Starting phenix.real_space_refine on Tue Aug 26 04:55:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t0l_40943/08_2025/8t0l_40943.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t0l_40943/08_2025/8t0l_40943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t0l_40943/08_2025/8t0l_40943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t0l_40943/08_2025/8t0l_40943.map" model { file = "/net/cci-nas-00/data/ceres_data/8t0l_40943/08_2025/8t0l_40943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t0l_40943/08_2025/8t0l_40943.cif" } resolution = 3.62 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= 0.004 sd= 0.055 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 Al 1 5.89 5 P 48 5.49 5 Mg 1 5.21 5 S 135 5.16 5 C 20878 2.51 5 N 5924 2.21 5 O 6538 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33530 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1706 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1667 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "J" Number of atoms: 10366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1333, 10366 Classifications: {'peptide': 1333} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1277} Chain breaks: 2 Chain: "K" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 577 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "F" Number of atoms: 7670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7670 Classifications: {'peptide': 966} Link IDs: {'PTRANS': 35, 'TRANS': 930} Chain: "A" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 483 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "B" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 460 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "J" 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} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14389 SG CYS J 70 128.451 108.473 118.746 1.00199.76 S ATOM 14403 SG CYS J 72 128.642 110.561 119.774 1.00190.32 S ATOM 14511 SG CYS J 85 127.611 110.374 122.280 1.00186.13 S ATOM 14535 SG CYS J 88 126.539 111.398 119.901 1.00185.19 S ATOM 20221 SG CYS J 814 70.656 79.718 121.443 1.00109.39 S ATOM 20786 SG CYS J 888 70.741 80.635 120.144 1.00105.52 S ATOM 20837 SG CYS J 895 71.470 79.782 120.501 1.00 92.47 S ATOM 20858 SG CYS J 898 68.424 78.432 117.696 1.00 92.21 S Time building chain proxies: 6.23, per 1000 atoms: 0.19 Number of scatterers: 33530 At special positions: 0 Unit cell: (197.984, 161.4, 171.084, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 135 16.00 P 48 15.00 Al 1 13.00 Mg 1 11.99 F 3 9.00 O 6538 8.00 N 5924 7.00 C 20878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM33521 O3A ADP F1000 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1402 " pdb="ZN ZN J1402 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1402 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1402 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1402 " - pdb=" SG CYS J 70 " pdb=" ZN J1403 " pdb="ZN ZN J1403 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1403 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1403 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1403 " - pdb=" SG CYS J 814 " Number of angles added : 12 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7704 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 54 sheets defined 41.5% alpha, 11.9% beta 23 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 4.40 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.739A pdb=" N SER G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 88 Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'G' and resid 154 through 159 removed outlier: 3.752A pdb=" N ARG G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 233 removed outlier: 3.779A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 212 through 230 removed outlier: 4.228A pdb=" N ALA H 230 " --> pdb=" O GLU H 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 10 removed outlier: 4.227A pdb=" N ARG I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.627A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 198 through 201 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.296A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 256 through 260 removed outlier: 4.095A pdb=" N GLY I 259 " --> pdb=" O GLU I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 288 through 294 removed outlier: 4.075A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 329 Processing helix chain 'I' and resid 345 through 354 removed outlier: 3.614A pdb=" N GLU I 349 " --> pdb=" O PRO I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.167A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 437 Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.558A pdb=" N MET I 459 " --> pdb=" O SER I 455 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 507 Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 608 through 614 removed outlier: 4.109A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 614' Processing helix chain 'I' and resid 662 through 667 Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 704 through 713 removed outlier: 4.303A pdb=" N GLY I 713 " --> pdb=" O ALA I 709 " (cutoff:3.500A) Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 865 removed outlier: 3.722A pdb=" N LEU I 862 " --> pdb=" O GLY I 858 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS I 864 " --> pdb=" O ALA I 860 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU I 865 " --> pdb=" O ALA I 861 " (cutoff:3.500A) Processing helix chain 'I' and resid 896 through 906 Processing helix chain 'I' and resid 942 through 981 removed outlier: 4.269A pdb=" N ALA I 981 " --> pdb=" O ALA I 977 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 992 removed outlier: 3.701A pdb=" N LEU I 992 " --> pdb=" O LYS I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 3.889A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.561A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1138 through 1151 removed outlier: 3.562A pdb=" N LEU I1151 " --> pdb=" O ARG I1147 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1177 removed outlier: 3.572A pdb=" N VAL I1169 " --> pdb=" O SER I1165 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.548A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1261 through 1265 removed outlier: 3.613A pdb=" N PHE I1265 " --> pdb=" O LYS I1262 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1281 removed outlier: 3.638A pdb=" N TYR I1281 " --> pdb=" O ALA I1277 " (cutoff:3.500A) Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.810A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU I1333 " --> pdb=" O GLU I1329 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 122 through 129 removed outlier: 3.753A pdb=" N LEU J 126 " --> pdb=" O SER J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 173 Processing helix chain 'J' and resid 181 through 191 Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 264 through 286 removed outlier: 3.588A pdb=" N LEU J 268 " --> pdb=" O ASP J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 309 Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 370 through 374 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 402 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.856A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 417 through 419 No H-bonds generated for 'chain 'J' and resid 417 through 419' Processing helix chain 'J' and resid 453 through 458 removed outlier: 4.075A pdb=" N TYR J 457 " --> pdb=" O VAL J 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 removed outlier: 3.985A pdb=" N ASN J 489 " --> pdb=" O SER J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.925A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 removed outlier: 3.721A pdb=" N ALA J 533 " --> pdb=" O GLY J 529 " (cutoff:3.500A) Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.788A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 593 removed outlier: 3.577A pdb=" N ASN J 593 " --> pdb=" O SER J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 removed outlier: 3.537A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER J 602 " --> pdb=" O LYS J 598 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 4.170A pdb=" N TYR J 631 " --> pdb=" O THR J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 729 Processing helix chain 'J' and resid 733 through 742 removed outlier: 3.628A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 805 removed outlier: 4.053A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) Processing helix chain 'J' and resid 836 through 840 removed outlier: 3.676A pdb=" N VAL J 839 " --> pdb=" O ARG J 836 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 884 through 888 removed outlier: 4.133A pdb=" N CYS J 888 " --> pdb=" O VAL J 885 " (cutoff:3.500A) Processing helix chain 'J' and resid 895 through 900 Processing helix chain 'J' and resid 915 through 923 removed outlier: 3.980A pdb=" N GLN J 921 " --> pdb=" O VAL J 917 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1217 through 1224 Processing helix chain 'J' and resid 1228 through 1245 removed outlier: 3.842A pdb=" N ASN J1235 " --> pdb=" O ARG J1231 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY J1245 " --> pdb=" O TYR J1241 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.103A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1325 Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1348 through 1354 Processing helix chain 'J' and resid 1360 through 1373 Processing helix chain 'K' and resid 6 through 13 removed outlier: 3.518A pdb=" N VAL K 10 " --> pdb=" O VAL K 6 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU K 11 " --> pdb=" O GLN K 7 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS K 12 " --> pdb=" O ASP K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.645A pdb=" N VAL K 32 " --> pdb=" O ARG K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 73 Processing helix chain 'F' and resid 14 through 18 removed outlier: 3.849A pdb=" N LEU F 17 " --> pdb=" O GLU F 14 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY F 18 " --> pdb=" O SER F 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 14 through 18' Processing helix chain 'F' and resid 100 through 102 No H-bonds generated for 'chain 'F' and resid 100 through 102' Processing helix chain 'F' and resid 111 through 117 removed outlier: 4.047A pdb=" N LEU F 115 " --> pdb=" O PRO F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 125 Processing helix chain 'F' and resid 126 through 140 removed outlier: 3.678A pdb=" N GLU F 138 " --> pdb=" O LYS F 134 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN F 139 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE F 140 " --> pdb=" O SER F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 167 removed outlier: 3.656A pdb=" N ARG F 167 " --> pdb=" O HIS F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 198 Processing helix chain 'F' and resid 210 through 223 removed outlier: 3.996A pdb=" N GLN F 214 " --> pdb=" O THR F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 242 Processing helix chain 'F' and resid 245 through 249 removed outlier: 3.578A pdb=" N THR F 248 " --> pdb=" O PRO F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 260 Processing helix chain 'F' and resid 262 through 271 Processing helix chain 'F' and resid 282 through 285 Processing helix chain 'F' and resid 293 through 305 Processing helix chain 'F' and resid 319 through 332 removed outlier: 4.380A pdb=" N SER F 323 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N HIS F 324 " --> pdb=" O GLY F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 340 No H-bonds generated for 'chain 'F' and resid 338 through 340' Processing helix chain 'F' and resid 341 through 350 Processing helix chain 'F' and resid 352 through 361 removed outlier: 3.978A pdb=" N VAL F 356 " --> pdb=" O VAL F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 377 removed outlier: 3.506A pdb=" N MET F 372 " --> pdb=" O ASP F 368 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU F 375 " --> pdb=" O ASN F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 391 removed outlier: 4.322A pdb=" N LEU F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA F 388 " --> pdb=" O PRO F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 412 removed outlier: 4.288A pdb=" N GLN F 401 " --> pdb=" O GLN F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 452 removed outlier: 3.500A pdb=" N GLN F 445 " --> pdb=" O PRO F 441 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL F 450 " --> pdb=" O THR F 446 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY F 452 " --> pdb=" O ILE F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 458 Processing helix chain 'F' and resid 459 through 468 Processing helix chain 'F' and resid 469 through 478 Processing helix chain 'F' and resid 483 through 487 removed outlier: 3.763A pdb=" N ASN F 486 " --> pdb=" O THR F 483 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE F 487 " --> pdb=" O TRP F 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 483 through 487' Processing helix chain 'F' and resid 488 through 501 removed outlier: 3.533A pdb=" N GLU F 492 " --> pdb=" O ASP F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 512 through 528 Processing helix chain 'F' and resid 539 through 552 Processing helix chain 'F' and resid 586 through 596 removed outlier: 3.719A pdb=" N LEU F 590 " --> pdb=" O ASN F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 616 through 628 removed outlier: 3.580A pdb=" N VAL F 620 " --> pdb=" O THR F 616 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 646 removed outlier: 3.820A pdb=" N ILE F 642 " --> pdb=" O THR F 638 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP F 644 " --> pdb=" O ALA F 640 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL F 646 " --> pdb=" O ILE F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 656 Processing helix chain 'F' and resid 663 through 684 Processing helix chain 'F' and resid 688 through 695 Processing helix chain 'F' and resid 695 through 711 Processing helix chain 'F' and resid 713 through 