D 688 " --> pdb=" O ASP D 684 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER D 694 " --> pdb=" O ASN D 690 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA D 696 " --> pdb=" O ARG D 692 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP D 699 " --> pdb=" O LYS D 695 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASN D 700 " --> pdb=" O ALA D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 728 Processing helix chain 'D' and resid 733 through 741 removed outlier: 5.086A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 740 " --> pdb=" O GLN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 782 removed outlier: 3.577A pdb=" N ILE D 774 " --> pdb=" O LEU D 770 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG D 780 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 782 through 804 removed outlier: 3.506A pdb=" N THR D 786 " --> pdb=" O GLY D 782 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR D 797 " --> pdb=" O SER D 793 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG D 799 " --> pdb=" O TYR D 795 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D 801 " --> pdb=" O THR D 797 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP D 802 " --> pdb=" O ARG D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 Processing helix chain 'D' and resid 867 through 875 Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.780A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 921 Processing helix chain 'D' and resid 1137 through 1146 removed outlier: 3.970A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.619A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1242 removed outlier: 3.737A pdb=" N ASN D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN D1238 " --> pdb=" O VAL D1234 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP D1239 " --> pdb=" O ASN D1235 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG D1242 " --> pdb=" O GLN D1238 " (cutoff:3.500A) Processing helix chain 'D' and resid 1243 through 1245 No H-bonds generated for 'chain 'D' and resid 1243 through 1245' Processing helix chain 'D' and resid 1280 through 1287 Processing helix chain 'D' and resid 1308 through 1313 removed outlier: 3.644A pdb=" N SER D1313 " --> pdb=" O ILE D1309 " (cutoff:3.500A) Processing helix chain 'D' and resid 1328 through 1339 removed outlier: 3.710A pdb=" N THR D1333 " --> pdb=" O THR D1329 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU D1334 " --> pdb=" O ARG D1330 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D1335 " --> pdb=" O VAL D1331 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1362 through 1370 removed outlier: 3.809A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 11 removed outlier: 3.703A pdb=" N VAL E 10 " --> pdb=" O GLN E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 30 removed outlier: 3.834A pdb=" N ARG E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 removed outlier: 3.645A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 62 through 80 removed outlier: 3.515A pdb=" N GLU E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN E 70 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU E 71 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 112 through 136 removed outlier: 3.827A pdb=" N ASN F 128 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU F 136 " --> pdb=" O CYS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 140 Processing helix chain 'F' and resid 141 through 152 removed outlier: 3.637A pdb=" N GLU F 146 " --> pdb=" O THR F 142 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU F 152 " --> pdb=" O TYR F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 221 removed outlier: 3.617A pdb=" N ARG F 218 " --> pdb=" O PRO F 214 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLU F 219 " --> pdb=" O GLU F 215 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE F 221 " --> pdb=" O ALA F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 231 removed outlier: 4.737A pdb=" N VAL F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 234 No H-bonds generated for 'chain 'F' and resid 232 through 234' Processing helix chain 'F' and resid 244 through 255 removed outlier: 4.170A pdb=" N ILE F 249 " --> pdb=" O ALA F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 259 Processing helix chain 'F' and resid 262 through 292 removed outlier: 3.669A pdb=" N PHE F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP F 267 " --> pdb=" O PRO F 263 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL F 275 " --> pdb=" O ASN F 271 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP F 278 " --> pdb=" O ARG F 274 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR F 282 " --> pdb=" O ASP F 278 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLN F 283 " --> pdb=" O ARG F 279 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS F 289 " --> pdb=" O ARG F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 307 removed outlier: 4.576A pdb=" N PHE F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE F 303 " --> pdb=" O LYS F 299 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE F 306 " --> pdb=" O PHE F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 318 Processing helix chain 'F' and resid 319 through 323 removed outlier: 3.619A pdb=" N ASN F 323 " --> pdb=" O ILE F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 331 removed outlier: 3.877A pdb=" N HIS F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 342 through 351 removed outlier: 3.543A pdb=" N GLU F 349 " --> pdb=" O GLN F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 381 removed outlier: 3.757A pdb=" N MET F 365 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER F 366 " --> pdb=" O ASN F 362 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE F 367 " --> pdb=" O ARG F 363 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY F 368 " --> pdb=" O ARG F 364 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 391 removed outlier: 3.991A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER F 389 " --> pdb=" O ARG F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 416 removed outlier: 3.655A pdb=" N GLN F 406 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU F 407 " --> pdb=" O ASP F 403 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN F 409 " --> pdb=" O ILE F 405 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE F 410 " --> pdb=" O GLN F 406 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS F 414 " --> pdb=" O ILE F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 443 removed outlier: 5.229A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA F 438 " --> pdb=" O TRP F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 474 removed outlier: 3.681A pdb=" N ILE F 457 " --> pdb=" O PRO F 453 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU F 458 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR F 459 " --> pdb=" O HIS F 455 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN F 469 " --> pdb=" O ARG F 465 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU F 471 " --> pdb=" O SER F 467 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN F 472 " --> pdb=" O ARG F 468 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU F 473 " --> pdb=" O GLN F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 481 through 487 Processing helix chain 'F' and resid 492 through 497 Processing helix chain 'F' and resid 511 through 515 removed outlier: 4.085A pdb=" N GLU F 515 " --> pdb=" O GLY F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 522 removed outlier: 3.552A pdb=" N ASP F 521 " --> pdb=" O HIS F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 547 removed outlier: 3.526A pdb=" N THR F 536 " --> pdb=" O LEU F 532 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR F 537 " --> pdb=" O ASP F 533 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG F 541 " --> pdb=" O THR F 537 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA F 542 " --> pdb=" O GLU F 538 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA F 543 " --> pdb=" O SER F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 551 removed outlier: 3.679A pdb=" N LEU F 551 " --> pdb=" O LEU F 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 548 through 551' Processing helix chain 'F' and resid 553 through 562 removed outlier: 4.029A pdb=" N VAL F 558 " --> pdb=" O ARG F 554 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU F 559 " --> pdb=" O GLU F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 581 removed outlier: 3.601A pdb=" N LYS F 578 " --> pdb=" O GLU F 574 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLN F 579 " --> pdb=" O GLU F 575 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE F 580 " --> pdb=" O VAL F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 600 removed outlier: 3.817A pdb=" N GLU F 591 " --> pdb=" O ILE F 587 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG F 596 " --> pdb=" O ALA F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 611 Processing sheet with id=AA1, first strand: chain 'I' and resid 62 through 63 Processing sheet with id=AA2, first strand: chain 'J' and resid 37 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 13 through 17 removed outlier: 4.680A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 198 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 202 " --> pdb=" O ASN A 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.532A pdb=" N VAL A 146 " --> pdb=" O VAL A 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA6, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA7, first strand: chain 'A' and resid 102 through 105 Processing sheet with id=AA8, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.925A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 23 through 24 removed outlier: 4.101A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 27 through 28 Processing sheet with id=AB2, first strand: chain 'B' and resid 97 through 