727 removed outlier: 3.584A pdb=" N ALA F 717 " --> pdb=" O THR F 713 " (cutoff:3.500A) Processing helix chain 'F' and resid 764 through 771 Processing helix chain 'F' and resid 781 through 794 Processing helix chain 'F' and resid 827 through 831 Processing helix chain 'F' and resid 857 through 863 removed outlier: 3.596A pdb=" N ARG F 863 " --> pdb=" O GLU F 859 " (cutoff:3.500A) Processing helix chain 'F' and resid 871 through 879 Processing helix chain 'F' and resid 881 through 904 removed outlier: 4.035A pdb=" N HIS F 885 " --> pdb=" O GLN F 881 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA F 886 " --> pdb=" O GLN F 882 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN F 889 " --> pdb=" O HIS F 885 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS F 897 " --> pdb=" O ALA F 893 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER F 898 " --> pdb=" O GLN F 894 " (cutoff:3.500A) Processing helix chain 'F' and resid 905 through 928 removed outlier: 3.652A pdb=" N GLU F 909 " --> pdb=" O ALA F 905 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS F 913 " --> pdb=" O GLU F 909 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL F 927 " --> pdb=" O ALA F 923 " (cutoff:3.500A) Processing helix chain 'F' and resid 932 through 952 removed outlier: 3.734A pdb=" N LEU F 936 " --> pdb=" O ARG F 932 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.819A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 98 through 102 removed outlier: 3.946A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 109 Processing sheet with id=AA5, first strand: chain 'H' and resid 15 through 19 removed outlier: 3.615A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR H 27 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU H 17 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 98 through 101 removed outlier: 6.717A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 90 through 91 removed outlier: 3.503A pdb=" N ARG H 91 " --> pdb=" O GLU H 122 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU H 122 " --> pdb=" O ARG H 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AA9, first strand: chain 'H' and resid 108 through 111 Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.872A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.681A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 155 Processing sheet with id=AB7, first strand: chain 'I' and resid 227 through 228 Processing sheet with id=AB8, first strand: chain 'I' and resid 238 through 239 Processing sheet with id=AB9, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.801A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 603 through 606 Processing sheet with id=AC2, first strand: chain 'I' and resid 733 through 736 removed outlier: 6.794A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 768 through 769 Processing sheet with id=AC4, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'I' and resid 801 through 802 Processing sheet with id=AC6, first strand: chain 'I' and resid 816 through 819 removed outlier: 7.148A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'I' and resid 836 through 841 removed outlier: 3.860A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 876 through 877 removed outlier: 3.895A pdb=" N GLY I 926 " --> pdb=" O VAL I 877 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.985A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 887 through 888 Processing sheet with id=AD2, first strand: chain 'I' and resid 1065 through 1067 removed outlier: 4.641A pdb=" N LYS I1065 " --> pdb=" O LEU I1235 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA I1067 " --> pdb=" O LEU I1233 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AD4, first strand: chain 'I' and resid 1209 through 1210 Processing sheet with id=AD5, first strand: chain 'J' and resid 83 through 84 removed outlier: 4.356A pdb=" N LEU F 42 " --> pdb=" O ILE J 84 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR F 29 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL F 25 " --> pdb=" O THR F 29 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR F 31 " --> pdb=" O VAL F 23 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 103 through 112 removed outlier: 9.939A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AD8, first strand: chain 'J' and resid 355 through 357 removed outlier: 6.478A pdb=" N THR J 356 " --> pdb=" O LEU J 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'J' and resid 365 through 369 Processing sheet with id=AE1, first strand: chain 'J' and resid 547 through 550 Processing sheet with id=AE2, first strand: chain 'J' and resid 553 through 559 removed outlier: 4.205A pdb=" N ASP J 558 " --> pdb=" O GLU J 562 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU J 562 " --> pdb=" O ASP J 558 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 705 through 708 removed outlier: 3.679A pdb=" N THR J 705 " --> pdb=" O GLN J 716 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 821 through 822 Processing sheet with id=AE5, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.307A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 991 through 997 removed outlier: 6.261A pdb=" N THR J 991 " --> pdb=" O ASP J 986 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASP J 986 " --> pdb=" O THR J 991 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 965 through 966 Processing sheet with id=AE8, first strand: chain 'J' and resid 1002 through 1003 Processing sheet with id=AE9, first strand: chain 'J' and resid 1025 through 1029 removed outlier: 4.076A pdb=" N ILE J1124 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL J1027 " --> pdb=" O ALA J1122 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA J1122 " --> pdb=" O VAL J1027 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N THR J1029 " --> pdb=" O THR J1120 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR J1120 " --> pdb=" O THR J1029 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1033 through 1034 Processing sheet with id=AF2, first strand: chain 'J' and resid 1046 through 1051 Processing sheet with id=AF3, first strand: chain 'J' and resid 1186 through 1191 removed outlier: 4.083A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.578A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 60 through 62 removed outlier: 6.822A pdb=" N ILE F 84 " --> pdb=" O GLU F 72 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL F 74 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR F 82 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU F 76 " --> pdb=" O LEU F 80 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU F 80 " --> pdb=" O GLU F 76 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 228 through 229 removed outlier: 6.153A pdb=" N ALA F 228 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL F 252 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU F 277 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU F 312 " --> pdb=" O LEU F 277 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL F 279 " --> pdb=" O LEU F 312 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL F 173 " --> pdb=" O VAL F 309 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 431 through 438 removed outlier: 7.157A pdb=" N GLU F 432 " --> pdb=" O ILE F 608 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N VAL F 610 " --> pdb=" O GLU F 432 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N HIS F 434 " --> pdb=" O VAL F 610 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N TYR F 612 " --> pdb=" O HIS F 434 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE F 436 " --> pdb=" O TYR F 612 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU F 507 " --> pdb=" O VAL F 579 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL F 506 " --> pdb=" O LEU F 560 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N CYS F 562 " --> pdb=" O VAL F 506 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL F 508 " --> pdb=" O CYS F 562 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 729 through 732 Processing sheet with id=AF9, first strand: chain 'F' and resid 839 through 845 removed outlier: 6.732A pdb=" N LEU F 815 " --> pdb=" O LEU F 962 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU F 962 " --> pdb=" O LEU F 815 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU F 817 " --> pdb=" O LEU F 960 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU F 960 " --> pdb=" O GLU F 817 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE F 819 " --> pdb=" O ASP F 958 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY F 954 " --> pdb=" O GLU F 823 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER F 802 " --> pdb=" O VAL F 964 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR F 966 " --> pdb=" O SER F 802 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU F 804 " --> pdb=" O THR F 966 " (cutoff:3.500A) 1345 hydrogen bonds defined for protein. 3786 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 6.38 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11227 1.34 - 1.46: 4850 1.46 - 1.58: 17741 1.58 - 1.70: 94 1.70 - 1.82: 236 Bond restraints: 34148 Sorted by residual: bond pdb=" CA MET I 800 " pdb=" CB MET I 800 " ideal model delta sigma weight residual 1.530 1.504 0.026 1.69e-02 3.50e+03 2.32e+00 bond pdb=" CB ARG I 528 " pdb=" CG ARG I 528 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.30e+00 bond pdb=" CA SER J 638 " pdb=" CB SER J 638 " ideal model delta sigma weight residual 1.534 1.497 0.037 2.47e-02 1.64e+03 2.25e+00 bond pdb=" CB TRP I1276 " pdb=" CG TRP I1276 " ideal model delta sigma weight residual 1.498 1.452 0.046 3.10e-02 1.04e+03 2.17e+00 bond pdb=" CB MET I1066 " pdb=" CG MET I1066 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.09e+00 ... (remaining 34143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 44388 1.43 - 2.86: 1628 2.86 - 4.29: 249 4.29 - 5.73: 75 5.73 - 7.16: 11 Bond angle restraints: 46351 Sorted by residual: angle pdb=" N GLU J 704 " pdb=" CA GLU J 704 " pdb=" CB GLU J 704 " ideal model delta sigma weight residual 114.17 110.14 4.03 1.14e+00 7.69e-01 1.25e+01 angle pdb=" N ARG J 77 " pdb=" CA ARG J 77 " pdb=" C ARG J 77 " ideal model delta sigma weight residual 110.80 117.96 -7.16 2.13e+00 2.20e-01 1.13e+01 angle pdb=" CA GLY F 954 " pdb=" C GLY F 954 " pdb=" N TRP F 955 " ideal model delta sigma weight residual 114.58 117.29 -2.71 8.60e-01 1.35e+00 9.90e+00 angle pdb=" N VAL I1138 " pdb=" CA VAL I1138 " pdb=" C VAL I1138 " ideal model delta sigma weight residual 109.34 115.42 -6.08 2.08e+00 2.31e-01 8.54e+00 angle pdb=" C GLU I1137 " pdb=" N VAL I1138 " pdb=" CA VAL I1138 " ideal model delta sigma weight residual 121.97 127.05 -5.08 1.80e+00 3.09e-01 7.96e+00 ... (remaining 46346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.22: 18889 18.22 - 36.43: 1431 36.43 - 54.65: 434 54.65 - 72.86: 109 72.86 - 91.08: 10 Dihedral angle restraints: 20873 sinusoidal: 8924 harmonic: 11949 Sorted by residual: dihedral pdb=" CA ARG F 870 " pdb=" C ARG F 870 " pdb=" N HIS F 871 " pdb=" CA HIS F 871 " ideal model delta harmonic sigma weight residual -180.00 -147.28 -32.72 0 5.00e+00 4.00e-02 4.28e+01 dihedral pdb=" CA LYS J 76 " pdb=" C LYS J 76 " pdb=" N ARG J 77 " pdb=" CA ARG J 77 " ideal model delta harmonic sigma weight residual 180.00 149.98 30.02 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA LEU I1151 " pdb=" C LEU I1151 " pdb=" N GLY I1152 " pdb=" CA GLY I1152 " ideal model delta harmonic sigma weight residual -180.00 -151.68 -28.32 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 20870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3360 0.032 - 0.064: 1233 0.064 - 0.096: 439 0.096 - 0.128: 197 0.128 - 0.160: 38 Chirality restraints: 5267 Sorted by residual: chirality pdb=" CA ILE I 668 " pdb=" N ILE I 668 " pdb=" C ILE I 668 " pdb=" CB ILE I 668 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CB VAL I 690 " pdb=" CA VAL I 690 " pdb=" CG1 VAL I 690 " pdb=" CG2 VAL I 690 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CA ILE J 500 " pdb=" N ILE J 500 " pdb=" C ILE J 500 " pdb=" CB ILE J 500 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 5264 not shown) Planarity restraints: 5930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR J1178 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO J1179 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO J1179 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO J1179 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE I 831 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C ILE I 831 " 0.032 2.00e-02 2.50e+03 pdb=" O ILE I 831 " -0.012 2.00e-02 2.50e+03 pdb=" N HIS I 832 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET I 488 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO I 489 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO I 489 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 489 " 0.025 5.00e-02 4.00e+02 ... (remaining 5927 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 57 2.24 - 2.91: 14542 2.91 - 3.57: 52185 3.57 - 4.24: 79132 4.24 - 4.90: 132608 Nonbonded interactions: 278524 Sorted by model distance: nonbonded pdb=" OD2 ASP J 460 " pdb=" OD1 ASP J 462 " model vdw 1.577 3.040 nonbonded pdb=" OD1 ASP I 826 " pdb=" OG1 THR I 829 " model vdw 1.991 3.040 nonbonded pdb=" O GLY F 727 " pdb=" OG SER F 743 " model vdw 2.001 3.040 nonbonded pdb=" O VAL J 347 " pdb=" OG SER J 350 " model vdw 2.027 3.040 nonbonded pdb=" OG SER F 11 " pdb=" O GLU F 14 " model vdw 2.030 3.040 ... (remaining 278519 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 'G' and (resid 6 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 149 or (resid 150 and (name N or \ name CA or name C or name O or name CB )) or resid 151 through 158 or resid 170 \ through 217 or (resid 218 and (name N or name CA or name C or name O or name CB \ )) or resid 219 through 232)) selection = (chain 'H' and (resid 6 through 190 or (resid 191 through 192 and (name N or nam \ e CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 232)) } 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.230 