99 removed outlier: 6.799A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.872A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 102 through 104 Processing sheet with id=AB5, first strand: chain 'B' and resid 108 through 110 Processing sheet with id=AB6, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.547A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 66 through 75 removed outlier: 5.298A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS C 115 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB9, first strand: chain 'C' and resid 451 through 453 removed outlier: 3.761A pdb=" N SER C 531 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AC2, first strand: chain 'C' and resid 195 through 196 Processing sheet with id=AC3, first strand: chain 'C' and resid 226 through 230 removed outlier: 4.422A pdb=" N GLU C 226 " --> pdb=" O PHE C 337 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AC5, first strand: chain 'C' and resid 250 through 251 removed outlier: 3.854A pdb=" N ARG C 267 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC7, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.502A pdb=" N THR C 589 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC9, first strand: chain 'C' and resid 633 through 637 Processing sheet with id=AD1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'C' and resid 731 through 732 Processing sheet with id=AD3, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD4, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 3.715A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET C1230 " --> pdb=" O MET C 800 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 832 through 837 removed outlier: 3.836A pdb=" N LEU C1054 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.733A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD8, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.553A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 422 " --> pdb=" O HIS D 469 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1268 through 1269 Processing sheet with id=AE1, first strand: chain 'C' and resid 1336 through 1339 Processing sheet with id=AE2, first strand: chain 'D' and resid 105 through 112 removed outlier: 6.948A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 9.987A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AE4, first strand: chain 'D' and resid 252 through 254 removed outlier: 4.055A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE D 260 " --> pdb=" O ILE F 505 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 547 through 549 Processing sheet with id=AE6, first strand: chain 'D' and resid 553 through 554 removed outlier: 3.602A pdb=" N GLU D 554 " --> pdb=" O LYS D 566 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AE8, first strand: chain 'D' and resid 820 through 821 Processing sheet with id=AE9, first strand: chain 'D' and resid 826 through 827 Processing sheet with id=AF1, first strand: chain 'D' and resid 966 through 967 removed outlier: 3.589A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1001 through 1003 Processing sheet with id=AF3, first strand: chain 'D' and resid 1035 through 1038 removed outlier: 4.453A pdb=" N LEU D1078 " --> pdb=" O TYR D1099 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1162 through 1164 removed outlier: 3.681A pdb=" N THR D1178 " --> pdb=" O ILE D1162 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER D1164 " --> pdb=" O VAL D1176 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU D1188 " --> pdb=" O LEU D1175 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 1277 through 1279 903 hydrogen bonds defined for protein. 2466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 8.12 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 531 1.03 - 1.23: 176 1.23 - 1.42: 14413 1.42 - 1.61: 20981 1.61 - 1.81: 260 Bond restraints: 36361 Sorted by residual: bond pdb=" C LYS C 697 " pdb=" N PRO C 698 " ideal model delta sigma weight residual 1.335 1.295 0.040 8.70e-03 1.32e+04 2.14e+01 bond pdb=" CA LEU C 27 " pdb=" C LEU C 27 " ideal model delta sigma weight residual 1.523 1.490 0.033 1.34e-02 5.57e+03 5.97e+00 bond pdb=" CA LYS D 332 " pdb=" C LYS D 332 " ideal model delta sigma weight residual 1.525 1.499 0.026 1.28e-02 6.10e+03 4.14e+00 bond pdb=" C VAL D 470 " pdb=" N PRO D 471 " ideal model delta sigma weight residual 1.335 1.317 0.018 8.70e-03 1.32e+04 4.09e+00 bond pdb=" C MET C 805 " pdb=" N PRO C 806 " ideal model delta sigma weight residual 1.335 1.319 0.016 8.70e-03 1.32e+04 3.27e+00 ... (remaining 36356 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 48650 2.07 - 4.15: 1312 4.15 - 6.22: 118 6.22 - 8.30: 10 8.30 - 10.37: 3 Bond angle restraints: 50093 Sorted by residual: angle pdb=" N VAL C1159 " pdb=" CA VAL C1159 " pdb=" C VAL C1159 " ideal model delta sigma weight residual 110.62 120.58 -9.96 1.02e+00 9.61e-01 9.53e+01 angle pdb=" N ASP C1160 " pdb=" CA ASP C1160 " pdb=" C ASP C1160 " ideal model delta sigma weight residual 109.41 119.78 -10.37 1.52e+00 4.33e-01 4.65e+01 angle pdb=" N LYS D 334 " pdb=" CA LYS D 334 " pdb=" C LYS D 334 " ideal model delta sigma weight residual 112.72 106.60 6.12 1.14e+00 7.69e-01 2.88e+01 angle pdb=" CA LEU C 27 " pdb=" C LEU C 27 " pdb=" N LEU C 28 " ideal model delta sigma weight residual 116.84 125.13 -8.29 1.71e+00 3.42e-01 2.35e+01 angle pdb=" N PHE D1274 " pdb=" CA PHE D1274 " pdb=" CB PHE D1274 " ideal model delta sigma weight residual 114.17 109.02 5.15 1.14e+00 7.69e-01 2.04e+01 ... (remaining 50088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 20825 35.82 - 71.64: 1058 71.64 - 107.47: 52 107.47 - 143.29: 0 143.29 - 179.11: 4 Dihedral angle restraints: 21939 sinusoidal: 9912 harmonic: 12027 Sorted by residual: dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual -180.00 -152.71 -27.29 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA THR K 263 " pdb=" C THR K 263 " pdb=" N VAL K 264 " pdb=" CA VAL K 264 " ideal model delta harmonic sigma weight residual -180.00 -154.45 -25.55 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA SER D 503 " pdb=" C SER D 503 " pdb=" N GLN D 504 " pdb=" CA GLN D 504 " ideal model delta harmonic sigma weight residual 180.00 -155.42 -24.58 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 21936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4784 0.063 - 0.125: 743 0.125 - 0.188: 27 0.188 - 0.251: 1 0.251 - 0.313: 1 Chirality restraints: 5556 Sorted by residual: chirality pdb=" CA ASP C1160 " pdb=" N ASP C1160 " pdb=" C ASP C1160 " pdb=" CB ASP C1160 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA VAL C1159 " pdb=" N VAL C1159 " pdb=" C VAL C1159 " pdb=" CB VAL C1159 " both_signs ideal model delta sigma weight residual False 2.44 2.24 0.20 2.00e-01 2.50e+01 9.77e-01 chirality pdb=" CA LEU C1161 " pdb=" N LEU C1161 " pdb=" C LEU C1161 " pdb=" CB LEU C1161 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.21e-01 ... (remaining 5553 not shown) Planarity restraints: 6055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C1257 " -0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO C1258 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO C1258 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C1258 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 551 " 0.041 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO C 552 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 552 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 552 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 615 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.12e+00 pdb=" N PRO D 616 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 616 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 616 " -0.032 5.00e-02 4.00e+02 ... (remaining 6052 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 245 2.26 - 2.85: 14684 2.85 - 3.43: 41308 3.43 - 4.02: 62895 4.02 - 4.60: 95232 Nonbonded interactions: 214364 Sorted by model distance: nonbonded pdb=" O VAL K 282 " pdb=" H MET K 316 " model vdw 1.681 2.450 nonbonded pdb=" O VAL K 264 " pdb="HD21 ASN K 268 " model vdw 1.748 2.450 nonbonded pdb=" O LEU K 307 " pdb=" H LEU K 312 " model vdw 1.769 2.450 nonbonded pdb=" OD1 ASP K 280 " pdb=" HE1 TRP K 321 " model vdw 1.941 2.450 nonbonded pdb=" O ASN K 320 " pdb="HD21 ASN K 320 " model vdw 1.968 2.450 ... (remaining 214359 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 19 or resid 22 through 233)) selection = (chain 'B' and resid 7 through 233) } ncs_group { reference = (chain 'I' and resid 10 through 209) selection = (chain 'J' and (resid 10 through 132 or (resid 133 and (name N or name CA or nam \ e C or name O or name CB )) or resid 134 through 209)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 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: 0.290 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 39.950 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.007 0.120 35836 Z= 0.323 Angle : 0.825 16.095 48882 Z= 0.485 Chirality : 0.044 0.313 5556 Planarity : 0.005 0.081 5994 Dihedral : 18.520 179.108 14026 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 33.