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 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 : 0.005 0.090 34156 Z= 0.228 Angle : 1.034 78.993 46363 Z= 0.386 Chirality : 0.042 0.160 5267 Planarity : 0.004 0.052 5930 Dihedral : 14.812 91.077 13169 Min Nonbonded Distance : 1.577 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.92 % Favored : 90.00 % Rotamer: Outliers : 5.67 % Allowed : 10.01 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.13), residues: 4132 helix: 0.49 (0.13), residues: 1515 sheet: -1.28 (0.23), residues: 470 loop : -1.86 (0.14), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 211 TYR 0.014 0.002 TYR J 360 PHE 0.019 0.002 PHE J1319 TRP 0.008 0.001 TRP I 807 HIS 0.007 0.001 HIS I1070 Details of bonding type rmsd covalent geometry : bond 0.00509 (34148) covalent geometry : angle 0.66555 (46351) hydrogen bonds : bond 0.14609 ( 1391) hydrogen bonds : angle 6.80573 ( 3878) metal coordination : bond 0.05402 ( 8) metal coordination : angle 49.20935 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 1022 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.8476 (mtmt) cc_final: 0.8210 (pttp) REVERT: G 46 ILE cc_start: 0.8585 (tp) cc_final: 0.8296 (tp) REVERT: G 50 SER cc_start: 0.9051 (m) cc_final: 0.8697 (p) REVERT: G 57 THR cc_start: 0.7991 (m) cc_final: 0.7099 (p) REVERT: G 68 TYR cc_start: 0.9139 (m-80) cc_final: 0.8477 (m-80) REVERT: G 103 ASN cc_start: 0.8734 (m-40) cc_final: 0.8316 (m-40) REVERT: G 145 LYS cc_start: 0.8091 (tttt) cc_final: 0.7881 (tttm) REVERT: G 152 TYR cc_start: 0.8818 (t80) cc_final: 0.8448 (t80) REVERT: G 178 SER cc_start: 0.9287 (t) cc_final: 0.8947 (m) REVERT: G 200 LYS cc_start: 0.8925 (ttmt) cc_final: 0.8530 (ttmm) REVERT: H 51 MET cc_start: 0.8810 (mmp) cc_final: 0.7988 (mpp) REVERT: H 61 ILE cc_start: 0.9379 (mm) cc_final: 0.9126 (mm) REVERT: H 84 ASN cc_start: 0.9061 (m-40) cc_final: 0.8518 (t0) REVERT: H 88 LEU cc_start: 0.8320 (mt) cc_final: 0.8077 (mt) REVERT: H 125 LYS cc_start: 0.9350 (mptt) cc_final: 0.8698 (tttp) REVERT: H 144 ILE cc_start: 0.8778 (mp) cc_final: 0.8512 (mp) REVERT: H 145 LYS cc_start: 0.9110 (tttt) cc_final: 0.8886 (tptt) REVERT: H 177 TYR cc_start: 0.8185 (m-80) cc_final: 0.7714 (m-80) REVERT: H 217 ILE cc_start: 0.8699 (mm) cc_final: 0.8087 (mm) REVERT: H 227 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8488 (mm-40) REVERT: I 185 ASP cc_start: 0.7573 (m-30) cc_final: 0.7181 (m-30) REVERT: I 340 ASP cc_start: 0.8918 (m-30) cc_final: 0.8565 (p0) REVERT: I 403 MET cc_start: 0.8253 (tmm) cc_final: 0.8047 (tpp) REVERT: I 434 ASP cc_start: 0.9228 (m-30) cc_final: 0.9016 (m-30) REVERT: I 639 LYS cc_start: 0.8463 (mtmm) cc_final: 0.7964 (mttm) REVERT: I 693 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8460 (tt) REVERT: I 708 VAL cc_start: 0.8830 (t) cc_final: 0.8629 (t) REVERT: I 768 MET cc_start: 0.7879 (ptm) cc_final: 0.7655 (ptp) REVERT: I 781 ASP cc_start: 0.7166 (m-30) cc_final: 0.6930 (m-30) REVERT: I 930 ASP cc_start: 0.7916 (t0) cc_final: 0.7332 (t0) REVERT: I 1029 LEU cc_start: 0.9470 (tt) cc_final: 0.9218 (mt) REVERT: I 1216 ARG cc_start: 0.8424 (ptp-170) cc_final: 0.7512 (ptt90) REVERT: I 1297 ASP cc_start: 0.7539 (t0) cc_final: 0.7324 (t0) REVERT: I 1339 LEU cc_start: 0.9233 (mp) cc_final: 0.8844 (mp) REVERT: J 29 MET cc_start: 0.8935 (tpp) cc_final: 0.8626 (tpp) REVERT: J 42 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.5833 (mt-10) REVERT: J 50 LYS cc_start: 0.7028 (tttp) cc_final: 0.6824 (tttp) REVERT: J 62 PHE cc_start: 0.9063 (m-80) cc_final: 0.8795 (m-10) REVERT: J 113 HIS cc_start: 0.8868 (t-90) cc_final: 0.8068 (t-90) REVERT: J 197 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8623 (mt-10) REVERT: J 238 ILE cc_start: 0.9086 (mm) cc_final: 0.8802 (tt) REVERT: J 265 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8632 (mm) REVERT: J 294 ASN cc_start: 0.9063 (t0) cc_final: 0.8473 (m-40) REVERT: J 303 VAL cc_start: 0.8938 (t) cc_final: 0.8705 (p) REVERT: J 431 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.8106 (ptt180) REVERT: J 441 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7560 (mm) REVERT: J 445 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7788 (pttt) REVERT: J 454 CYS cc_start: 0.8580 (t) cc_final: 0.8308 (t) REVERT: J 458 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7274 (t0) REVERT: J 485 MET cc_start: 0.8768 (ttt) cc_final: 0.8455 (ttt) REVERT: J 705 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7686 (p) REVERT: J 759 ILE cc_start: 0.8610 (mm) cc_final: 0.8266 (mt) REVERT: J 800 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8221 (mm) REVERT: J 817 HIS cc_start: 0.7827 (m-70) cc_final: 0.7598 (m-70) REVERT: J 818 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6135 (pm20) REVERT: J 834 PRO cc_start: 0.9053 (Cg_endo) cc_final: 0.8498 (Cg_exo) REVERT: J 913 GLU cc_start: 0.8274 (tt0) cc_final: 0.7822 (tt0) REVERT: J 1275 LEU cc_start: 0.9021 (tp) cc_final: 0.8710 (tp) REVERT: K 37 PRO cc_start: 0.8943 (Cg_endo) cc_final: 0.7025 (Cg_exo) REVERT: K 66 VAL cc_start: 0.9353 (t) cc_final: 0.9116 (t) REVERT: F 9 TRP cc_start: 0.8801 (m100) cc_final: 0.8155 (m100) REVERT: F 34 PHE cc_start: 0.8596 (m-80) cc_final: 0.8048 (m-10) REVERT: F 99 GLU cc_start: 0.4828 (OUTLIER) cc_final: 0.4601 (pm20) REVERT: F 160 ASN cc_start: 0.8840 (t0) cc_final: 0.8561 (t0) REVERT: F 219 MET cc_start: 0.8198 (mmt) cc_final: 0.7713 (mmm) REVERT: F 229 LEU cc_start: 0.9114 (tp) cc_final: 0.8683 (tp) REVERT: F 252 VAL cc_start: 0.7494 (t) cc_final: 0.6851 (t) REVERT: F 281 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8126 (mm-30) REVERT: F 395 ASP cc_start: 0.8923 (t0) cc_final: 0.8624 (p0) REVERT: F 401 GLN cc_start: 0.8988 (tp40) cc_final: 0.8676 (mm-40) REVERT: F 407 LEU cc_start: 0.8978 (mt) cc_final: 0.8697 (mm) REVERT: F 450 VAL cc_start: 0.8907 (t) cc_final: 0.8693 (m) REVERT: F 553 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8515 (mp0) REVERT: F 608 ILE cc_start: 0.8088 (tt) cc_final: 0.7273 (tt) REVERT: F 688 LEU cc_start: 0.8127 (tp) cc_final: 0.7614 (mp) REVERT: F 776 PHE cc_start: 0.7738 (t80) cc_final: 0.7251 (t80) REVERT: F 820 TYR cc_start: 0.8950 (m-80) cc_final: 0.8588 (m-80) REVERT: F 835 PHE cc_start: 0.8096 (m-80) cc_final: 0.7620 (m-80) REVERT: F 941 SER cc_start: 0.9199 (m) cc_final: 0.8841 (p) REVERT: F 944 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8756 (mm-40) REVERT: F 949 SER cc_start: 0.9336 (t) cc_final: 0.9042 (p) REVERT: F 958 ASP cc_start: 0.6318 (OUTLIER) cc_final: 0.5910 (m-30) outliers start: 200 outliers final: 65 residues processed: 1162 average time/residue: 0.2156 time to fit residues: 385.9296 Evaluate side-chains 772 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 694 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain I residue 31 GLN Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 150 HIS Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 226 GLU Chi-restraints excluded: chain I residue 283 LYS Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 486 THR Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 504 GLU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 757 THR Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1268 GLN Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 445 LYS Chi-restraints excluded: chain J residue 458 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 562 GLU Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 917 VAL Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1123 ARG Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 469 TYR Chi-restraints excluded: chain F residue 553 GLU Chi-restraints excluded: chain F residue 707 GLU Chi-restraints excluded: chain F residue 958 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 GLN ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN I 148 GLN I 510 GLN I 517 GLN I 649 GLN I 894 GLN I 952 GLN J 45 ASN ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 419 HIS J 430 HIS J1023 HIS ** J1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 GLN F 240 HIS F 250 GLN ** F 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 HIS F 420 ASN ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 571 ASN ** F 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 729 ASN F 745 HIS F 775 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.217157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.131515 restraints weight = 52502.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130374 restraints weight = 28941.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.130247 restraints weight = 22811.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.130614 restraints weight = 21347.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.131825 restraints weight = 18030.902| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 34156 Z= 0.247 Angle : 0.872 50.264 46363 Z= 0.412 Chirality : 0.048 0.312 5267 Planarity : 0.006 0.069 5930 Dihedral : 13.339 112.791 5249 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.79 % Favored : 92.11 % Rotamer: Outliers : 6.13 % Allowed : 16.14 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.13), residues: 4132 helix: 0.39 (0.13), residues: 1551 sheet: -1.22 (0.23), residues: 485 loop : -1.85 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 3 TYR 0.035 0.002 TYR I 367 PHE 0.027 0.002 PHE G 35 TRP 0.023 0.002 TRP F 955 HIS 0.012 0.002 HIS H 128 Details of bonding type rmsd covalent geometry : bond 0.00573 (34148) covalent geometry : angle 0.79252 (46351) hydrogen bonds : bond 0.04890 ( 1391) hydrogen bonds : angle 5.70393 ( 3878) metal coordination : bond 0.02152 ( 8) metal coordination : angle 22.64373 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 740 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.8404 (mtmt) cc_final: 0.8138 (pttp) REVERT: G 46 ILE cc_start: 0.8747 (tp) cc_final: 0.8354 (tp) REVERT: G 50 SER cc_start: 0.9129 (m) cc_final: 0.8740 (p) REVERT: G 51 MET cc_start: 0.8651 (mmm) cc_final: 0.8377 (mmm) REVERT: G 103 ASN cc_start: 0.8799 (m-40) cc_final: 0.8401 (m-40) REVERT: G 152 TYR cc_start: 0.8802 (t80) cc_final: 0.8509 (t80) REVERT: G 178 SER cc_start: 0.9270 (t) cc_final: 0.8919 (m) REVERT: G 200 LYS cc_start: 0.8850 (ttmt) cc_final: 0.8444 (ttmm) REVERT: H 41 ASN cc_start: 0.8860 (t0) cc_final: 0.8596 (t0) REVERT: H 84 ASN cc_start: 0.9150 (m-40) cc_final: 0.8564 (t0) REVERT: H 95 LYS cc_start: 0.8334 (mtmm) cc_final: 0.8133 (mtmm) REVERT: H 121 VAL cc_start: 0.9238 (t) cc_final: 0.9027 (t) REVERT: H 125 LYS cc_start: 0.9295 (mptt) cc_final: 0.8666 (tttp) REVERT: H 145 LYS cc_start: 0.9315 (tttt) cc_final: 0.8912 (tptt) REVERT: H 146 VAL cc_start: 0.9444 (OUTLIER) cc_final: 0.8589 (p) REVERT: H 180 VAL cc_start: 0.9387 (p) cc_final: 0.9167 (p) REVERT: H 181 GLU cc_start: 0.8228 (tp30) cc_final: 0.7655 (tp30) REVERT: H 206 GLU cc_start: 0.8729 (tt0) cc_final: 0.8446 (tp30) REVERT: H 232 VAL cc_start: 0.6486 (OUTLIER) cc_final: 0.6235 (m) REVERT: I 46 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8769 (mm-40) REVERT: I 47 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.7349 (p90) REVERT: I 87 ILE cc_start: 0.9010 (mm) cc_final: 0.8761 (mp) REVERT: I 158 ASP cc_start: 0.8513 (t0) cc_final: 0.8231 (t0) REVERT: I 192 ASP cc_start: 0.8570 (m-30) cc_final: 0.7837 (m-30) REVERT: I 340 ASP cc_start: 0.9248 (m-30) cc_final: 0.8767 (p0) REVERT: I 346 TYR cc_start: 0.7514 (m-10) cc_final: 0.7020 (m-80) REVERT: I 367 TYR cc_start: 0.7758 (t80) cc_final: 0.7366 (t80) REVERT: I 368 ARG cc_start: 0.9034 (mmm-85) cc_final: 0.8372 (mmm160) REVERT: I 403 MET cc_start: 0.8433 (tmm) cc_final: 0.8219 (tpp) REVERT: I 431 LYS cc_start: 0.9288 (ttmt) cc_final: 0.8790 (mtmt) REVERT: I 565 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7075 (tt0) REVERT: I 622 ASN cc_start: 0.8068 (t0) cc_final: 0.7741 (t0) REVERT: I 623 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8190 (tp) REVERT: I 649 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7356 (mp10) REVERT: I 693 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8304 (tt) REVERT: I 697 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8554 (pttm) REVERT: I 704 MET cc_start: 0.7553 (mmm) cc_final: 0.6992 (mmm) REVERT: I 708 VAL cc_start: 0.8787 (t) cc_final: 0.8492 (t) REVERT: I 737 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.7859 (m110) REVERT: I 781 ASP cc_start: 0.7053 (m-30) cc_final: 0.6838 (m-30) REVERT: I 930 ASP cc_start: 0.7974 (t0) cc_final: 0.7564 (t0) REVERT: I 960 LEU cc_start: 0.9226 (mp) cc_final: 0.8406 (tp) REVERT: I 1034 ARG cc_start: 0.9468 (ttp-110) cc_final: 0.9143 (ttm110) REVERT: I 1038 GLN cc_start: 0.8910 (pp30) cc_final: 0.8609 (pp30) REVERT: I 1177 ARG cc_start: 0.8619 (ptm160) cc_final: 0.8239 (ttm170) REVERT: I 1297 ASP cc_start: 0.7807 (t0) cc_final: 0.7580 (t0) REVERT: I 1316 GLU cc_start: 0.8377 (tp30) cc_final: 0.7972 (tm-30) REVERT: J 42 GLU cc_start: 0.6109 (OUTLIER) cc_final: 0.5863 (mt-10) REVERT: J 50 LYS cc_start: 0.7320 (tttp) cc_final: 0.6910 (tttp) REVERT: J 118 LYS cc_start: 0.9285 (mttt) cc_final: 0.9012 (mmmm) REVERT: J 195 GLU cc_start: 0.9362 (mp0) cc_final: 0.9075 (pm20) REVERT: J 265 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8071 (mm) REVERT: J 281 ARG cc_start: 0.9420 (mmm160) cc_final: 0.9153 (mmm160) REVERT: J 294 ASN cc_start: 0.9193 (t0) cc_final: 0.8939 (t0) REVERT: J 301 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8786 (pp20) REVERT: J 303 VAL cc_start: 0.9066 (t) cc_final: 0.8800 (p) REVERT: J 330 MET cc_start: 0.9114 (mmm) cc_final: 0.8606 (mpp) REVERT: J 441 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7970 (mt) REVERT: J 445 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.7893 (mtpt) REVERT: J 454 CYS cc_start: 0.8588 (t) cc_final: 0.8350 (t) REVERT: J 478 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7784 (mt) REVERT: J 484 MET cc_start: 0.8373 (mtm) cc_final: 0.8115 (mtm) REVERT: J 485 MET cc_start: 0.8802 (ttt) cc_final: 0.8509 (ttt) REVERT: J 610 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7769 (ttp80) REVERT: J 697 MET cc_start: 0.7683 (ppp) cc_final: 0.7434 (ttp) REVERT: J 797 THR cc_start: 0.8435 (m) cc_final: 0.7703 (p) REVERT: J 818 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6237 (pm20) REVERT: J 830 ASP cc_start: 0.8486 (t0) cc_final: 0.8051 (t70) REVERT: J 913 GLU cc_start: 0.8330 (tt0) cc_final: 0.7810 (tt0) REVERT: J 1311 LYS cc_start: 0.9219 (mmmt) cc_final: 0.8996 (mtmm) REVERT: K 11 GLU cc_start: 0.8845 (pp20) cc_final: 0.8576 (pp20) REVERT: K 26 ARG cc_start: 0.8941 (tpt170) cc_final: 0.8361 (tpm170) REVERT: K 30 MET cc_start: 0.7483 (ttm) cc_final: 0.7095 (tpp) REVERT: K 35 LYS cc_start: 0.8459 (ptpp) cc_final: 0.8246 (ptpp) REVERT: K 44 ASP cc_start: 0.8292 (m-30) cc_final: 0.7999 (p0) REVERT: K 53 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7985 (mm-30) REVERT: K 58 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8258 (pp) REVERT: K 64 LEU cc_start: 0.7582 (mt) cc_final: 0.7304 (tt) REVERT: F 10 ILE cc_start: 0.9120 (pt) cc_final: 0.8872 (tp) REVERT: F 34 PHE cc_start: 0.8577 (m-80) cc_final: 0.7842 (m-10) REVERT: F 160 ASN cc_start: 0.8777 (t0) cc_final: 0.8503 (t0) REVERT: F 204 LEU cc_start: 0.9115 (mt) cc_final: 0.8854 (mt) REVERT: F 211 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8733 (mm) REVERT: F 221 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7231 (tpp80) REVERT: F 281 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8176 (mm-30) REVERT: F 376 MET cc_start: -0.1719 (mmm) cc_final: -0.1986 (mmm) REVERT: F 407 LEU cc_start: 0.8799 (mt) cc_final: 0.8552 (mm) REVERT: F 444 TYR cc_start: 0.8153 (m-80) cc_final: 0.7835 (m-10) REVERT: F 534 PHE cc_start: 0.6742 (m-80) cc_final: 0.6487 (m-80) REVERT: F 543 ARG cc_start: 0.8546 (mmt-90) cc_final: 0.8270 (mtt180) REVERT: F 553 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8769 (mp0) REVERT: F 558 GLN cc_start: 0.8597 (tt0) cc_final: 0.8205 (tp-100) REVERT: F 723 PHE cc_start: 0.8798 (m-10) cc_final: 0.8523 (m-10) REVERT: F 766 GLU cc_start: 0.9418 (mm-30) cc_final: 0.9148 (mm-30) REVERT: F 776 PHE cc_start: 0.7959 (t80) cc_final: 0.7245 (t80) REVERT: F 820 TYR cc_start: 0.9216 (m-80) cc_final: 0.8894 (m-80) REVERT: F 941 SER cc_start: 0.9325 (m) cc_final: 0.9072 (p) REVERT: F 948 GLU cc_start: 0.9531 (tp30) cc_final: 0.9311 (pt0) REVERT: F 949 SER cc_start: 0.9442 (t) cc_final: 0.9083 (p) REVERT: F 956 ARG cc_start: 0.8155 (ttp-170) cc_final: 0.7932 (mtp180) REVERT: F 957 LEU cc_start: 0.8679 (tp) cc_final: 0.8254 (tp) outliers start: 216 outliers final: 116 residues processed: 884 average time/residue: 0.2299 time to fit residues: 321.2564 Evaluate side-chains 757 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 621 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 147 GLN Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 31 GLN Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 150 HIS Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 226 GLU Chi-restraints excluded: chain I residue 283 LYS Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 486 THR Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 649 GLN Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 737 ASN Chi-restraints excluded: chain I residue 757 THR Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 807 TRP Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain I residue 883 LEU Chi-restraints excluded: chain I residue 901 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1268 GLN Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 334 LYS Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 445 LYS Chi-restraints excluded: chain J residue 458 ASN Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 610 ARG Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 917 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1098 GLN Chi-restraints excluded: chain J residue 1123 ARG Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1325 PHE Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 254 CYS Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 321 MET Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 469 TYR Chi-restraints excluded: chain F residue 507 LEU Chi-restraints excluded: chain F residue 553 GLU Chi-restraints excluded: chain F residue 647 TYR Chi-restraints excluded: chain F residue 745 HIS Chi-restraints excluded: chain F residue 799 SER Chi-restraints excluded: chain F residue 841 VAL Chi-restraints excluded: chain F residue 869 ASN Chi-restraints excluded: chain F residue 908 ASN Chi-restraints excluded: chain F residue 921 LEU Chi-restraints excluded: chain F residue 935 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 370 optimal weight: 40.0000 chunk 260 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 327 optimal weight: 30.0000 chunk 102 optimal weight: 0.9980 chunk 270 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 111 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN I 46 GLN I 83 GLN I 86 GLN I 760 ASN ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 768 ASN ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1235 ASN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 HIS F 194 GLN F 244 ASN F 268 HIS ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 626 HIS ** F 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.218152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.132918 restraints weight = 52456.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.132551 restraints weight = 31221.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.131776 restraints weight = 22111.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.132576 restraints weight = 21041.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134263 restraints weight = 17695.471| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34156 Z= 0.181 Angle : 0.787 42.520 46363 Z= 0.377 Chirality : 0.045 0.284 5267 Planarity : 0.005 0.092 5930 Dihedral : 13.163 118.543 5199 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.43 % Favored : 92.50 % Rotamer: Outliers : 5.79 % Allowed : 17.62 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.13), residues: 4132 helix: 0.49 (0.13), residues: 1531 sheet: -1.18 (0.23), residues: 505 loop : -1.75 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 221 TYR 0.032 0.002 TYR I 367 PHE 0.035 0.002 PHE J 62 TRP 0.023 0.002 TRP J 115 HIS 0.012 0.001 HIS F 213 Details of bonding type rmsd covalent geometry : bond 0.00417 (34148) covalent geometry : angle 0.73408 (46351) hydrogen bonds : bond 0.04340 ( 1391) hydrogen bonds : angle 5.40389 ( 3878) metal coordination : bond 0.01837 ( 8) metal coordination : angle 17.67130 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 686 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: G 25 LYS cc_start: 0.8378 (mtmt) cc_final: 0.8119 (pttp) REVERT: G 46 ILE cc_start: 0.8661 (tp) cc_final: 0.8221 (tp) REVERT: G 50 SER cc_start: 0.9134 (m) cc_final: 0.8651 (p) REVERT: G 51 MET cc_start: 0.8567 (mmm) cc_final: 0.8257 (mmm) REVERT: G 103 ASN cc_start: 0.8691 (m-40) cc_final: 0.8347 (m-40) REVERT: G 152 TYR cc_start: 0.8819 (t80) cc_final: 0.8552 (t80) REVERT: G 178 SER cc_start: 0.9252 (t) cc_final: 0.8972 (m) REVERT: G 200 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8316 (ttmm) REVERT: H 51 MET cc_start: 0.9132 (mmm) cc_final: 0.8644 (tpp) REVERT: H 84 ASN cc_start: 0.9184 (m-40) cc_final: 0.8631 (t0) REVERT: H 95 LYS cc_start: 0.8238 (mtmm) cc_final: 0.7868 (mtmm) REVERT: H 125 LYS cc_start: 0.9280 (mptt) cc_final: 0.8654 (tttp) REVERT: H 133 LEU cc_start: 0.8486 (tp) cc_final: 0.8155 (tp) REVERT: H 147 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8371 (mm-40) REVERT: H 181 GLU cc_start: 0.8353 (tp30) cc_final: 0.7766 (tp30) REVERT: H 206 GLU cc_start: 0.8777 (tt0) cc_final: 0.8243 (tp30) REVERT: H 212 ASP cc_start: 0.8217 (p0) cc_final: 0.7660 (p0) REVERT: I 46 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8469 (mm110) REVERT: I 47 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.7262 (p90) REVERT: I 81 ASP cc_start: 0.6982 (t0) cc_final: 0.6330 (t0) REVERT: I 83 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6443 (pm20) REVERT: I 87 ILE cc_start: 0.9069 (mm) cc_final: 0.8812 (mp) REVERT: I 158 ASP cc_start: 0.8429 (t0) cc_final: 0.8043 (t0) REVERT: I 160 ASP cc_start: 0.8702 (m-30) cc_final: 0.8226 (m-30) REVERT: I 185 ASP cc_start: 0.6770 (m-30) cc_final: 0.6469 (m-30) REVERT: I 192 ASP cc_start: 0.8635 (m-30) cc_final: 0.7806 (m-30) REVERT: I 195 PHE cc_start: 0.6990 (m-80) cc_final: 0.6627 (t80) REVERT: I 340 ASP cc_start: 0.9212 (m-30) cc_final: 0.8745 (p0) REVERT: I 346 TYR cc_start: 0.7546 (m-10) cc_final: 0.6709 (m-80) REVERT: I 403 MET cc_start: 0.8401 (tmm) cc_final: 0.8186 (tpp) REVERT: I 488 MET cc_start: 0.8598 (mmm) cc_final: 0.7153 (mmm) REVERT: I 492 MET cc_start: 0.7946 (ptp) cc_final: 0.7482 (tpp) REVERT: I 549 ASP cc_start: 0.7714 (t0) cc_final: 0.7438 (m-30) REVERT: I 565 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6937 (tt0) REVERT: I 622 ASN cc_start: 0.8116 (t0) cc_final: 0.7781 (t0) REVERT: I 623 LEU cc_start: 0.8418 (mt) cc_final: 0.8193 (tp) REVERT: I 639 LYS cc_start: 0.8433 (mtmm) cc_final: 0.7903 (mttm) REVERT: I 693 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8274 (tt) REVERT: I 697 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8264 (pttm) REVERT: I 699 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8180 (mp) REVERT: I 704 MET cc_start: 0.7303 (mmm) cc_final: 0.7099 (mmm) REVERT: I 737 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7979 (m110) REVERT: I 760 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8471 (m-40) REVERT: I 761 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7837 (mp10) REVERT: I 790 ASP cc_start: 0.7850 (t70) cc_final: 0.7567 (t0) REVERT: I 814 ASP cc_start: 0.7812 (m-30) cc_final: 0.7601 (m-30) REVERT: I 817 LEU cc_start: 0.8868 (mm) cc_final: 0.8621 (mt) REVERT: I 898 GLU cc_start: 0.9634 (pp20) cc_final: 0.9296 (pp20) REVERT: I 930 ASP cc_start: 0.8159 (t0) cc_final: 0.7949 (t0) REVERT: I 960 LEU cc_start: 0.9243 (mp) cc_final: 0.8349 (tp) REVERT: I 1038 GLN cc_start: 0.8951 (pp30) cc_final: 0.8720 (pp30) REVERT: I 1131 MET cc_start: 0.7504 (mtp) cc_final: 0.7275 (ttm) REVERT: I 1174 GLU cc_start: 0.8393 (tp30) cc_final: 0.8143 (tp30) REVERT: I 1177 ARG cc_start: 0.8639 (ptm160) cc_final: 0.8103 (ttm170) REVERT: I 1231 TYR cc_start: 0.8527 (t80) cc_final: 0.8238 (t80) REVERT: I 1297 ASP cc_start: 0.7810 (t0) cc_final: 0.7170 (t0) REVERT: I 1302 THR cc_start: 0.9036 (p) cc_final: 0.8755 (t) REVERT: I 1316 GLU cc_start: 0.8539 (tp30) cc_final: 0.7951 (tm-30) REVERT: J 42 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.5504 (mt-10) REVERT: J 62 PHE cc_start: 0.9070 (m-80) cc_final: 0.8791 (m-80) REVERT: J 127 LEU cc_start: 0.9500 (tp) cc_final: 0.9174 (tt) REVERT: J 237 MET cc_start: 0.8335 (mtp) cc_final: 0.7944 (mtp) REVERT: J 238 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8006 (tt) REVERT: J 265 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8229 (mm) REVERT: J 281 ARG cc_start: 0.9381 (mmm160) cc_final: 0.9105 (mmm160) REVERT: J 296 LYS cc_start: 0.9520 (mttt) cc_final: 0.9271 (mtmt) REVERT: J 301 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8892 (tm-30) REVERT: J 303 VAL cc_start: 0.9061 (t) cc_final: 0.8805 (p) REVERT: J 330 MET cc_start: 0.9093 (mmm) cc_final: 0.8774 (mpp) REVERT: J 343 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6703 (mp) REVERT: J 417 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.7015 (tpp80) REVERT: J 441 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7474 (mm) REVERT: J 445 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7946 (ptpt) REVERT: J 454 CYS cc_start: 0.8602 (t) cc_final: 0.8325 (t) REVERT: J 478 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8000 (mt) REVERT: J 484 MET cc_start: 0.8288 (mtm) cc_final: 0.7999 (mtm) REVERT: J 485 MET cc_start: 0.8651 (ttt) cc_final: 0.8381 (ttt) REVERT: J 500 ILE cc_start: 0.8647 (mt) cc_final: 0.8230 (tt) REVERT: J 508 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7730 (tp) REVERT: J 610 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7724 (ttp80) REVERT: J 797 THR cc_start: 0.8423 (m) cc_final: 0.7641 (p) REVERT: J 811 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7932 (mt-10) REVERT: J 818 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6402 (pm20) REVERT: J 830 ASP cc_start: 0.8454 (t0) cc_final: 0.8008 (t70) REVERT: J 913 GLU cc_start: 0.8262 (tt0) cc_final: 0.8051 (tt0) REVERT: J 960 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8202 (tt) REVERT: J 1023 HIS cc_start: 0.8471 (OUTLIER) cc_final: 0.8200 (t70) REVERT: J 1040 MET cc_start: 0.0930 (mmm) cc_final: 0.0474 (mmp) REVERT: J 1219 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7853 (p0) REVERT: J 1289 ASN cc_start: 0.9158 (t0) cc_final: 0.8950 (t0) REVERT: K 11 GLU cc_start: 0.8970 (pp20) cc_final: 0.8615 (pp20) REVERT: K 12 LYS cc_start: 0.9134 (mmmt) cc_final: 0.8794 (mmmt) REVERT: K 26 ARG cc_start: 0.8930 (tpt170) cc_final: 0.8271 (tpm170) REVERT: K 30 MET cc_start: 0.7346 (ttm) cc_final: 0.7106 (tpp) REVERT: K 52 ARG cc_start: 0.8413 (ttp-170) cc_final: 0.7729 (ttp-170) REVERT: F 9 TRP cc_start: 0.8598 (m100) cc_final: 0.7727 (m100) REVERT: F 10 ILE cc_start: 0.9056 (pt) cc_final: 0.8781 (tp) REVERT: F 34 PHE cc_start: 0.8428 (m-80) cc_final: 0.7693 (m-10) REVERT: F 47 ASP cc_start: 0.5857 (OUTLIER) cc_final: 0.5239 (p0) REVERT: F 99 GLU cc_start: 0.3443 (OUTLIER) cc_final: 0.3078 (pt0) REVERT: F 116 PHE cc_start: 0.4117 (OUTLIER) cc_final: 0.3823 (m-80) REVERT: F 160 ASN cc_start: 0.8764 (t0) cc_final: 0.8535 (t0) REVERT: F 204 LEU cc_start: 0.9009 (mt) cc_final: 0.8794 (mt) REVERT: F 213 HIS cc_start: 0.9321 (m170) cc_final: 0.9093 (m90) REVERT: F 244 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.6631 (t0) REVERT: F 252 VAL cc_start: 0.7465 (OUTLIER) cc_final: 0.7127 (p) REVERT: F 281 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8002 (mm-30) REVERT: F 358 MET cc_start: 0.7880 (ptt) cc_final: 0.7615 (ppp) REVERT: F 401 GLN cc_start: 0.9129 (tp-100) cc_final: 0.8472 (mm-40) REVERT: F 407 LEU cc_start: 0.8742 (mt) cc_final: 0.8539 (mt) REVERT: F 418 PHE cc_start: 0.8019 (m-80) cc_final: 0.7691 (m-80) REVERT: F 444 TYR cc_start: 0.7826 (m-80) cc_final: 0.7221 (m-80) REVERT: F 534 PHE cc_start: 0.7467 (m-80) cc_final: 0.6687 (m-80) REVERT: F 543 ARG cc_start: 0.8635 (mmt-90) cc_final: 0.8237 (mtt180) REVERT: F 553 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8573 (mp0) REVERT: F 723 PHE cc_start: 0.8788 (m-10) cc_final: 0.8556 (m-10) REVERT: F 766 GLU cc_start: 0.9377 (mm-30) cc_final: 0.9111 (mm-30) REVERT: F 776 PHE cc_start: 0.7751 (t80) cc_final: 0.7156 (t80) REVERT: F 949 SER cc_start: 0.9395 (t) cc_final: 0.9131 (p) REVERT: F 957 LEU cc_start: 0.8494 (tp) cc_final: 0.8271 (tp) outliers start: 204 outliers final: 106 residues processed: 824 average time/residue: 0.2379 time to fit residues: 310.1713 Evaluate side-chains 736 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 599 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 147 GLN Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 150 HIS Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 226 GLU Chi-restraints excluded: chain I residue 283 LYS Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 486 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 737 ASN Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 760 ASN Chi-restraints excluded: chain I residue 761 GLN Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 807 TRP Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain I residue 883 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1268 GLN Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 334 LYS Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 417 ARG Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 445 LYS Chi-restraints excluded: chain J residue 458 ASN Chi-restraints excluded: chain J residue 460 ASP Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 610 ARG Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1123 ARG Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1325 PHE Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 116 PHE Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 244 ASN Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 254 CYS Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 321 MET Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 469 TYR Chi-restraints excluded: chain F residue 535 HIS Chi-restraints excluded: chain F residue 553 GLU Chi-restraints excluded: chain F residue 626 HIS Chi-restraints excluded: chain F residue 647 TYR Chi-restraints excluded: chain F residue 869 ASN Chi-restraints excluded: chain F residue 935 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 56 optimal weight: 0.6980 chunk 326 optimal weight: 40.0000 chunk 157 optimal weight: 1.9990 chunk 341 optimal weight: 0.5980 chunk 325 optimal weight: 7.9990 chunk 239 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 300 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS I 760 ASN ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS ** I1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN K 72 GLN ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 GLN F 626 HIS F 674 HIS F 885 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.217077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.130114 restraints weight = 52405.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.128701 restraints weight = 29990.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.131781 restraints weight = 19283.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.131928 restraints weight = 13769.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.132062 restraints weight = 14356.391| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34156 Z= 0.175 Angle : 0.758 30.560 46363 Z= 0.372 Chirality : 0.045 0.211 5267 Planarity : 0.005 0.083 5930 Dihedral : 13.014 119.794 5184 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.53 % Favored : 92.45 % Rotamer: Outliers : 5.82 % Allowed : 19.60 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 aren not related in a simple way. whole: -1.16 (0.13), residues: 4132 helix: 0.49 (0.13), residues: 1536 sheet: -1.07 (0.23), residues: 509 loop : -1.67 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 900 TYR 0.027 0.002 TYR H 177 PHE 0.027 0.002 PHE F 572 TRP 0.016 0.001 TRP J 115 HIS 0.011 0.001 HIS F 885 Details of bonding type rmsd covalent geometry : bond 0.00399 (34148) covalent geometry : angle 0.72917 (46351) hydrogen bonds : bond 0.04178 ( 1391) hydrogen bonds : angle 5.25822 ( 3878) metal coordination : bond 0.01700 ( 8) metal coordination : angle 12.85497 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 654 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.8404 (mtmt) cc_final: 0.8136 (pttp) REVERT: G 46 ILE cc_start: 0.8632 (tp) cc_final: 0.8155 (tp) REVERT: G 50 SER cc_start: 0.9068 (m) cc_final: 0.8571 (p) REVERT: G 51 MET cc_start: 0.8580 (mmm) cc_final: 0.8189 (mmm) REVERT: G 80 GLU cc_start: 0.8078 (tt0) cc_final: 0.7828 (tt0) REVERT: G 103 ASN cc_start: 0.8721 (m-40) cc_final: 0.8356 (m-40) REVERT: G 152 TYR cc_start: 0.8800 (t80) cc_final: 0.8501 (t80) REVERT: G 185 TYR cc_start: 0.9053 (p90) cc_final: 0.8699 (p90) REVERT: G 200 LYS cc_start: 0.8743 (ttmt) cc_final: 0.8328 (ttmm) REVERT: H 84 ASN cc_start: 0.9064 (m-40) cc_final: 0.8547 (t0) REVERT: H 125 LYS cc_start: 0.9276 (mptt) cc_final: 0.8688 (tttp) REVERT: H 145 LYS cc_start: 0.9294 (tttt) cc_final: 0.8820 (tptm) REVERT: H 177 TYR cc_start: 0.8375 (m-80) cc_final: 0.7360 (m-80) REVERT: H 181 GLU cc_start: 0.8402 (tp30) cc_final: 0.7773 (tp30) REVERT: H 206 GLU cc_start: 0.8620 (tt0) cc_final: 0.8320 (tp30) REVERT: H 212 ASP cc_start: 0.8117 (p0) cc_final: 0.7504 (p0) REVERT: H 232 VAL cc_start: 0.6361 (OUTLIER) cc_final: 0.6101 (m) REVERT: I 47 TYR cc_start: 0.7706 (OUTLIER) cc_final: 0.7207 (p90) REVERT: I 83 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7186 (pm20) REVERT: I 87 ILE cc_start: 0.9072 (mm) cc_final: 0.8854 (mp) REVERT: I 158 ASP cc_start: 0.8459 (t0) cc_final: 0.8020 (t70) REVERT: I 160 ASP cc_start: 0.8712 (m-30) cc_final: 0.8185 (m-30) REVERT: I 191 LYS cc_start: 0.9201 (mmmm) cc_final: 0.8584 (tptp) REVERT: I 192 ASP cc_start: 0.8685 (m-30) cc_final: 0.7826 (m-30) REVERT: I 340 ASP cc_start: 0.9186 (m-30) cc_final: 0.8750 (p0) REVERT: I 346 TYR cc_start: 0.7537 (m-10) cc_final: 0.7027 (m-80) REVERT: I 359 ARG cc_start: 0.8536 (ttm-80) cc_final: 0.7673 (ttt-90) REVERT: I 371 ARG cc_start: 0.8582 (tpp-160) cc_final: 0.8370 (tpp-160) REVERT: I 403 MET cc_start: 0.8382 (tmm) cc_final: 0.8165 (tpp) REVERT: I 477 GLU cc_start: 0.9419 (tp30) cc_final: 0.8843 (tm-30) REVERT: I 488 MET cc_start: 0.8379 (mmm) cc_final: 0.7755 (mmp) REVERT: I 492 MET cc_start: 0.8061 (ptp) cc_final: 0.7123 (tpp) REVERT: I 549 ASP cc_start: 0.7881 (t0) cc_final: 0.7517 (m-30) REVERT: I 565 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7041 (tt0) REVERT: I 622 ASN cc_start: 0.8195 (t0) cc_final: 0.7774 (t0) REVERT: I 623 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8133 (tp) REVERT: I 693 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8331 (tt) REVERT: I 697 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8360 (pttm) REVERT: I 737 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.7998 (m110) REVERT: I 790 ASP cc_start: 0.7960 (t70) cc_final: 0.7619 (t0) REVERT: I 814 ASP cc_start: 0.7778 (m-30) cc_final: 0.7557 (m-30) REVERT: I 1038 GLN cc_start: 0.8965 (pp30) cc_final: 0.8748 (pp30) REVERT: I 1089 GLU cc_start: 0.7509 (pp20) cc_final: 0.7185 (pp20) REVERT: I 1131 MET cc_start: 0.7649 (mtp) cc_final: 0.7428 (ttm) REVERT: I 1177 ARG cc_start: 0.8703 (ptm160) cc_final: 0.8163 (ttm170) REVERT: I 1203 ASP cc_start: 0.7823 (t0) cc_final: 0.7436 (t0) REVERT: I 1214 ASP cc_start: 0.8247 (t0) cc_final: 0.7841 (t0) REVERT: I 1231 TYR cc_start: 0.8582 (t80) cc_final: 0.8233 (t80) REVERT: I 1316 GLU cc_start: 0.8476 (tp30) cc_final: 0.8002 (tm-30) REVERT: J 62 PHE cc_start: 0.9185 (m-80) cc_final: 0.8931 (m-80) REVERT: J 238 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8127 (tt) REVERT: J 265 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8348 (mm) REVERT: J 281 ARG cc_start: 0.9359 (mmm160) cc_final: 0.9080 (mmm160) REVERT: J 298 MET cc_start: 0.8954 (mmm) cc_final: 0.7794 (tmm) REVERT: J 301 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8148 (pp20) REVERT: J 303 VAL cc_start: 0.9104 (t) cc_final: 0.8845 (p) REVERT: J 330 MET cc_start: 0.9047 (mmm) cc_final: 0.8754 (mpp) REVERT: J 343 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6746 (mp) REVERT: J 441 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7584 (mm) REVERT: J 445 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8312 (ptpt) REVERT: J 454 CYS cc_start: 0.8529 (t) cc_final: 0.8259 (t) REVERT: J 478 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7810 (mt) REVERT: J 484 MET cc_start: 0.8396 (mtm) cc_final: 0.8166 (mtm) REVERT: J 485 MET cc_start: 0.8584 (ttt) cc_final: 0.8326 (ttt) REVERT: J 500 ILE cc_start: 0.8631 (mt) cc_final: 0.8276 (tt) REVERT: J 508 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7648 (tp) REVERT: J 610 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7930 (ttp80) REVERT: J 797 THR cc_start: 0.8404 (m) cc_final: 0.7550 (p) REVERT: J 811 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7819 (mt-10) REVERT: J 818 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6653 (pm20) REVERT: J 830 ASP cc_start: 0.8482 (t0) cc_final: 0.8019 (t70) REVERT: J 923 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8143 (tp) REVERT: J 960 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8292 (tt) REVERT: J 983 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8395 (mppt) REVERT: J 1040 MET cc_start: 0.0641 (mmm) cc_final: 0.0426 (mmp) REVERT: J 1189 MET cc_start: 0.7928 (mtt) cc_final: 0.7351 (tpp) REVERT: J 1202 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7853 (pm20) REVERT: J 1218 HIS cc_start: 0.7706 (m90) cc_final: 0.7362 (m90) REVERT: K 12 LYS cc_start: 0.9215 (mmmt) cc_final: 0.9015 (mmmt) REVERT: K 26 ARG cc_start: 0.8975 (tpt170) cc_final: 0.8334 (tpm170) REVERT: K 29 GLN cc_start: 0.8359 (mt0) cc_final: 0.8062 (mt0) REVERT: K 30 MET cc_start: 0.7360 (ttm) cc_final: 0.6986 (tpp) REVERT: K 35 LYS cc_start: 0.8474 (ptpp) cc_final: 0.8273 (ptpp) REVERT: K 52 ARG cc_start: 0.8207 (ttp-170) cc_final: 0.7727 (ttp-170) REVERT: F 9 TRP cc_start: 0.8580 (m100) cc_final: 0.7679 (m100) REVERT: F 10 ILE cc_start: 0.8939 (pt) cc_final: 0.8662 (tp) REVERT: F 34 PHE cc_start: 0.8436 (m-80) cc_final: 0.7697 (m-10) REVERT: F 47 ASP cc_start: 0.5657 (OUTLIER) cc_final: 0.5085 (p0) REVERT: F 69 MET cc_start: 0.5619 (tpp) cc_final: 0.5215 (tpp) REVERT: F 116 PHE cc_start: 0.5056 (OUTLIER) cc_final: 0.4764 (m-80) REVERT: F 167 ARG cc_start: 0.8995 (mtm180) cc_final: 0.8761 (mtm180) REVERT: F 204 LEU cc_start: 0.8949 (mt) cc_final: 0.8722 (mt) REVERT: F 213 HIS cc_start: 0.9315 (m170) cc_final: 0.9110 (m-70) REVERT: F 221 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7125 (mtp85) REVERT: F 240 HIS cc_start: 0.8458 (OUTLIER) cc_final: 0.8010 (p90) REVERT: F 247 ASP cc_start: 0.8718 (m-30) cc_final: 0.8131 (m-30) REVERT: F 252 VAL cc_start: 0.7426 (OUTLIER) cc_final: 0.7078 (p) REVERT: F 281 GLU cc_start: 0.8541 (mm-30) cc_final: 0.7961 (mm-30) REVERT: F 358 MET cc_start: 0.7755 (ptt) cc_final: 0.7259 (ppp) REVERT: F 401 GLN cc_start: 0.9096 (tp-100) cc_final: 0.8317 (mm-40) REVERT: F 407 LEU cc_start: 0.8866 (mt) cc_final: 0.8642 (mt) REVERT: F 444 TYR cc_start: 0.7788 (m-80) cc_final: 0.7506 (m-10) REVERT: F 534 PHE cc_start: 0.7427 (m-80) cc_final: 0.6552 (m-80) REVERT: F 538 MET cc_start: 0.8798 (mmm) cc_final: 0.8577 (mmt) REVERT: F 543 ARG cc_start: 0.8666 (mmm-85) cc_final: 0.8296 (mtt180) REVERT: F 553 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8589 (mp0) REVERT: F 707 GLU cc_start: 0.9136 (pt0) cc_final: 0.8887 (tm-30) REVERT: F 723 PHE cc_start: 0.8679 (m-10) cc_final: 0.8447 (m-10) REVERT: F 766 GLU cc_start: 0.9384 (mm-30) cc_final: 0.9121 (mm-30) REVERT: F 775 GLN cc_start: 0.8708 (mp10) cc_final: 0.8374 (mp10) REVERT: F 776 PHE cc_start: 0.7633 (t80) cc_final: 0.7277 (t80) REVERT: F 949 SER cc_start: 0.9393 (t) cc_final: 0.9123 (p) outliers start: 205 outliers final: 124 residues processed: 805 average time/residue: 0.2389 time to fit residues: 304.9513 Evaluate side-chains 745 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 595 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 147 GLN Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 150 HIS Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 226 GLU Chi-restraints excluded: chain I residue 283 LYS Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 486 THR Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 737 ASN Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 757 THR Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 807 TRP Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain I residue 883 LEU Chi-restraints excluded: chain I residue 931 VAL Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1268 GLN Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 445 LYS Chi-restraints excluded: chain J residue 458 ASN Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 562 GLU Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 610 ARG Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 983 LYS Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1123 ARG Chi-restraints excluded: chain J residue 1124 ILE Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1202 GLU Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1325 PHE Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 116 PHE Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 254 CYS Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 321 MET Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 469 TYR Chi-restraints excluded: chain F residue 553 GLU Chi-restraints excluded: chain F residue 739 VAL Chi-restraints excluded: chain F residue 869 ASN Chi-restraints excluded: chain F residue 935 GLU Chi-restraints excluded: chain F residue 941 SER Chi-restraints excluded: chain F residue 956 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 44 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 311 optimal weight: 8.9990 chunk 347 optimal weight: 50.0000 chunk 8 optimal weight: 0.7980 chunk 176 optimal weight: 0.2980 chunk 217 optimal weight: 2.9990 chunk 284 optimal weight: 0.0870 chunk 286 optimal weight: 6.9990 chunk 329 optimal weight: 8.9990 chunk 328 optimal weight: 9.9990 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN I 649 GLN ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1157 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS ** I1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1295 ASN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN K 72 GLN F 160 ASN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 626 HIS F 745 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.231816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.152818 restraints weight = 55769.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.149700 restraints weight = 32414.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.151603 restraints weight = 23438.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.152357 restraints weight = 21801.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.152557 restraints weight = 18255.641| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34156 Z= 0.153 Angle : 0.728 19.612 46363 Z= 0.360 Chirality : 0.044 0.206 5267 Planarity : 0.005 0.085 5930 Dihedral : 12.867 119.055 5176 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.21 % Favored : 92.76 % Rotamer: Outliers : 5.50 % Allowed : 20.94 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.13), residues: 4132 helix: 0.58 (0.13), residues: 1546 sheet: -1.01 (0.23), residues: 508 loop : -1.65 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 221 TYR 0.022 0.002 TYR H 177 PHE 0.026 0.002 PHE I 225 TRP 0.031 0.001 TRP J 115 HIS 0.026 0.001 HIS H 132 Details of bonding type rmsd covalent geometry : bond 0.00348 (34148) covalent geometry : angle 0.71416 (46351) hydrogen bonds : bond 0.03995 ( 1391) hydrogen bonds : angle 5.11293 ( 3878) metal coordination : bond 0.01298 ( 8) metal coordination : angle 8.88287 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 656 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.8424 (mtmt) cc_final: 0.8191 (pttp) REVERT: G 46 ILE cc_start: 0.8669 (tp) cc_final: 0.8203 (tp) REVERT: G 50 SER cc_start: 0.9052 (m) cc_final: 0.8586 (p) REVERT: G 51 MET cc_start: 0.8540 (mmm) cc_final: 0.8123 (mmm) REVERT: G 80 GLU cc_start: 0.8020 (tt0) cc_final: 0.7799 (tt0) REVERT: G 103 ASN cc_start: 0.8740 (m-40) cc_final: 0.8385 (m-40) REVERT: G 105 SER cc_start: 0.8755 (p) cc_final: 0.8504 (m) REVERT: G 152 TYR cc_start: 0.8830 (t80) cc_final: 0.8538 (t80) REVERT: G 185 TYR cc_start: 0.8997 (p90) cc_final: 0.8643 (p90) REVERT: G 200 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8338 (ttmm) REVERT: H 57 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8070 (p) REVERT: H 84 ASN cc_start: 0.9078 (m-40) cc_final: 0.8632 (t0) REVERT: H 125 LYS cc_start: 0.9267 (mptt) cc_final: 0.8723 (tttp) REVERT: H 132 HIS cc_start: 0.8826 (m-70) cc_final: 0.8326 (m-70) REVERT: H 145 LYS cc_start: 0.9277 (tttt) cc_final: 0.8875 (tptm) REVERT: H 174 ASP cc_start: 0.9156 (OUTLIER) cc_final: 0.8812 (m-30) REVERT: H 181 GLU cc_start: 0.8304 (tp30) cc_final: 0.7796 (tp30) REVERT: H 212 ASP cc_start: 0.7929 (p0) cc_final: 0.7372 (p0) REVERT: H 232 VAL cc_start: 0.6333 (OUTLIER) cc_final: 0.5330 (p) REVERT: I 81 ASP cc_start: 0.6919 (t0) cc_final: 0.6639 (t0) REVERT: I 83 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.6598 (pm20) REVERT: I 87 ILE cc_start: 0.9131 (mm) cc_final: 0.8912 (mp) REVERT: I 158 ASP cc_start: 0.8358 (t0) cc_final: 0.7891 (t70) REVERT: I 160 ASP cc_start: 0.8662 (m-30) cc_final: 0.8061 (m-30) REVERT: I 191 LYS cc_start: 0.9266 (mmmm) cc_final: 0.8634 (tptp) REVERT: I 192 ASP cc_start: 0.8647 (m-30) cc_final: 0.7893 (m-30) REVERT: I 204 LEU cc_start: 0.7524 (mp) cc_final: 0.7293 (mp) REVERT: I 340 ASP cc_start: 0.9225 (m-30) cc_final: 0.8759 (p0) REVERT: I 346 TYR cc_start: 0.7508 (m-10) cc_final: 0.7065 (m-80) REVERT: I 359 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7851 (ttt-90) REVERT: I 368 ARG cc_start: 0.9135 (mmm-85) cc_final: 0.8903 (mmt90) REVERT: I 403 MET cc_start: 0.8408 (tmm) cc_final: 0.8205 (tpp) REVERT: I 427 ASP cc_start: 0.9018 (m-30) cc_final: 0.8777 (t0) REVERT: I 477 GLU cc_start: 0.9426 (tp30) cc_final: 0.8846 (tm-30) REVERT: I 488 MET cc_start: 0.8536 (mmm) cc_final: 0.7984 (mmp) REVERT: I 492 MET cc_start: 0.8235 (ptp) cc_final: 0.7322 (tpp) REVERT: I 549 ASP cc_start: 0.7766 (t0) cc_final: 0.7527 (m-30) REVERT: I 565 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7040 (tt0) REVERT: I 697 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8365 (pttm) REVERT: I 790 ASP cc_start: 0.7952 (t70) cc_final: 0.7599 (t0) REVERT: I 814 ASP cc_start: 0.7681 (m-30) cc_final: 0.7474 (m-30) REVERT: I 960 LEU cc_start: 0.9219 (mm) cc_final: 0.7948 (tp) REVERT: I 962 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8406 (tp30) REVERT: I 971 LEU cc_start: 0.7485 (tp) cc_final: 0.7130 (mt) REVERT: I 1025 PHE cc_start: 0.9193 (t80) cc_final: 0.8805 (t80) REVERT: I 1038 GLN cc_start: 0.9054 (pp30) cc_final: 0.8842 (pp30) REVERT: I 1149 TYR cc_start: 0.7877 (m-80) cc_final: 0.7457 (m-80) REVERT: I 1177 ARG cc_start: 0.8647 (ptm160) cc_final: 0.8184 (ttm170) REVERT: I 1203 ASP cc_start: 0.7732 (t0) cc_final: 0.7297 (t0) REVERT: I 1231 TYR cc_start: 0.8481 (t80) cc_final: 0.8189 (t80) REVERT: I 1290 MET cc_start: 0.8091 (mmt) cc_final: 0.7756 (mmp) REVERT: I 1316 GLU cc_start: 0.8451 (tp30) cc_final: 0.7949 (tm-30) REVERT: J 17 PHE cc_start: 0.6786 (t80) cc_final: 0.6442 (t80) REVERT: J 44 ILE cc_start: 0.7191 (OUTLIER) cc_final: 0.6894 (tp) REVERT: J 99 ARG cc_start: 0.9376 (ttm110) cc_final: 0.9105 (mtm-85) REVERT: J 189 LEU cc_start: 0.9546 (mm) cc_final: 0.9341 (mm) REVERT: J 202 ARG cc_start: 0.8992 (mmm160) cc_final: 0.8791 (mmm-85) REVERT: J 238 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8090 (tt) REVERT: J 281 ARG cc_start: 0.9396 (mmm160) cc_final: 0.9099 (mmm160) REVERT: J 296 LYS cc_start: 0.9562 (mttt) cc_final: 0.9289 (mtmt) REVERT: J 297 ARG cc_start: 0.9118 (ttp80) cc_final: 0.8696 (ttp80) REVERT: J 298 MET cc_start: 0.9005 (mmm) cc_final: 0.7961 (tmm) REVERT: J 301 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8759 (pt0) REVERT: J 303 VAL cc_start: 0.9108 (t) cc_final: 0.8857 (p) REVERT: J 418 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: J 441 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7494 (mm) REVERT: J 445 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7753 (mtmt) REVERT: J 478 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7719 (mt) REVERT: J 485 MET cc_start: 0.8500 (ttt) cc_final: 0.8251 (ttt) REVERT: J 500 ILE cc_start: 0.8662 (mt) cc_final: 0.8429 (tt) REVERT: J 508 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7720 (tp) REVERT: J 610 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7876 (ttp80) REVERT: J 697 MET cc_start: 0.8685 (ttp) cc_final: 0.8472 (ttp) REVERT: J 698 MET cc_start: 0.8082 (tpt) cc_final: 0.7748 (tpt) REVERT: J 754 ILE cc_start: 0.8886 (mm) cc_final: 0.8672 (mm) REVERT: J 797 THR cc_start: 0.8423 (m) cc_final: 0.7532 (p) REVERT: J 818 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6652 (pm20) REVERT: J 822 MET cc_start: 0.7818 (tpt) cc_final: 0.7541 (tpt) REVERT: J 830 ASP cc_start: 0.8546 (t0) cc_final: 0.8083 (t70) REVERT: J 923 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8139 (tp) REVERT: J 932 MET cc_start: 0.4336 (tpt) cc_final: 0.3583 (ttt) REVERT: J 960 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8430 (tt) REVERT: J 983 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8439 (mppt) REVERT: J 1202 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8002 (pm20) REVERT: J 1218 HIS cc_start: 0.7567 (m90) cc_final: 0.7360 (m90) REVERT: K 26 ARG cc_start: 0.8888 (tpt170) cc_final: 0.8446 (tpm170) REVERT: F 9 TRP cc_start: 0.8632 (m100) cc_final: 0.7798 (m100) REVERT: F 10 ILE cc_start: 0.8943 (pt) cc_final: 0.8640 (tp) REVERT: F 34 PHE cc_start: 0.8635 (m-80) cc_final: 0.8374 (m-10) REVERT: F 175 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6388 (tp) REVERT: F 204 LEU cc_start: 0.8970 (mt) cc_final: 0.8733 (mt) REVERT: F 214 GLN cc_start: 0.9421 (tm-30) cc_final: 0.8893 (pp30) REVERT: F 233 GLU cc_start: 0.9613 (mp0) cc_final: 0.9290 (mp0) REVERT: F 240 HIS cc_start: 0.8479 (OUTLIER) cc_final: 0.8158 (p90) REVERT: F 252 VAL cc_start: 0.7466 (OUTLIER) cc_final: 0.7176 (p) REVERT: F 345 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8179 (pt0) REVERT: F 401 GLN cc_start: 0.9138 (tp-100) cc_final: 0.8303 (mm-40) REVERT: F 407 LEU cc_start: 0.8833 (mt) cc_final: 0.8613 (mt) REVERT: F 444 TYR cc_start: 0.7905 (m-80) cc_final: 0.7345 (m-80) REVERT: F 553 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8693 (mp0) REVERT: F 708 GLU cc_start: 0.9611 (tp30) cc_final: 0.9204 (mm-30) REVERT: F 723 PHE cc_start: 0.8833 (m-10) cc_final: 0.8610 (m-10) REVERT: F 766 GLU cc_start: 0.9459 (mm-30) cc_final: 0.9202 (mm-30) REVERT: F 776 PHE cc_start: 0.7602 (t80) cc_final: 0.7304 (t80) REVERT: F 900 ARG cc_start: 0.9102 (ttp80) cc_final: 0.8872 (ttp80) REVERT: F 949 SER cc_start: 0.9408 (t) cc_final: 0.9139 (p) outliers start: 194 outliers final: 117 residues processed: 785 average time/residue: 0.2353 time to fit residues: 292.4167 Evaluate side-chains 735 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 593 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 147 GLN Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 150 HIS Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 226 GLU Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 359 ARG Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 486 THR Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 807 TRP Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain I residue 883 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1268 GLN Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 418 GLU Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 445 LYS Chi-restraints excluded: chain J residue 458 ASN Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 562 GLU Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 610 ARG Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 915 ILE Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 983 LYS Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1123 ARG Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1202 GLU Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1325 PHE Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 110 LYS Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 254 CYS Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 321 MET Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 469 TYR Chi-restraints excluded: chain F residue 535 HIS Chi-restraints excluded: chain F residue 553 GLU Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain F residue 626 HIS Chi-restraints excluded: chain F residue 739 VAL Chi-restraints excluded: chain F residue 869 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 301 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 193 optimal weight: 30.0000 chunk 277 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 327 optimal weight: 40.0000 chunk 380 optimal weight: 30.0000 chunk 368 optimal weight: 6.9990 chunk 285 optimal weight: 8.9990 chunk 391 optimal weight: 9.9990 chunk 279 optimal weight: 50.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 702 GLN ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1235 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1252 HIS ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 626 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.215726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.161491 restraints weight = 54884.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.142857 restraints weight = 73727.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.140183 restraints weight = 55392.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.139342 restraints weight = 45073.