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.28 % Favored : 87.58 % Rotamer: Outliers : 11.86 % Allowed : 13.41 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % 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: -5.70 (0.10), residues: 4130 helix: -4.29 (0.07), residues: 1437 sheet: -3.87 (0.21), residues: 389 loop : -3.51 (0.11), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 195 TYR 0.017 0.002 TYR C 578 PHE 0.013 0.002 PHE D 380 TRP 0.007 0.001 TRP F 326 HIS 0.005 0.001 HIS C 673 Details of bonding type rmsd covalent geometry : bond 0.00719 (35829) covalent geometry : angle 0.80987 (48876) hydrogen bonds : bond 0.32756 ( 948) hydrogen bonds : angle 11.79859 ( 2552) metal coordination : bond 0.07805 ( 7) metal coordination : angle 14.02232 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 422 poor density : 630 time to evaluate : 1.250 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: I 11 MET cc_start: 0.7442 (ppp) cc_final: 0.5741 (ppp) REVERT: I 57 GLN cc_start: 0.5676 (mt0) cc_final: 0.4821 (tp40) REVERT: I 101 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8790 (tm) REVERT: I 189 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.5436 (ttm-80) REVERT: I 192 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6859 (pm20) REVERT: J 14 PHE cc_start: 0.7286 (m-10) cc_final: 0.6838 (m-10) REVERT: J 184 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7513 (tptt) REVERT: K 289 LEU cc_start: -0.1890 (OUTLIER) cc_final: -0.2158 (tt) REVERT: A 25 LYS cc_start: 0.8867 (mtpt) cc_final: 0.8605 (mtpp) REVERT: B 7 GLU cc_start: 0.4675 (OUTLIER) cc_final: 0.4365 (pm20) REVERT: B 18 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7714 (mm-40) REVERT: B 49 SER cc_start: 0.8092 (p) cc_final: 0.7771 (p) REVERT: B 77 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7321 (m-30) REVERT: B 83 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8672 (mt) REVERT: B 205 MET cc_start: 0.7348 (ttp) cc_final: 0.7148 (ttt) REVERT: C 8 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8031 (mttm) REVERT: C 9 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8538 (mtpp) REVERT: C 32 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8756 (tp) REVERT: C 81 ASP cc_start: 0.7971 (m-30) cc_final: 0.7613 (m-30) REVERT: C 197 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7833 (ttt180) REVERT: C 299 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6632 (ptmt) REVERT: C 332 ARG cc_start: 0.7028 (mmt-90) cc_final: 0.6672 (mmm-85) REVERT: C 370 MET cc_start: 0.7427 (tpt) cc_final: 0.6991 (tpt) REVERT: C 403 MET cc_start: 0.7199 (tmm) cc_final: 0.6901 (tmt) REVERT: C 626 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7097 (mm-30) REVERT: C 704 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8872 (tmm) REVERT: C 827 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8145 (ptm160) REVERT: C 915 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8485 (t70) REVERT: C 1057 LYS cc_start: 0.9440 (OUTLIER) cc_final: 0.9128 (ttpt) REVERT: C 1134 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.6972 (mm-40) REVERT: C 1155 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8510 (m) REVERT: C 1194 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7225 (mt-10) REVERT: D 172 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.5224 (m-80) REVERT: D 255 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7860 (mt) REVERT: D 290 ILE cc_start: 0.9261 (tp) cc_final: 0.8937 (tt) REVERT: D 298 MET cc_start: 0.8165 (ttp) cc_final: 0.7849 (ttp) REVERT: D 368 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8839 (tp) REVERT: D 558 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7069 (p0) REVERT: D 619 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8997 (tp) REVERT: D 634 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7509 (mtp85) REVERT: D 652 GLU cc_start: 0.8047 (mp0) cc_final: 0.7827 (mt-10) REVERT: D 679 TYR cc_start: 0.8258 (t80) cc_final: 0.8000 (t80) REVERT: D 700 ASN cc_start: 0.7745 (t0) cc_final: 0.7464 (t0) REVERT: D 821 MET cc_start: 0.6325 (tpp) cc_final: 0.6073 (mtm) REVERT: D 929 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.6751 (pm20) REVERT: D 930 LEU cc_start: 0.7403 (mt) cc_final: 0.7088 (mt) REVERT: D 999 TYR cc_start: 0.1032 (OUTLIER) cc_final: 0.0128 (m-80) REVERT: D 1023 HIS cc_start: 0.3567 (OUTLIER) cc_final: 0.2060 (p-80) REVERT: D 1052 GLU cc_start: 0.5207 (OUTLIER) cc_final: 0.4700 (mt-10) REVERT: D 1156 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8349 (mm) REVERT: D 1197 ASN cc_start: 0.8001 (m110) cc_final: 0.7262 (m-40) REVERT: D 1282 TYR cc_start: 0.7428 (m-10) cc_final: 0.7217 (m-10) REVERT: D 1325 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.8201 (p90) REVERT: E 18 ASP cc_start: 0.8349 (p0) cc_final: 0.7964 (p0) REVERT: E 56 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: F 131 GLN cc_start: 0.7182 (OUTLIER) cc_final: 0.5402 (pp30) REVERT: F 152 GLU cc_start: 0.2605 (OUTLIER) cc_final: 0.1888 (tp30) REVERT: F 232 ARG cc_start: 0.3572 (OUTLIER) cc_final: 0.2697 (tpt-90) REVERT: F 252 LEU cc_start: 0.5089 (OUTLIER) cc_final: 0.4564 (tp) REVERT: F 316 PHE cc_start: 0.3054 (OUTLIER) cc_final: 0.2755 (m-80) REVERT: F 446 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8858 (pm20) REVERT: F 472 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.7113 (mp10) REVERT: F 500 ILE cc_start: 0.7746 (mm) cc_final: 0.7519 (mt) REVERT: F 507 MET cc_start: 0.8829 (ttp) cc_final: 0.8554 (ttm) REVERT: F 540 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8838 (tt) REVERT: F 573 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7739 (mt) REVERT: F 579 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: F 589 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7284 (mp10) outliers start: 422 outliers final: 239 residues processed: 991 average time/residue: 0.2488 time to fit residues: 388.9246 Evaluate side-chains 753 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 282 poor density : 471 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 192 GLU Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 289 LEU Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 827 ARG Chi-restraints excluded: chain C residue 835 GLU Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 991 LYS Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1057 LYS Chi-restraints excluded: chain C residue 1058 ARG Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1134 GLN Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1246 ARG Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1259 LEU Chi-restraints excluded: chain C residue 1268 GLN Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 634 ARG Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 765 GLU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 797 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 925 GLU Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 986 ASP Chi-restraints excluded: chain D residue 999 TYR Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1052 GLU Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1187 GLU Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1342 ASP Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 152 GLU Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 301 ASN Chi-restraints excluded: chain F residue 316 PHE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 446 GLN Chi-restraints excluded: chain F residue 472 GLN Chi-restraints excluded: chain F residue 525 ASP Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 537 THR Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 573 LEU Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 591 GLU Chi-restraints excluded: chain F residue 604 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.0870 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 23 HIS ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 GLN J 115 ASN K 283 GLN A 37 HIS A 147 GLN A 194 GLN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN B 103 ASN B 147 GLN C 120 GLN C 219 GLN ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN C 673 HIS C 808 ASN C 834 GLN C 955 GLN C1111 GLN C1264 GLN C1268 GLN D 186 GLN D 294 ASN D 365 GLN D 419 HIS ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN D 805 GLN D 865 HIS D 867 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN D1279 GLN E 43 ASN E 73 GLN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 HIS F 464 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.153509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.125649 restraints weight = 58091.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.125891 restraints weight = 145804.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126529 restraints weight = 105015.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126614 restraints weight = 65263.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128542 restraints weight = 52645.171| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 35836 Z= 0.108 Angle : 0.523 9.380 48882 Z= 0.285 Chirality : 0.039 0.138 5556 Planarity : 0.004 0.050 5994 Dihedral : 18.407 175.935 6362 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 36.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 6.80 % Allowed : 19.00 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -4.63 (0.11), residues: 4130 helix: -2.93 (0.10), residues: 1535 sheet: -3.29 (0.23), residues: 373 loop : -3.20 (0.11), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 232 TYR 0.014 0.001 TYR K 277 PHE 0.020 0.001 PHE B 8 TRP 0.014 0.001 TRP D 33 HIS 0.004 0.001 HIS I 85 Details of bonding type rmsd covalent geometry : bond 0.00228 (35829) covalent geometry : angle 0.51911 (48876) hydrogen bonds : bond 0.05900 ( 948) hydrogen bonds : angle 6.10212 ( 2552) metal coordination : bond 0.00806 ( 7) metal coordination : angle 6.04346 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 531 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 42 GLU cc_start: 0.5458 (OUTLIER) cc_final: 0.4599 (tm-30) REVERT: I 57 GLN cc_start: 0.6036 (mt0) cc_final: 0.5144 (tp40) REVERT: J 11 MET cc_start: 0.7930 (ttm) cc_final: 0.7557 (ttp) REVERT: J 14 PHE cc_start: 0.7389 (m-10) cc_final: 0.7174 (m-10) REVERT: J 19 ASP cc_start: 0.5322 (t0) cc_final: 0.4133 (m-30) REVERT: J 20 ILE cc_start: 0.7906 (tt) cc_final: 0.7570 (tt) REVERT: J 81 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7472 (mt-10) REVERT: J 184 LYS cc_start: 0.7969 (mtpt) cc_final: 0.6989 (tptt) REVERT: A 25 LYS cc_start: 0.8972 (mtpt) cc_final: 0.8766 (ttmm) REVERT: B 18 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7518 (mm-40) REVERT: B 77 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7266 (m-30) REVERT: B 162 GLU cc_start: 0.2094 (OUTLIER) cc_final: 0.1173 (tm-30) REVERT: C 8 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7516 (mttm) REVERT: C 245 ARG cc_start: 0.8300 (ttm170) cc_final: 0.7792 (ttm170) REVERT: C 299 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6657 (ptmt) REVERT: C 332 ARG cc_start: 0.6888 (mmt-90) cc_final: 0.6656 (mmm-85) REVERT: C 370 MET cc_start: 0.7283 (tpt) cc_final: 0.7048 (tpt) REVERT: C 626 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7116 (mm-30) REVERT: C 841 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.7659 (mpp80) REVERT: C 903 ARG cc_start: 0.7554 (mmt-90) cc_final: 0.6983 (mmt-90) REVERT: C 1240 ASP cc_start: 0.8099 (p0) cc_final: 0.7812 (p0) REVERT: D 172 PHE cc_start: 0.7054 (OUTLIER) cc_final: 0.4955 (m-80) REVERT: D 223 LEU cc_start: 0.8457 (tp) cc_final: 0.8083 (tp) REVERT: D 255 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7721 (mt) REVERT: D 458 ASN cc_start: 0.8924 (t0) cc_final: 0.8703 (t0) REVERT: D 531 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8964 (mttm) REVERT: D 619 ILE cc_start: 0.9209 (tt) cc_final: 0.8979 (tp) REVERT: D 654 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8705 (mp) REVERT: D 677 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6864 (mm-30) REVERT: D 678 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.5792 (tmm160) REVERT: D 777 HIS cc_start: 0.7558 (t-90) cc_final: 0.7275 (t-90) REVERT: D 788 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8411 (tp) REVERT: D 821 MET cc_start: 0.6488 (tpp) cc_final: 0.6262 (mtm) REVERT: D 849 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6350 (pp) REVERT: D 999 TYR cc_start: 0.0568 (OUTLIER) cc_final: -0.0068 (m-80) REVERT: D 1023 HIS cc_start: 0.3574 (OUTLIER) cc_final: 0.2188 (p-80) REVERT: D 1325 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8067 (p90) REVERT: E 56 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: E 61 ASN cc_start: 0.8327 (t0) cc_final: 0.8080 (t0) REVERT: F 131 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.6405 (pp30) REVERT: F 218 ARG cc_start: 0.6797 (mtm110) cc_final: 0.6428 (tpp80) REVERT: F 266 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.6270 (t80) REVERT: F 316 PHE cc_start: 0.2974 (OUTLIER) cc_final: 0.2408 (m-80) REVERT: F 322 MET cc_start: 0.2959 (tpt) cc_final: 0.2126 (mmm) REVERT: F 446 GLN cc_start: 0.9313 (OUTLIER) cc_final: 0.8986 (pm20) REVERT: F 500 ILE cc_start: 0.7579 (mm) cc_final: 0.7377 (mt) REVERT: F 507 MET cc_start: 0.8860 (ttp) cc_final: 0.8563 (ttm) REVERT: F 579 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7261 (tp40) REVERT: F 589 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.6952 (mp10) outliers start: 242 outliers final: 145 residues processed: 733 average time/residue: 0.2231 time to fit residues: 266.5282 Evaluate side-chains 627 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 457 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 92 TYR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 841 ARG Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 925 GLU Chi-restraints excluded: chain D residue 986 ASP Chi-restraints excluded: chain D residue 999 TYR Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 301 ASN Chi-restraints excluded: chain F residue 316 PHE Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 446 GLN Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 604 SER Chi-restraints excluded: chain F residue 611 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 224 optimal weight: 5.9990 chunk 186 optimal weight: 0.0370 chunk 362 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 348 optimal weight: 0.0970 chunk 72 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 414 optimal weight: 9.9990 overall best weight: 2.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 HIS ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN B 93 GLN ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN C 490 GLN C 677 ASN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 477 GLN D 495 ASN D 865 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN E 70 GLN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.150707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.116750 restraints weight = 58625.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.115106 restraints weight = 75612.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.116353 restraints weight = 75352.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.116689 restraints weight = 41835.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.118296 restraints weight = 36495.853| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35836 Z= 0.150 Angle : 0.515 7.488 48882 Z= 0.275 Chirality : 0.039 0.178 5556 Planarity : 0.003 0.039 5994 Dihedral : 17.763 175.854 6072 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 37.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 6.83 % Allowed : 19.76 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % 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: -4.03 (0.12), residues: 4130 helix: -2.19 (0.12), residues: 1550 sheet: -3.09 (0.23), residues: 398 loop : -3.01 (0.12), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 764 TYR 0.013 0.001 TYR C1018 PHE 0.013 0.001 PHE B 8 TRP 0.009 0.001 TRP I 70 HIS 0.005 0.001 HIS J 23 Details of bonding type rmsd covalent geometry : bond 0.00344 (35829) covalent geometry : angle 0.51133 (48876) hydrogen bonds : bond 0.04733 ( 948) hydrogen bonds : angle 5.44570 ( 2552) metal coordination : bond 0.01077 ( 7) metal coordination : angle 5.27005 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 243 poor density : 474 time to evaluate : 1.304 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: I 42 GLU cc_start: 0.5407 (OUTLIER) cc_final: 0.4445 (tm-30) REVERT: I 57 GLN cc_start: 0.6087 (mt0) cc_final: 0.5511 (tm-30) REVERT: I 85 HIS cc_start: 0.7098 (m170) cc_final: 0.5693 (m170) REVERT: I 112 THR cc_start: 0.7675 (m) cc_final: 0.7437 (t) REVERT: J 81 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7686 (mt-10) REVERT: J 184 LYS cc_start: 0.7841 (mtpt) cc_final: 0.6695 (tptt) REVERT: J 192 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6725 (mm-30) REVERT: J 195 SER cc_start: 0.9050 (p) cc_final: 0.8700 (t) REVERT: A 25 LYS cc_start: 0.9001 (mtpt) cc_final: 0.8470 (mtpp) REVERT: B 7 GLU cc_start: 0.4325 (OUTLIER) cc_final: 0.4124 (pm20) REVERT: B 77 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7304 (m-30) REVERT: C 8 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7832 (mttm) REVERT: C 30 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.9104 (tt) REVERT: C 245 ARG cc_start: 0.8412 (ttm170) cc_final: 0.7934 (ttm170) REVERT: C 278 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6568 (mp0) REVERT: C 299 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6704 (ptmt) REVERT: C 332 ARG cc_start: 0.7012 (mmt-90) cc_final: 0.6758 (mmm-85) REVERT: C 626 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7125 (mm-30) REVERT: C 761 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.8907 (mp10) REVERT: C 808 ASN cc_start: 0.9279 (OUTLIER) cc_final: 0.8736 (t0) REVERT: D 172 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.5162 (m-80) REVERT: D 368 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8670 (tp) REVERT: D 422 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8868 (mp) REVERT: D 458 ASN cc_start: 0.8937 (t0) cc_final: 0.8729 (t0) REVERT: D 619 ILE cc_start: 0.9248 (tt) cc_final: 0.9025 (tp) REVERT: D 654 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.8919 (mp) REVERT: D 677 GLU cc_start: 0.7260 (mm-30) cc_final: 0.7021 (mm-30) REVERT: D 678 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.5942 (tmm160) REVERT: D 781 LYS cc_start: 0.8767 (tptt) cc_final: 0.8086 (mttt) REVERT: D 788 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8343 (tp) REVERT: D 821 MET cc_start: 0.6597 (tpp) cc_final: 0.6296 (mtm) REVERT: D 849 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6514 (pp) REVERT: D 999 TYR cc_start: 0.0682 (OUTLIER) cc_final: 0.0021 (m-80) REVERT: D 1023 HIS cc_start: 0.3417 (OUTLIER) cc_final: 0.2144 (p-80) REVERT: D 1325 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8288 (p90) REVERT: E 56 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: E 61 ASN cc_start: 0.8458 (t0) cc_final: 0.8180 (t0) REVERT: F 220 LYS cc_start: 0.3983 (OUTLIER) cc_final: 0.3775 (mmmt) REVERT: F 322 MET cc_start: 0.2414 (tpt) cc_final: 0.1989 (mmt) REVERT: F 507 MET cc_start: 0.8806 (ttp) cc_final: 0.8504 (ttm) REVERT: F 523 ILE cc_start: 0.9352 (pt) cc_final: 0.8963 (mt) REVERT: F 561 MET cc_start: 0.8085 (ttm) cc_final: 0.7842 (tpp) REVERT: F 579 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7479 (tp40) REVERT: F 589 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7092 (mp10) outliers start: 243 outliers final: 174 residues processed: 671 average time/residue: 0.2171 time to fit residues: 239.5174 Evaluate side-chains 647 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 447 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 761 GLN Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 808 ASN Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1058 ARG Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 925 GLU Chi-restraints excluded: chain D residue 986 ASP Chi-restraints excluded: chain D residue 999 TYR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 301 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 604 SER Chi-restraints excluded: chain F residue 611 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 76 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 243 optimal weight: 9.9990 chunk 408 optimal weight: 3.9990 chunk 246 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 320 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS C 677 ASN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 560 ASN D 777 HIS D 865 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN E 70 GLN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.150260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122091 restraints weight = 57600.