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.139889 restraints weight = 36657.288| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.140 34156 Z= 0.374 Angle : 0.862 21.945 46363 Z= 0.434 Chirality : 0.048 0.271 5267 Planarity : 0.006 0.089 5930 Dihedral : 13.002 119.309 5164 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 6.52 % Allowed : 21.53 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 aren not related in a simple way. whole: -1.32 (0.13), residues: 4132 helix: 0.30 (0.13), residues: 1544 sheet: -0.87 (0.24), residues: 495 loop : -1.81 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J1345 TYR 0.030 0.003 TYR I1087 PHE 0.039 0.003 PHE J 62 TRP 0.026 0.002 TRP J 115 HIS 0.012 0.002 HIS F 626 Details of bonding type rmsd covalent geometry : bond 0.00875 (34148) covalent geometry : angle 0.84802 (46351) hydrogen bonds : bond 0.04601 ( 1391) hydrogen bonds : angle 5.44478 ( 3878) metal coordination : bond 0.02433 ( 8) metal coordination : angle 9.75324 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 621 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 46 ILE cc_start: 0.8846 (tp) cc_final: 0.8419 (tp) REVERT: G 50 SER cc_start: 0.9131 (m) cc_final: 0.8749 (p) REVERT: G 103 ASN cc_start: 0.8666 (m-40) cc_final: 0.8072 (m110) REVERT: G 141 SER cc_start: 0.8178 (m) cc_final: 0.7556 (m) REVERT: G 152 TYR cc_start: 0.8831 (t80) cc_final: 0.8488 (t80) REVERT: G 178 SER cc_start: 0.9233 (t) cc_final: 0.8797 (m) REVERT: G 185 TYR cc_start: 0.9019 (p90) cc_final: 0.8818 (p90) REVERT: G 200 LYS cc_start: 0.9005 (ttmt) cc_final: 0.8606 (ttmm) REVERT: G 224 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8232 (tp) REVERT: H 84 ASN cc_start: 0.9102 (m-40) cc_final: 0.8612 (t0) REVERT: H 145 LYS cc_start: 0.9167 (tttt) cc_final: 0.8940 (tptm) REVERT: H 206 GLU cc_start: 0.8477 (tt0) cc_final: 0.8091 (tp30) REVERT: H 212 ASP cc_start: 0.7822 (p0) cc_final: 0.7417 (p0) REVERT: I 32 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8552 (mm) REVERT: I 47 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.7578 (p90) REVERT: I 158 ASP cc_start: 0.8528 (t0) cc_final: 0.7999 (t70) REVERT: I 160 ASP cc_start: 0.8414 (m-30) cc_final: 0.7944 (m-30) REVERT: I 191 LYS cc_start: 0.9217 (mmmm) cc_final: 0.8585 (tptp) REVERT: I 192 ASP cc_start: 0.8477 (m-30) cc_final: 0.7688 (m-30) REVERT: I 195 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6833 (t80) REVERT: I 346 TYR cc_start: 0.7321 (m-10) cc_final: 0.6573 (m-80) REVERT: I 359 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7681 (ttt-90) REVERT: I 477 GLU cc_start: 0.9264 (tp30) cc_final: 0.8873 (tm-30) REVERT: I 492 MET cc_start: 0.7119 (ptp) cc_final: 0.6874 (tpp) REVERT: I 622 ASN cc_start: 0.8098 (t0) cc_final: 0.7854 (t0) REVERT: I 708 VAL cc_start: 0.8964 (t) cc_final: 0.8694 (t) REVERT: I 760 ASN cc_start: 0.8951 (OUTLIER) cc_final: 0.8749 (m-40) REVERT: I 761 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8126 (mp10) REVERT: I 960 LEU cc_start: 0.9125 (mm) cc_final: 0.7892 (tp) REVERT: I 962 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8299 (tp30) REVERT: I 1032 LYS cc_start: 0.9448 (mmtp) cc_final: 0.9117 (mmtp) REVERT: I 1177 ARG cc_start: 0.8666 (ptm160) cc_final: 0.8378 (ptm-80) REVERT: I 1302 THR cc_start: 0.8921 (p) cc_final: 0.8549 (t) REVERT: I 1316 GLU cc_start: 0.8330 (tp30) cc_final: 0.7704 (tm-30) REVERT: J 44 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6698 (tp) REVERT: J 96 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8474 (ttpp) REVERT: J 196 GLN cc_start: 0.9496 (OUTLIER) cc_final: 0.9272 (pt0) REVERT: J 296 LYS cc_start: 0.9556 (mttt) cc_final: 0.9330 (mtmt) REVERT: J 301 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8457 (pp20) REVERT: J 303 VAL cc_start: 0.9258 (t) cc_final: 0.8974 (p) REVERT: J 343 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6913 (mp) REVERT: J 360 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.6254 (p90) REVERT: J 424 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.7847 (t0) REVERT: J 441 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8231 (mt) REVERT: J 445 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8423 (ptpt) REVERT: J 457 TYR cc_start: 0.8255 (m-80) cc_final: 0.8048 (m-80) REVERT: J 478 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7903 (mt) REVERT: J 508 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8298 (tp) REVERT: J 642 ASP cc_start: 0.8186 (m-30) cc_final: 0.7721 (t0) REVERT: J 697 MET cc_start: 0.8784 (ttp) cc_final: 0.8183 (ttp) REVERT: J 702 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: J 754 ILE cc_start: 0.9071 (mm) cc_final: 0.8837 (mm) REVERT: J 797 THR cc_start: 0.8657 (m) cc_final: 0.7861 (p) REVERT: J 818 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6695 (pm20) REVERT: J 830 ASP cc_start: 0.7984 (t0) cc_final: 0.7351 (t0) REVERT: J 913 GLU cc_start: 0.8333 (tt0) cc_final: 0.7968 (tp30) REVERT: J 960 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8035 (tt) REVERT: J 983 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8489 (mppt) REVERT: J 1025 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7241 (ptp) REVERT: J 1202 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: K 11 GLU cc_start: 0.8853 (pp20) cc_final: 0.8627 (pm20) REVERT: K 26 ARG cc_start: 0.8756 (tpt170) cc_final: 0.8288 (tpm170) REVERT: K 67 ARG cc_start: 0.9143 (mmt-90) cc_final: 0.8770 (mmp80) REVERT: F 9 TRP cc_start: 0.8412 (m100) cc_final: 0.7614 (m100) REVERT: F 10 ILE cc_start: 0.8516 (pt) cc_final: 0.8247 (tp) REVERT: F 34 PHE cc_start: 0.8094 (m-80) cc_final: 0.7777 (m-10) REVERT: F 159 LEU cc_start: 0.8852 (mt) cc_final: 0.8220 (pp) REVERT: F 175 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.5824 (tp) REVERT: F 233 GLU cc_start: 0.9356 (mp0) cc_final: 0.8976 (mp0) REVERT: F 240 HIS cc_start: 0.7991 (OUTLIER) cc_final: 0.7682 (p90) REVERT: F 472 ARG cc_start: 0.8252 (tpp-160) cc_final: 0.7954 (tpp-160) REVERT: F 766 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8867 (mm-30) REVERT: F 775 GLN cc_start: 0.8693 (mp10) cc_final: 0.8381 (mp10) REVERT: F 776 PHE cc_start: 0.7233 (t80) cc_final: 0.6995 (t80) REVERT: F 888 LEU cc_start: 0.8830 (mt) cc_final: 0.8248 (pp) REVERT: F 900 ARG cc_start: 0.8884 (ttp80) cc_final: 0.8653 (ttp80) REVERT: F 949 SER cc_start: 0.9219 (t) cc_final: 0.8950 (p) outliers start: 230 outliers final: 146 residues processed: 789 average time/residue: 0.2331 time to fit residues: 293.2217 Evaluate side-chains 748 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 577 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 147 GLN Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 150 HIS Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 195 PHE Chi-restraints excluded: chain I residue 226 GLU Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 359 ARG Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 486 THR Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 666 SER Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 757 THR Chi-restraints excluded: chain I residue 760 ASN Chi-restraints excluded: chain I residue 761 GLN Chi-restraints excluded: chain I residue 807 TRP Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain I residue 883 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1268 GLN Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 334 LYS Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 360 TYR Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 424 ASN Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 445 LYS Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 458 ASN Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 562 GLU Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 610 ARG Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 702 GLN Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 816 THR Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 865 HIS Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 915 ILE Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 983 LYS Chi-restraints excluded: chain J residue 1025 MET Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1123 ARG Chi-restraints excluded: chain J residue 1168 GLU Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1202 GLU Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1325 PHE Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 254 CYS Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 469 TYR Chi-restraints excluded: chain F residue 535 HIS Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain F residue 586 ASN Chi-restraints excluded: chain F residue 626 HIS Chi-restraints excluded: chain F residue 647 TYR Chi-restraints excluded: chain F residue 739 VAL Chi-restraints excluded: chain F residue 792 LEU Chi-restraints excluded: chain F residue 799 SER Chi-restraints excluded: chain F residue 869 ASN Chi-restraints excluded: chain F residue 941 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 359 optimal weight: 50.0000 chunk 229 optimal weight: 2.9990 chunk 295 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 353 optimal weight: 50.0000 chunk 385 optimal weight: 10.0000 chunk 278 optimal weight: 50.0000 chunk 220 optimal weight: 1.9990 chunk 234 optimal weight: 0.9980 chunk 313 optimal weight: 20.0000 chunk 384 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS ** I1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 702 GLN ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 626 HIS ** F 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.219034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.166648 restraints weight = 55582.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.150155 restraints weight = 74396.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.145403 restraints weight = 58327.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.146086 restraints weight = 47615.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.146176 restraints weight = 36855.324| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 34156 Z= 0.234 Angle : 0.798 17.970 46363 Z= 0.399 Chirality : 0.046 0.266 5267 Planarity : 0.005 0.089 5930 Dihedral : 12.941 118.707 5159 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 5.82 % Allowed : 22.95 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.13), residues: 4132 helix: 0.34 (0.13), residues: 1543 sheet: -1.11 (0.23), residues: 520 loop : -1.75 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J1345 TYR 0.025 0.002 TYR H 177 PHE 0.035 0.002 PHE J 35 TRP 0.022 0.002 TRP F 215 HIS 0.018 0.001 HIS F 626 Details of bonding type rmsd covalent geometry : bond 0.00547 (34148) covalent geometry : angle 0.79213 (46351) hydrogen bonds : bond 0.04269 ( 1391) hydrogen bonds : angle 5.31100 ( 3878) metal coordination : bond 0.01359 ( 8) metal coordination : angle 6.23432 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 625 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: G 10 LYS cc_start: 0.8928 (mmmt) cc_final: 0.8664 (mmmt) REVERT: G 25 LYS cc_start: 0.8531 (pttp) cc_final: 0.8270 (pttp) REVERT: G 46 ILE cc_start: 0.8792 (tp) cc_final: 0.8490 (mt) REVERT: G 152 TYR cc_start: 0.8768 (t80) cc_final: 0.8364 (t80) REVERT: G 178 SER cc_start: 0.9147 (t) cc_final: 0.8749 (m) REVERT: G 185 TYR cc_start: 0.8998 (p90) cc_final: 0.8787 (p90) REVERT: G 200 LYS cc_start: 0.8990 (ttmt) cc_final: 0.8615 (ttmm) REVERT: H 57 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7927 (p) REVERT: H 84 ASN cc_start: 0.9036 (m-40) cc_final: 0.8576 (t0) REVERT: H 145 LYS cc_start: 0.9118 (tttt) cc_final: 0.8911 (tptm) REVERT: H 181 GLU cc_start: 0.7921 (tp30) cc_final: 0.6922 (tp30) REVERT: H 212 ASP cc_start: 0.7806 (p0) cc_final: 0.7369 (p0) REVERT: I 32 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8457 (mm) REVERT: I 50 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7908 (tp30) REVERT: I 158 ASP cc_start: 0.8365 (t0) cc_final: 0.7856 (t70) REVERT: I 160 ASP cc_start: 0.8420 (m-30) cc_final: 0.7953 (m-30) REVERT: I 185 ASP cc_start: 0.7042 (m-30) cc_final: 0.6767 (m-30) REVERT: I 191 LYS cc_start: 0.9194 (mmmm) cc_final: 0.8589 (tptp) REVERT: I 192 ASP cc_start: 0.8370 (m-30) cc_final: 0.7557 (m-30) REVERT: I 204 LEU cc_start: 0.7823 (mp) cc_final: 0.7504 (mp) REVERT: I 346 TYR cc_start: 0.7330 (m-10) cc_final: 0.6545 (m-80) REVERT: I 359 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7724 (ttt-90) REVERT: I 477 GLU cc_start: 0.9196 (tp30) cc_final: 0.8812 (tm-30) REVERT: I 685 MET cc_start: 0.7406 (mtm) cc_final: 0.7017 (ttm) REVERT: I 708 VAL cc_start: 0.8920 (t) cc_final: 0.8704 (t) REVERT: I 761 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7991 (mp10) REVERT: I 955 GLN cc_start: 0.9286 (tp-100) cc_final: 0.9057 (tp-100) REVERT: I 960 LEU cc_start: 0.9110 (mm) cc_final: 0.7963 (tp) REVERT: I 962 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8393 (tp30) REVERT: I 964 LEU cc_start: 0.9246 (tp) cc_final: 0.8842 (tp) REVERT: I 1025 PHE cc_start: 0.8504 (t80) cc_final: 0.7732 (t80) REVERT: I 1032 LYS cc_start: 0.9408 (mmtp) cc_final: 0.9089 (mmtp) REVERT: I 1177 ARG cc_start: 0.8571 (ptm160) cc_final: 0.8353 (ptm-80) REVERT: I 1231 TYR cc_start: 0.8734 (t80) cc_final: 0.8480 (t80) REVERT: I 1302 THR cc_start: 0.8816 (p) cc_final: 0.8418 (t) REVERT: I 1316 GLU cc_start: 0.8252 (tp30) cc_final: 0.7656 (tm-30) REVERT: J 44 ILE cc_start: 0.6646 (OUTLIER) cc_final: 0.6212 (tp) REVERT: J 189 LEU cc_start: 0.9333 (mm) cc_final: 0.9052 (mm) REVERT: J 296 LYS cc_start: 0.9537 (mttt) cc_final: 0.9328 (mtmt) REVERT: J 298 MET cc_start: 0.8674 (mmm) cc_final: 0.7342 (tmm) REVERT: J 303 VAL cc_start: 0.9235 (t) cc_final: 0.8970 (p) REVERT: J 343 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6861 (mp) REVERT: J 360 TYR cc_start: 0.7123 (OUTLIER) cc_final: 0.6170 (p90) REVERT: J 441 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8066 (mt) REVERT: J 445 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8286 (ptpt) REVERT: J 457 TYR cc_start: 0.8081 (m-80) cc_final: 0.7879 (m-80) REVERT: J 478 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7704 (mt) REVERT: J 508 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8234 (tp) REVERT: J 642 ASP cc_start: 0.8138 (m-30) cc_final: 0.7700 (t0) REVERT: J 697 MET cc_start: 0.8727 (ttp) cc_final: 0.8061 (ttp) REVERT: J 797 THR cc_start: 0.8633 (m) cc_final: 0.7779 (p) REVERT: J 830 ASP cc_start: 0.7696 (t0) cc_final: 0.7177 (t0) REVERT: J 913 GLU cc_start: 0.8286 (tt0) cc_final: 0.7927 (tp30) REVERT: J 960 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8047 (tt) REVERT: J 1040 MET cc_start: 0.1211 (mmm) cc_final: 0.0891 (mmp) REVERT: J 1189 MET cc_start: 0.7807 (tpp) cc_final: 0.7219 (tpp) REVERT: K 11 GLU cc_start: 0.8658 (pp20) cc_final: 0.8419 (pm20) REVERT: F 9 TRP cc_start: 0.8367 (m100) cc_final: 0.7641 (m100) REVERT: F 10 ILE cc_start: 0.8455 (pt) cc_final: 0.8114 (tp) REVERT: F 34 PHE cc_start: 0.7963 (m-80) cc_final: 0.7738 (m-80) REVERT: F 123 MET cc_start: 0.7023 (mmm) cc_final: 0.6647 (mmm) REVERT: F 159 LEU cc_start: 0.8878 (mt) cc_final: 0.8483 (pp) REVERT: F 175 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.5832 (tp) REVERT: F 233 GLU cc_start: 0.9302 (mp0) cc_final: 0.8925 (mp0) REVERT: F 240 HIS cc_start: 0.7864 (OUTLIER) cc_final: 0.7527 (p90) REVERT: F 401 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8127 (mm-40) REVERT: F 444 TYR cc_start: 0.7239 (m-10) cc_final: 0.6697 (m-10) REVERT: F 472 ARG cc_start: 0.8104 (tpp-160) cc_final: 0.7898 (tpp-160) REVERT: F 629 LEU cc_start: 0.8403 (tt) cc_final: 0.7939 (pt) REVERT: F 765 ARG cc_start: 0.8534 (tpt-90) cc_final: 0.7819 (tpt-90) REVERT: F 766 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8822 (mm-30) REVERT: F 775 GLN cc_start: 0.8622 (mp10) cc_final: 0.8310 (mp10) REVERT: F 900 ARG cc_start: 0.8923 (ttp80) cc_final: 0.8716 (ttp80) REVERT: F 949 SER cc_start: 0.9132 (t) cc_final: 