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.121921 restraints weight = 146583.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.123029 restraints weight = 107273.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123002 restraints weight = 67820.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123566 restraints weight = 57995.076| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 35836 Z= 0.198 Angle : 0.553 9.078 48882 Z= 0.292 Chirality : 0.040 0.161 5556 Planarity : 0.004 0.039 5994 Dihedral : 17.686 174.919 6014 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 39.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 7.76 % Allowed : 20.64 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % 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: -3.77 (0.12), residues: 4130 helix: -1.89 (0.12), residues: 1554 sheet: -2.93 (0.23), residues: 407 loop : -2.93 (0.12), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 764 TYR 0.017 0.001 TYR C1018 PHE 0.015 0.001 PHE C 405 TRP 0.007 0.001 TRP J 166 HIS 0.005 0.001 HIS C 673 Details of bonding type rmsd covalent geometry : bond 0.00459 (35829) covalent geometry : angle 0.54994 (48876) hydrogen bonds : bond 0.04693 ( 948) hydrogen bonds : angle 5.34546 ( 2552) metal coordination : bond 0.01242 ( 7) metal coordination : angle 5.14744 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 276 poor density : 461 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 42 GLU cc_start: 0.5520 (OUTLIER) cc_final: 0.4563 (tm-30) REVERT: I 57 GLN cc_start: 0.5395 (mt0) cc_final: 0.5088 (tm-30) REVERT: I 85 HIS cc_start: 0.6973 (m170) cc_final: 0.6245 (m170) REVERT: I 89 MET cc_start: 0.8000 (mmm) cc_final: 0.7531 (mmm) REVERT: J 51 ILE cc_start: 0.7545 (pt) cc_final: 0.7259 (pt) REVERT: J 103 MET cc_start: 0.7797 (mtt) cc_final: 0.7570 (mtt) REVERT: J 184 LYS cc_start: 0.7897 (mtpt) cc_final: 0.6969 (tptm) REVERT: J 192 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6587 (mm-30) REVERT: J 195 SER cc_start: 0.8890 (p) cc_final: 0.8595 (t) REVERT: A 25 LYS cc_start: 0.9069 (mtpt) cc_final: 0.8531 (mtpp) REVERT: B 27 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8243 (m) REVERT: B 77 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.7041 (m-30) REVERT: C 8 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7677 (mttm) REVERT: C 270 THR cc_start: 0.1185 (OUTLIER) cc_final: 0.0859 (p) REVERT: C 278 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: C 299 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6443 (ptmt) REVERT: C 626 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7145 (mm-30) REVERT: C 754 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8896 (p) REVERT: C 761 GLN cc_start: 0.9320 (OUTLIER) cc_final: 0.8875 (mp10) REVERT: C 808 ASN cc_start: 0.9338 (OUTLIER) cc_final: 0.8883 (t0) REVERT: C 919 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8559 (mtp85) REVERT: D 172 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.5457 (m-80) REVERT: D 422 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9005 (mp) REVERT: D 458 ASN cc_start: 0.8939 (t0) cc_final: 0.8731 (t0) REVERT: D 619 ILE cc_start: 0.9194 (tt) cc_final: 0.8981 (tp) REVERT: D 654 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.8974 (mp) REVERT: D 678 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.5819 (tmm160) REVERT: D 781 LYS cc_start: 0.8825 (tptt) cc_final: 0.8196 (mttt) REVERT: D 788 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8378 (tp) REVERT: D 849 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6365 (pp) REVERT: D 929 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7463 (pp30) REVERT: D 999 TYR cc_start: 0.1033 (OUTLIER) cc_final: 0.0182 (m-80) REVERT: D 1023 HIS cc_start: 0.3289 (OUTLIER) cc_final: 0.2166 (p-80) REVERT: D 1325 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.8270 (p90) REVERT: E 56 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: E 61 ASN cc_start: 0.8497 (t0) cc_final: 0.8164 (t0) REVERT: F 322 MET cc_start: 0.1345 (tpt) cc_final: 0.1059 (mmt) REVERT: F 507 MET cc_start: 0.8829 (ttp) cc_final: 0.8608 (ttm) REVERT: F 554 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7990 (ptp-170) REVERT: F 589 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7046 (mp10) outliers start: 276 outliers final: 201 residues processed: 686 average time/residue: 0.2167 time to fit residues: 243.4122 Evaluate side-chains 674 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 447 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 761 GLN Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 808 ASN Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1058 ARG Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1167 GLU Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1336 ASN Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 986 ASP Chi-restraints excluded: chain D residue 999 TYR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 301 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 554 ARG Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 611 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 196 optimal weight: 0.2980 chunk 78 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 309 optimal weight: 2.9990 chunk 400 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 336 optimal weight: 30.0000 chunk 63 optimal weight: 7.9990 chunk 408 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS D 865 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN E 70 GLN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.150590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.112965 restraints weight = 58228.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.111584 restraints weight = 50987.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.112463 restraints weight = 52991.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.112989 restraints weight = 34314.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114022 restraints weight = 29806.921| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35836 Z= 0.143 Angle : 0.494 6.754 48882 Z= 0.263 Chirality : 0.039 0.139 5556 Planarity : 0.003 0.039 5994 Dihedral : 17.492 175.033 5993 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 37.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 7.00 % Allowed : 21.98 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % 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: -3.45 (0.12), residues: 4130 helix: -1.57 (0.13), residues: 1558 sheet: -2.77 (0.25), residues: 387 loop : -2.79 (0.12), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 764 TYR 0.014 0.001 TYR C1018 PHE 0.021 0.001 PHE C 545 TRP 0.008 0.001 TRP I 70 HIS 0.003 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00331 (35829) covalent geometry : angle 0.49165 (48876) hydrogen bonds : bond 0.04144 ( 948) hydrogen bonds : angle 5.01444 ( 2552) metal coordination : bond 0.00978 ( 7) metal coordination : angle 4.21412 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 461 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 19 ASP cc_start: 0.7672 (t0) cc_final: 0.7426 (m-30) REVERT: I 42 GLU cc_start: 0.5617 (OUTLIER) cc_final: 0.4646 (tm-30) REVERT: I 57 GLN cc_start: 0.6243 (mt0) cc_final: 0.5675 (tm-30) REVERT: I 85 HIS cc_start: 0.6888 (m170) cc_final: 0.6244 (m170) REVERT: I 89 MET cc_start: 0.8387 (mmm) cc_final: 0.7735 (mmm) REVERT: J 81 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: J 103 MET cc_start: 0.7882 (mtt) cc_final: 0.7607 (mtt) REVERT: J 184 LYS cc_start: 0.7735 (mtpt) cc_final: 0.6604 (tptm) REVERT: J 192 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6714 (mm-30) REVERT: J 195 SER cc_start: 0.9093 (p) cc_final: 0.8693 (t) REVERT: A 25 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8401 (mtpp) REVERT: B 27 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8245 (m) REVERT: B 233 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6666 (m-30) REVERT: C 8 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7825 (mttm) REVERT: C 30 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9160 (tt) REVERT: C 270 THR cc_start: 0.1585 (OUTLIER) cc_final: 0.1277 (p) REVERT: C 278 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6377 (mp0) REVERT: C 299 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6365 (ptmt) REVERT: C 626 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7183 (mm-30) REVERT: C 754 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8867 (p) REVERT: C 761 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.8891 (mp10) REVERT: C 808 ASN cc_start: 0.9286 (OUTLIER) cc_final: 0.8798 (t0) REVERT: C 919 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8696 (mtp85) REVERT: D 368 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8642 (tp) REVERT: D 458 ASN cc_start: 0.8963 (t0) cc_final: 0.8758 (t0) REVERT: D 619 ILE cc_start: 0.9296 (tt) cc_final: 0.9081 (tp) REVERT: D 678 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.5879 (tmm160) REVERT: D 781 LYS cc_start: 0.8822 (tptt) cc_final: 0.8068 (mttt) REVERT: D 788 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8318 (tp) REVERT: D 849 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6494 (pp) REVERT: D 867 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8006 (tp40) REVERT: D 929 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7570 (pp30) REVERT: D 999 TYR cc_start: 0.1165 (OUTLIER) cc_final: 0.0452 (m-80) REVERT: D 1189 MET cc_start: 0.6506 (ppp) cc_final: 0.6071 (ppp) REVERT: D 1325 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8256 (p90) REVERT: E 3 ARG cc_start: 0.8177 (tpp80) cc_final: 0.7865 (tpp80) REVERT: E 56 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: E 61 ASN cc_start: 0.8475 (t0) cc_final: 0.8120 (t0) REVERT: E 71 GLU cc_start: 0.8049 (tp30) cc_final: 0.7848 (tm-30) REVERT: F 266 PHE cc_start: 0.6620 (OUTLIER) cc_final: 0.6258 (t80) REVERT: F 507 MET cc_start: 0.8860 (ttp) cc_final: 0.8621 (ttm) REVERT: F 561 MET cc_start: 0.8416 (tpp) cc_final: 0.7820 (tpp) REVERT: F 579 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7290 (tp40) outliers start: 249 outliers final: 195 residues processed: 658 average time/residue: 0.2159 time to fit residues: 233.3247 Evaluate side-chains 665 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 445 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 761 GLN Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 808 ASN Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1058 ARG Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1210 ILE Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 986 ASP Chi-restraints excluded: chain D residue 999 TYR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 301 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 611 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 410 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 288 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 147 optimal weight: 8.9990 chunk 348 optimal weight: 0.0070 chunk 196 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 159 optimal weight: 0.0970 overall best weight: 1.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS B 147 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 865 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1114 GLN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.152126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.119774 restraints weight = 58450.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116346 restraints weight = 78995.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117909 restraints weight = 75640.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118286 restraints weight = 46817.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.121006 restraints weight = 39392.545| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 35836 Z= 0.101 Angle : 0.447 7.133 48882 Z= 0.239 Chirality : 0.038 0.137 5556 Planarity : 0.003 0.036 5994 Dihedral : 17.203 175.802 5984 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 36.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 5.57 % Allowed : 23.70 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % 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: -3.00 (0.13), residues: 4130 helix: -1.13 (0.13), residues: 1561 sheet: -2.58 (0.25), residues: 392 loop : -2.59 (0.12), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1034 TYR 0.012 0.001 TYR F 148 PHE 0.022 0.001 PHE C 545 TRP 0.009 0.001 TRP I 70 HIS 0.003 0.000 HIS D 865 Details of bonding type rmsd covalent geometry : bond 0.00231 (35829) covalent geometry : angle 0.44569 (48876) hydrogen bonds : bond 0.03486 ( 948) hydrogen bonds : angle 4.57802 ( 2552) metal coordination : bond 0.00639 ( 7) metal coordination : angle 2.81015 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 489 time to evaluate : 1.300 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: I 19 ASP cc_start: 0.7457 (t0) cc_final: 0.7232 (m-30) REVERT: I 42 GLU cc_start: 0.5592 (OUTLIER) cc_final: 0.4663 (tm-30) REVERT: I 57 GLN cc_start: 0.6255 (mt0) cc_final: 0.5763 (tm-30) REVERT: I 85 HIS cc_start: 0.6752 (m170) cc_final: 0.6252 (m170) REVERT: J 81 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7652 (mt-10) REVERT: J 103 MET cc_start: 0.7828 (mtt) cc_final: 0.7564 (mtt) REVERT: J 184 LYS cc_start: 0.7773 (mtpt) cc_final: 0.6756 (tptm) REVERT: J 192 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6594 (mm-30) REVERT: J 195 SER cc_start: 0.8956 (p) cc_final: 0.8576 (t) REVERT: A 25 LYS cc_start: 0.8933 (mtpt) cc_final: 0.8489 (mttp) REVERT: B 27 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8173 (m) REVERT: B 233 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6502 (m-30) REVERT: C 8 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7767 (mttm) REVERT: C 163 LYS cc_start: 0.7005 (OUTLIER) cc_final: 0.5925 (pttt) REVERT: C 278 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6431 (mp0) REVERT: C 299 LYS cc_start: 0.6883 (OUTLIER) cc_final: 0.6322 (ptmt) REVERT: C 626 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7060 (mm-30) REVERT: C 761 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8920 (mp10) REVERT: C 808 ASN cc_start: 0.9263 (OUTLIER) cc_final: 0.8977 (t0) REVERT: C 919 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8730 (mtp85) REVERT: C 957 LYS cc_start: 0.8377 (pttt) cc_final: 0.8007 (pttp) REVERT: D 619 ILE cc_start: 0.9166 (tt) cc_final: 0.8938 (tp) REVERT: D 678 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.5628 (tmm160) REVERT: D 781 LYS cc_start: 0.8816 (tptt) cc_final: 0.8096 (mttt) REVERT: D 795 TYR cc_start: 0.8120 (t80) cc_final: 0.7663 (t80) REVERT: D 849 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6476 (pp) REVERT: D 867 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8023 (tp40) REVERT: D 999 TYR cc_start: 0.1067 (OUTLIER) cc_final: 0.0465 (m-80) REVERT: D 1052 GLU cc_start: 0.4628 (OUTLIER) cc_final: 0.4416 (mt-10) REVERT: D 1189 MET cc_start: 0.6239 (ppp) cc_final: 0.5905 (ppp) REVERT: D 1325 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.8249 (p90) REVERT: E 3 ARG cc_start: 0.8076 (tpp80) cc_final: 0.7017 (tpp80) REVERT: E 61 ASN cc_start: 0.8470 (t0) cc_final: 0.8179 (t0) REVERT: F 266 PHE cc_start: 0.6473 (OUTLIER) cc_final: 0.6238 (t80) REVERT: F 446 GLN cc_start: 0.9418 (OUTLIER) cc_final: 0.9107 (pm20) REVERT: F 561 MET cc_start: 0.8327 (tpp) cc_final: 0.7866 (tpp) REVERT: F 579 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7358 (tp40) REVERT: F 589 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7223 (mp10) outliers start: 198 outliers final: 151 residues processed: 647 average time/residue: 0.2137 time to fit residues: 225.2644 Evaluate side-chains 638 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 465 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 285 THR Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 761 GLN Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 808 ASN Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 999 TYR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1052 GLU Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 301 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 446 GLN Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 611 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 204 optimal weight: 4.9990 chunk 396 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 354 optimal weight: 10.0000 chunk 397 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 259 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 368 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 ASN ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 865 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.149702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.116275 restraints weight = 58680.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114566 restraints weight = 82940.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.115829 restraints weight = 78360.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116246 restraints weight = 45803.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.117769 restraints weight = 39205.515| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 35836 Z= 0.180 Angle : 0.524 7.826 48882 Z= 0.275 Chirality : 0.040 0.144 5556 Planarity : 0.003 0.042 5994 Dihedral : 17.247 175.991 5950 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 38.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 6.78 % Allowed : 23.14 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % 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: -3.03 (0.13), residues: 4130 helix: -1.11 (0.13), residues: 1545 sheet: -2.53 (0.24), residues: 419 loop : -2.64 (0.12), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1373 TYR 0.013 0.001 TYR C1281 PHE 0.014 0.001 PHE C 405 TRP 0.010 0.001 TRP F 433 HIS 0.003 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00419 (35829) covalent geometry : angle 0.52177 (48876) hydrogen bonds : bond 0.03947 ( 948) hydrogen bonds : angle 4.83263 ( 2552) metal coordination : bond 0.01086 ( 7) metal coordination : angle 4.69885 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 456 time to evaluate : 1.176 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: I 19 ASP cc_start: 0.7492 (t0) cc_final: 0.7275 (m-30) REVERT: I 42 GLU cc_start: 0.5654 (OUTLIER) cc_final: 0.4689 (tm-30) REVERT: I 57 GLN cc_start: 0.6013 (mt0) cc_final: 0.5577 (tm-30) REVERT: J 81 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7656 (mt-10) REVERT: J 103 MET cc_start: 0.7861 (mtt) cc_final: 0.7612 (mtt) REVERT: J 184 LYS cc_start: 0.7768 (mtpt) cc_final: 0.6966 (tptp) REVERT: J 192 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6694 (mm-30) REVERT: J 195 SER cc_start: 0.9024 (p) cc_final: 0.8632 (t) REVERT: A 25 LYS cc_start: 0.9014 (mtpt) cc_final: 0.8556 (mttp) REVERT: B 27 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8240 (m) REVERT: B 233 ASP cc_start: 0.7140 (OUTLIER) cc_final: 0.6650 (m-30) REVERT: C 8 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7884 (mttm) REVERT: C 270 THR cc_start: 0.1259 (OUTLIER) cc_final: 0.1019 (p) REVERT: C 278 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6660 (mp0) REVERT: C 299 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6373 (ptmt) REVERT: C 484 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7149 (mt) REVERT: C 626 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7035 (mm-30) REVERT: C 761 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8821 (mp10) REVERT: C 808 ASN cc_start: 0.9317 (OUTLIER) cc_final: 0.8824 (t0) REVERT: C 919 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8639 (mtp85) REVERT: D 368 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8675 (tp) REVERT: D 422 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8946 (mp) REVERT: D 619 ILE cc_start: 0.9196 (tt) cc_final: 0.8931 (tp) REVERT: D 678 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.5762 (tmm160) REVERT: D 781 LYS cc_start: 0.8858 (tptt) cc_final: 0.8140 (mttt) REVERT: D 788 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8375 (tp) REVERT: D 849 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6510 (pp) REVERT: D 867 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8061 (tp40) REVERT: D 929 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.6626 (pm20) REVERT: D 999 TYR cc_start: 0.1519 (OUTLIER) cc_final: 0.0589 (m-80) REVERT: D 1189 MET cc_start: 0.6310 (ppp) cc_final: 0.5967 (ppp) REVERT: D 1325 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8275 (p90) REVERT: E 3 ARG cc_start: 0.8063 (tpp80) cc_final: 0.7056 (tpp80) REVERT: E 56 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: E 61 ASN cc_start: 0.8522 (t0) cc_final: 0.8185 (t0) REVERT: F 446 GLN cc_start: 0.9420 (OUTLIER) cc_final: 0.9171 (pm20) REVERT: F 579 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7373 (tp40) REVERT: F 589 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7223 (mp10) outliers start: 241 outliers final: 196 residues processed: 647 average time/residue: 0.2050 time to fit residues: 219.6476 Evaluate side-chains 672 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 450 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 285 THR Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 761 GLN Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 808 ASN Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 999 TYR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 301 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 446 GLN Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 611 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 157 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 225 optimal weight: 0.0870 chunk 30 optimal weight: 10.0000 chunk 372 optimal weight: 10.0000 chunk 326 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 321 optimal weight: 0.9980 chunk 337 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 overall best weight: 3.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 ASN ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.150083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117310 restraints weight = 58414.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.115468 restraints weight = 88929.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116857 restraints weight = 78491.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117248 restraints weight = 47078.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119075 restraints weight = 39592.633| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 35836 Z= 0.155 Angle : 0.496 7.702 48882 Z= 0.262 Chirality : 0.039 0.140 5556 Planarity : 0.003 0.037 5994 Dihedral : 17.210 176.013 5948 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 38.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 6.83 % Allowed : 23.36 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % 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: -2.90 (0.13), residues: 4130 helix: -1.00 (0.14), residues: 1548 sheet: -2.45 (0.25), residues: 393 loop : -2.58 (0.12), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1373 TYR 0.012 0.001 TYR C1281 PHE 0.012 0.001 PHE C 405 TRP 0.006 0.001 TRP I 70 HIS 0.005 0.001 HIS D 907 Details of bonding type rmsd covalent geometry : bond 0.00361 (35829) covalent geometry : angle 0.49395 (48876) hydrogen bonds : bond 0.03748 ( 948) hydrogen bonds : angle 4.72810 ( 2552) metal coordination : bond 0.00994 ( 7) metal coordination : angle 4.48348 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 243 poor density : 455 time to evaluate : 1.118 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: I 19 ASP cc_start: 0.7440 (t0) cc_final: 0.7233 (m-30) REVERT: I 42 GLU cc_start: 0.5651 (OUTLIER) cc_final: 0.4680 (tm-30) REVERT: I 57 GLN cc_start: 0.6040 (mt0) cc_final: 0.5650 (tm-30) REVERT: J 81 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7624 (mt-10) REVERT: J 103 MET cc_start: 0.7854 (mtt) cc_final: 0.7550 (mtt) REVERT: J 184 LYS cc_start: 0.7900 (mtpt) cc_final: 0.7054 (tptp) REVERT: J 192 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6683 (mm-30) REVERT: J 195 SER cc_start: 0.8992 (p) cc_final: 0.8595 (t) REVERT: A 25 LYS cc_start: 0.9023 (mtpt) cc_final: 0.8605 (mttp) REVERT: B 27 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8247 (m) REVERT: B 233 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.6680 (m-30) REVERT: C 8 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7946 (mttm) REVERT: C 270 THR cc_start: 0.1179 (OUTLIER) cc_final: 0.0934 (p) REVERT: C 278 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: C 299 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6259 (ptmt) REVERT: C 484 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7133 (mt) REVERT: C 626 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6949 (mm-30) REVERT: C 754 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8845 (p) REVERT: C 761 GLN cc_start: 0.9251 (OUTLIER) cc_final: 0.8812 (mp10) REVERT: C 808 ASN cc_start: 0.9298 (OUTLIER) cc_final: 0.8799 (t0) REVERT: C 835 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6979 (tp30) REVERT: C 915 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8488 (t70) REVERT: C 919 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8619 (mtp85) REVERT: D 368 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8663 (tp) REVERT: D 619 ILE cc_start: 0.9189 (tt) cc_final: 0.8935 (tp) REVERT: D 678 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.5738 (tmm160) REVERT: D 781 LYS cc_start: 0.8844 (tptt) cc_final: 0.8125 (mttt) REVERT: D 849 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6535 (pp) REVERT: D 867 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8067 (tp40) REVERT: D 929 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.6785 (pm20) REVERT: D 999 TYR cc_start: 0.1302 (OUTLIER) cc_final: 0.0591 (m-80) REVERT: D 1189 MET cc_start: 0.6281 (ppp) cc_final: 0.5960 (ppp) REVERT: D 1325 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.8326 (p90) REVERT: E 3 ARG cc_start: 0.7790 (tpp80) cc_final: 0.7239 (mmp-170) REVERT: E 19 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9104 (tp) REVERT: E 61 ASN cc_start: 0.8528 (t0) cc_final: 0.8210 (t0) REVERT: F 446 GLN cc_start: 0.9413 (OUTLIER) cc_final: 0.9091 (pm20) REVERT: F 579 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7368 (tp40) outliers start: 243 outliers final: 199 residues processed: 645 average time/residue: 0.2163 time to fit residues: 229.8148 Evaluate side-chains 667 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 442 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 285 THR Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 761 GLN Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 808 ASN Chi-restraints excluded: chain C residue 835 GLU Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 999 TYR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 301 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 446 GLN Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 611 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 215 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 205 optimal weight: 10.0000 chunk 243 optimal weight: 8.9990 chunk 406 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 283 optimal weight: 7.9990 chunk 372 optimal weight: 0.0050 chunk 200 optimal weight: 0.0170 chunk 34 optimal weight: 0.5980 overall best weight: 2.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 ASN ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.150595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.117359 restraints weight = 58103.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.115606 restraints weight = 82304.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.116922 restraints weight = 77174.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117265 restraints weight = 45392.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119052 restraints weight = 39000.513| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35836 Z= 0.136 Angle : 0.478 7.783 48882 Z= 0.253 Chirality : 0.039 0.138 5556 Planarity : 0.003 0.041 5994 Dihedral : 17.107 176.995 5945 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 37.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 6.63 % Allowed : 23.67 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % 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: -2.73 (0.13), residues: 4130 helix: -0.81 (0.14), residues: 1555 sheet: -2.32 (0.25), residues: 408 loop : -2.52 (0.13), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1373 TYR 0.011 0.001 TYR F 148 PHE 0.023 0.001 PHE C 545 TRP 0.006 0.001 TRP I 70 HIS 0.009 0.001 HIS I 85 Details of bonding type rmsd covalent geometry : bond 0.00315 (35829) covalent geometry : angle 0.47615 (48876) hydrogen bonds : bond 0.03538 ( 948) hydrogen bonds : angle 4.59613 ( 2552) metal coordination : bond 0.00847 ( 7) metal coordination : angle 3.91116 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 448 time to evaluate : 1.317 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: I 57 GLN cc_start: 0.6383 (mt0) cc_final: 0.5882 (tm-30) REVERT: I 110 TRP cc_start: 0.7480 (m-10) cc_final: 0.6707 (m-10) REVERT: J 81 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: J 103 MET cc_start: 0.7865 (mtt) cc_final: 0.7610 (mtt) REVERT: J 184 LYS cc_start: 0.8059 (mtpt) cc_final: 0.7231 (tptp) REVERT: J 192 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6714 (mm-30) REVERT: J 207 MET cc_start: 0.4683 (mpp) cc_final: 0.4423 (mtt) REVERT: A 25 LYS cc_start: 0.9009 (mtpt) cc_final: 0.8610 (mttp) REVERT: B 27 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8229 (m) REVERT: B 233 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6656 (m-30) REVERT: C 8 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7945 (mttm) REVERT: C 97 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8253 (mmt90) REVERT: C 270 THR cc_start: 0.1246 (OUTLIER) cc_final: 0.0995 (p) REVERT: C 299 LYS cc_start: 0.6832 (OUTLIER) cc_final: 0.6246 (ptmt) REVERT: C 484 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7198 (mt) REVERT: C 754 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8867 (p) REVERT: C 761 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.8865 (mp10) REVERT: C 808 ASN cc_start: 0.9295 (OUTLIER) cc_final: 0.8769 (t0) REVERT: C 915 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8486 (t70) REVERT: C 919 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8644 (mtp85) REVERT: C 1018 TYR cc_start: 0.5424 (OUTLIER) cc_final: 0.5194 (p90) REVERT: C 1019 ASP cc_start: 0.3833 (OUTLIER) cc_final: 0.3352 (t70) REVERT: C 1069 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8612 (mtp180) REVERT: D 368 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8668 (tp) REVERT: D 422 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8951 (mp) REVERT: D 619 ILE cc_start: 0.9152 (tt) cc_final: 0.8916 (tp) REVERT: D 678 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.5740 (tmm160) REVERT: D 781 LYS cc_start: 0.8816 (tptt) cc_final: 0.8063 (mttt) REVERT: D 788 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8338 (tp) REVERT: D 822 MET cc_start: 0.8595 (mmm) cc_final: 0.8001 (mmp) REVERT: D 849 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6493 (pp) REVERT: D 867 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8040 (tp40) REVERT: D 929 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7598 (pp30) REVERT: D 999 TYR cc_start: 0.1239 (OUTLIER) cc_final: 0.0527 (m-80) REVERT: D 1189 MET cc_start: 0.6253 (ppp) cc_final: 0.5931 (ppp) REVERT: D 1325 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8299 (p90) REVERT: E 3 ARG cc_start: 0.7768 (tpp80) cc_final: 0.7223 (mmp-170) REVERT: E 19 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9105 (tp) REVERT: E 61 ASN cc_start: 0.8570 (t0) cc_final: 0.8274 (t0) REVERT: F 561 MET cc_start: 0.8498 (tpp) cc_final: 0.8251 (tpp) REVERT: F 579 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7373 (tp40) outliers start: 236 outliers final: 194 residues processed: 638 average time/residue: 0.2128 time to fit residues: 223.5657 Evaluate side-chains 665 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 444 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 285 THR Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 761 GLN Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 808 ASN Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 929 GLN Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 999 TYR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1332 LEU Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 301 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 611 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 190 optimal weight: 0.0970 chunk 146 optimal weight: 7.9990 chunk 388 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 361 optimal weight: 0.7980 chunk 329 optimal weight: 0.0670 chunk 61 optimal weight: 2.9990 chunk 416 optimal weight: 9.9990 chunk 323 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 overall best weight: 1.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 865 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.151823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118721 restraints weight = 58617.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.116640 restraints weight = 82990.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.118165 restraints weight = 76546.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.118413 restraints weight = 46045.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.120335 restraints weight = 39383.764| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 35836 Z= 0.102 Angle : 0.451 7.775 48882 Z= 0.240 Chirality : 0.038 0.139 5556 Planarity : 0.003 0.039 5994 Dihedral : 16.934 177.371 5938 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 36.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 5.17 % Allowed : 24.96 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % 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: -2.47 (0.13), residues: 4130 helix: -0.57 (0.14), residues: 1556 sheet: -2.20 (0.26), residues: 373 loop : -2.40 (0.13), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1034 TYR 0.010 0.001 TYR F 148 PHE 0.008 0.001 PHE C1025 TRP 0.007 0.001 TRP I 70 HIS 0.005 0.000 HIS I 85 Details of bonding type rmsd covalent geometry : bond 0.00235 (35829) covalent geometry : angle 0.44996 (48876) hydrogen bonds : bond 0.03236 ( 948) hydrogen bonds : angle 4.35257 ( 2552) metal coordination : bond 0.00661 ( 7) metal coordination : angle 3.30389 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 464 time to evaluate : 1.312 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: I 57 GLN cc_start: 0.6299 (mt0) cc_final: 0.5712 (tm-30) REVERT: I 109 ASP cc_start: 0.7709 (t0) cc_final: 0.7321 (t70) REVERT: I 110 TRP cc_start: 0.7485 (m-10) cc_final: 0.6644 (m-10) REVERT: J 81 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7723 (mt-10) REVERT: J 103 MET cc_start: 0.7919 (mtt) cc_final: 0.7627 (mtt) REVERT: J 184 LYS cc_start: 0.8021 (mtpt) cc_final: 0.7194 (tptp) REVERT: A 25 LYS cc_start: 0.8977 (mtpt) cc_final: 0.8656 (mttp) REVERT: B 27 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8207 (m) REVERT: C 8 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8007 (mttm) REVERT: C 163 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.5849 (pttt) REVERT: C 270 THR cc_start: 0.1096 (OUTLIER) cc_final: 0.0875 (p) REVERT: C 299 LYS cc_start: 0.6792 (OUTLIER) cc_final: 0.6271 (ptmt) REVERT: C 484 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7168 (mt) REVERT: C 754 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8819 (p) REVERT: C 761 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8852 (mp10) REVERT: C 808 ASN cc_start: 0.9266 (OUTLIER) cc_final: 0.8979 (t0) REVERT: C 919 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8707 (mtp85) REVERT: D 678 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.5448 (tmm160) REVERT: D 781 LYS cc_start: 0.8814 (tptt) cc_final: 0.8057 (mttt) REVERT: D 788 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8303 (tp) REVERT: D 795 TYR cc_start: 0.8146 (t80) cc_final: 0.7768 (t80) REVERT: D 849 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6537 (pp) REVERT: D 867 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8068 (tp40) REVERT: D 999 TYR cc_start: 0.1011 (OUTLIER) cc_final: 0.0391 (m-80) REVERT: D 1034 PHE cc_start: 0.4871 (OUTLIER) cc_final: 0.3991 (m-80) REVERT: D 1172 LYS cc_start: 0.5577 (mtmt) cc_final: 0.5351 (mtmt) REVERT: D 1189 MET cc_start: 0.6235 (ppp) cc_final: 0.5940 (ppp) REVERT: D 1325 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.8252 (p90) REVERT: E 3 ARG cc_start: 0.7774 (tpp80) cc_final: 0.6820 (tpp80) REVERT: E 61 ASN cc_start: 0.8512 (t0) cc_final: 0.8239 (t0) REVERT: F 579 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7332 (tp40) outliers start: 184 outliers final: 158 residues processed: 614 average time/residue: 0.2085 time to fit residues: 211.5438 Evaluate side-chains 623 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 447 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 761 GLN Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 808 ASN Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 999 TYR Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1041 ILE Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1332 LEU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 301 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 611 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 413 optimal weight: 0.4980 chunk 303 optimal weight: 0.9990 chunk 88 optimal weight: 20.0000 chunk 330 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 282 optimal weight: 7.9990 chunk 342 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 24 GLN ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN F 258 GLN ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.153327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.120205 restraints weight = 58045.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.118175 restraints weight = 74753.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119298 restraints weight = 74795.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.119759 restraints weight = 41848.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.121605 restraints weight = 35539.231| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35836 Z= 0.082 Angle : 0.436 11.639 48882 Z= 0.231 Chirality : 0.037 0.137 5556 Planarity : 0.003 0.038 5994 Dihedral : 16.747 178.112 5928 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 36.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.16 % Allowed : 26.12 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % 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: -2.18 (0.13), residues: 4130 helix: -0.26 (0.14), residues: 1547 sheet: -2.11 (0.25), residues: 393 loop : -2.26 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1373 TYR 0.010 0.001 TYR F 148 PHE 0.020 0.001 PHE C 545 TRP 0.008 0.001 TRP D 33 HIS 0.005 0.000 HIS I 85 Details of bonding type rmsd covalent geometry : bond 0.00188 (35829) covalent geometry : angle 0.43522 (48876) hydrogen bonds : bond 0.02973 ( 948) hydrogen bonds : angle 4.11394 ( 2552) metal coordination : bond 0.00477 ( 7) metal coordination : angle 2.58720 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6076.20 seconds wall clock time: 105 minutes 56.87 seconds (6356.87 seconds total)