0.8899 (p) outliers start: 205 outliers final: 144 residues processed: 777 average time/residue: 0.2350 time to fit residues: 291.5649 Evaluate side-chains 741 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 583 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 147 GLN Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 150 HIS Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 359 ARG Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain I residue 486 THR Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 757 THR Chi-restraints excluded: chain I residue 761 GLN Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 807 TRP Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain I residue 856 ASN Chi-restraints excluded: chain I residue 883 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1268 GLN Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 334 LYS Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 360 TYR Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 445 LYS Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 458 ASN Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 562 GLU Chi-restraints excluded: chain J residue 571 ASP Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 610 ARG Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 840 LEU Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 865 HIS Chi-restraints excluded: chain J residue 915 ILE Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1019 ASN Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1123 ARG Chi-restraints excluded: chain J residue 1168 GLU Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1325 PHE Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1342 ASP Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 254 CYS Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 469 TYR Chi-restraints excluded: chain F residue 535 HIS Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain F residue 586 ASN Chi-restraints excluded: chain F residue 647 TYR Chi-restraints excluded: chain F residue 739 VAL Chi-restraints excluded: chain F residue 754 LEU Chi-restraints excluded: chain F residue 792 LEU Chi-restraints excluded: chain F residue 799 SER Chi-restraints excluded: chain F residue 811 VAL Chi-restraints excluded: chain F residue 869 ASN Chi-restraints excluded: chain F residue 941 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 142 optimal weight: 8.9990 chunk 302 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 351 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 255 optimal weight: 0.9990 chunk 328 optimal weight: 40.0000 chunk 249 optimal weight: 1.9990 chunk 394 optimal weight: 8.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 GLN I 580 GLN ** I 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 196 GLN ** J 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1195 GLN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 GLN ** 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 = 0.4611 r_free = 0.4611 target = 0.221897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.164958 restraints weight = 55793.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.158740 restraints weight = 70221.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.149843 restraints weight = 44234.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.149482 restraints weight = 48304.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.149778 restraints weight = 36920.754| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34156 Z= 0.151 Angle : 0.808 20.081 46363 Z= 0.398 Chirality : 0.046 0.284 5267 Planarity : 0.005 0.104 5930 Dihedral : 12.729 118.105 5148 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.34 % Allowed : 24.82 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.13), residues: 4132 helix: 0.39 (0.13), residues: 1541 sheet: -1.07 (0.23), residues: 514 loop : -1.68 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 197 TYR 0.037 0.002 TYR I1229 PHE 0.055 0.002 PHE I 195 TRP 0.030 0.002 TRP J 115 HIS 0.009 0.001 HIS F 692 Details of bonding type rmsd covalent geometry : bond 0.00341 (34148) covalent geometry : angle 0.80134 (46351) hydrogen bonds : bond 0.04096 ( 1391) hydrogen bonds : angle 5.19690 ( 3878) metal coordination : bond 0.00987 ( 8) metal coordination : angle 6.42261 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 626 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 LYS cc_start: 0.8876 (mmmt) cc_final: 0.8665 (mmmt) REVERT: G 25 LYS cc_start: 0.8486 (pttp) cc_final: 0.8237 (pttp) REVERT: G 103 ASN cc_start: 0.8178 (m-40) cc_final: 0.7697 (t0) REVERT: G 152 TYR cc_start: 0.8705 (t80) cc_final: 0.8287 (t80) REVERT: G 185 TYR cc_start: 0.8897 (p90) cc_final: 0.8637 (p90) REVERT: G 200 LYS cc_start: 0.8937 (ttmt) cc_final: 0.8546 (ttmm) REVERT: H 84 ASN cc_start: 0.8920 (m-40) cc_final: 0.8526 (t0) REVERT: H 125 LYS cc_start: 0.9086 (mptt) cc_final: 0.8688 (tttp) REVERT: H 212 ASP cc_start: 0.7753 (p0) cc_final: 0.7252 (p0) REVERT: I 32 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8374 (mm) REVERT: I 50 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7807 (tp30) REVERT: I 158 ASP cc_start: 0.8328 (t0) cc_final: 0.7900 (t70) REVERT: I 160 ASP cc_start: 0.8408 (m-30) cc_final: 0.8049 (m-30) REVERT: I 185 ASP cc_start: 0.6491 (m-30) cc_final: 0.6267 (m-30) REVERT: I 192 ASP cc_start: 0.8359 (m-30) cc_final: 0.7461 (m-30) REVERT: I 346 TYR cc_start: 0.7265 (m-10) cc_final: 0.6461 (m-80) REVERT: I 359 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7875 (ttt-90) REVERT: I 431 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8806 (ttpt) REVERT: I 472 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8347 (tm-30) REVERT: I 488 MET cc_start: 0.7488 (mmm) cc_final: 0.7007 (mmm) REVERT: I 639 LYS cc_start: 0.8447 (mtmm) cc_final: 0.7861 (mttm) REVERT: I 685 MET cc_start: 0.7002 (mtm) cc_final: 0.6653 (ttm) REVERT: I 704 MET cc_start: 0.7138 (mmm) cc_final: 0.6602 (tpp) REVERT: I 761 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7977 (mp10) REVERT: I 960 LEU cc_start: 0.9134 (mm) cc_final: 0.8649 (mm) REVERT: I 962 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8366 (tp30) REVERT: I 1024 GLU cc_start: 0.8695 (pt0) cc_final: 0.8346 (pt0) REVERT: I 1025 PHE cc_start: 0.8564 (t80) cc_final: 0.8236 (t80) REVERT: I 1149 TYR cc_start: 0.7866 (m-80) cc_final: 0.7425 (m-80) REVERT: I 1203 ASP cc_start: 0.7750 (t0) cc_final: 0.7445 (t0) REVERT: I 1290 MET cc_start: 0.7992 (mmt) cc_final: 0.7792 (mmp) REVERT: I 1302 THR cc_start: 0.8733 (p) cc_final: 0.8514 (t) REVERT: I 1316 GLU cc_start: 0.8094 (tp30) cc_final: 0.7587 (tm-30) REVERT: J 140 TYR cc_start: 0.6749 (m-80) cc_final: 0.5114 (m-10) REVERT: J 189 LEU cc_start: 0.9335 (mm) cc_final: 0.9079 (mm) REVERT: J 281 ARG cc_start: 0.9116 (mmm160) cc_final: 0.8688 (tpm170) REVERT: J 296 LYS cc_start: 0.9539 (mttt) cc_final: 0.9326 (mtmt) REVERT: J 303 VAL cc_start: 0.9212 (t) cc_final: 0.8945 (p) REVERT: J 418 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6995 (tt0) REVERT: J 445 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8120 (ptpt) REVERT: J 478 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7673 (mt) REVERT: J 500 ILE cc_start: 0.8591 (mt) cc_final: 0.8356 (tt) REVERT: J 508 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.7962 (tp) REVERT: J 610 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7664 (ttp80) REVERT: J 697 MET cc_start: 0.8648 (ttp) cc_final: 0.8038 (ttp) REVERT: J 698 MET cc_start: 0.8139 (tpt) cc_final: 0.7818 (tpt) REVERT: J 797 THR cc_start: 0.8548 (m) cc_final: 0.7743 (p) REVERT: J 913 GLU cc_start: 0.8230 (tt0) cc_final: 0.7969 (tp30) REVERT: J 960 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8171 (tt) REVERT: J 983 LYS cc_start: 0.9217 (mmmm) cc_final: 0.8852 (tppt) REVERT: J 1189 MET cc_start: 0.7707 (tpp) cc_final: 0.7139 (tpp) REVERT: F 9 TRP cc_start: 0.8301 (m100) cc_final: 0.7532 (m100) REVERT: F 10 ILE cc_start: 0.8500 (pt) cc_final: 0.8276 (tp) REVERT: F 123 MET cc_start: 0.7157 (mmm) cc_final: 0.6934 (mmm) REVERT: F 159 LEU cc_start: 0.8972 (mt) cc_final: 0.8571 (pp) REVERT: F 175 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.5863 (tp) REVERT: F 233 GLU cc_start: 0.9336 (mp0) cc_final: 0.8960 (mp0) REVERT: F 240 HIS cc_start: 0.7787 (OUTLIER) cc_final: 0.7437 (p90) REVERT: F 401 GLN cc_start: 0.8760 (tp-100) cc_final: 0.8112 (mm-40) REVERT: F 444 TYR cc_start: 0.7348 (m-10) cc_final: 0.6839 (m-10) REVERT: F 472 ARG cc_start: 0.8140 (tpp-160) cc_final: 0.7901 (tpp-160) REVERT: F 629 LEU cc_start: 0.8470 (tt) cc_final: 0.7971 (pt) REVERT: F 766 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8836 (mm-30) REVERT: F 775 GLN cc_start: 0.8700 (mp10) cc_final: 0.8377 (mp10) REVERT: F 943 ARG cc_start: 0.8383 (tmm-80) cc_final: 0.8102 (tmm-80) outliers start: 153 outliers final: 114 residues processed: 734 average time/residue: 0.2078 time to fit residues: 242.3047 Evaluate side-chains 707 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 580 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 147 GLN Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 359 ARG Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain I residue 486 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 761 GLN Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 807 TRP Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain I residue 856 ASN Chi-restraints excluded: chain I residue 883 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1217 THR Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1268 GLN Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 418 GLU Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 445 LYS Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 458 ASN Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 562 GLU Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 610 ARG Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 840 LEU Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 915 ILE Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1019 ASN Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1123 ARG Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1325 PHE Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 215 TRP Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 469 TYR Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 535 HIS Chi-restraints excluded: chain F residue 586 ASN Chi-restraints excluded: chain F residue 739 VAL Chi-restraints excluded: chain F residue 748 VAL Chi-restraints excluded: chain F residue 754 LEU Chi-restraints excluded: chain F residue 799 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 185 optimal weight: 8.9990 chunk 190 optimal weight: 0.4980 chunk 301 optimal weight: 0.7980 chunk 174 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 255 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 246 optimal weight: 5.9990 chunk 353 optimal weight: 50.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS ** I1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN ** J 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.223338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.158576 restraints weight = 56800.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.158909 restraints weight = 61368.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.159308 restraints weight = 47934.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.157245 restraints weight = 37735.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.157674 restraints weight = 38900.799| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 34156 Z= 0.190 Angle : 0.821 17.581 46363 Z= 0.407 Chirality : 0.046 0.272 5267 Planarity : 0.005 0.089 5930 Dihedral : 12.705 117.534 5145 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.14 % Allowed : 25.82 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.13), residues: 4132 helix: 0.38 (0.13), residues: 1539 sheet: -0.93 (0.24), residues: 486 loop : -1.71 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 221 TYR 0.039 0.002 TYR I1229 PHE 0.038 0.002 PHE I 195 TRP 0.024 0.002 TRP J 115 HIS 0.011 0.001 HIS I1244 Details of bonding type rmsd covalent geometry : bond 0.00442 (34148) covalent geometry : angle 0.81456 (46351) hydrogen bonds : bond 0.04155 ( 1391) hydrogen bonds : angle 5.26272 ( 3878) metal coordination : bond 0.01308 ( 8) metal coordination : angle 6.19198 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 615 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.8504 (pttp) cc_final: 0.8250 (pttp) REVERT: G 103 ASN cc_start: 0.8225 (m-40) cc_final: 0.7703 (t0) REVERT: G 152 TYR cc_start: 0.8742 (t80) cc_final: 0.8397 (t80) REVERT: G 185 TYR cc_start: 0.8903 (p90) cc_final: 0.8641 (p90) REVERT: G 200 LYS cc_start: 0.8904 (ttmt) cc_final: 0.8528 (ttmm) REVERT: H 15 ASP cc_start: 0.7789 (m-30) cc_final: 0.7282 (m-30) REVERT: H 84 ASN cc_start: 0.8840 (m-40) cc_final: 0.8281 (t0) REVERT: H 125 LYS cc_start: 0.8837 (mptt) cc_final: 0.8591 (tttp) REVERT: H 181 GLU cc_start: 0.7947 (tp30) cc_final: 0.7234 (tp30) REVERT: H 212 ASP cc_start: 0.7679 (p0) cc_final: 0.7224 (p0) REVERT: I 32 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8522 (mm) REVERT: I 50 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7788 (tp30) REVERT: I 157 PHE cc_start: 0.7911 (m-80) cc_final: 0.7500 (m-80) REVERT: I 158 ASP cc_start: 0.8238 (t0) cc_final: 0.7869 (t70) REVERT: I 160 ASP cc_start: 0.8246 (m-30) cc_final: 0.8034 (m-30) REVERT: I 183 TRP cc_start: 0.8213 (m-10) cc_final: 0.7999 (m-10) REVERT: I 185 ASP cc_start: 0.6419 (m-30) cc_final: 0.6180 (m-30) REVERT: I 192 ASP cc_start: 0.8048 (m-30) cc_final: 0.7080 (m-30) REVERT: I 204 LEU cc_start: 0.7439 (mp) cc_final: 0.7136 (mp) REVERT: I 346 TYR cc_start: 0.7199 (m-10) cc_final: 0.6165 (m-80) REVERT: I 359 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7751 (ttt-90) REVERT: I 431 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8604 (ttmt) REVERT: I 472 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8178 (tm-30) REVERT: I 639 LYS cc_start: 0.8460 (mtmm) cc_final: 0.7850 (mttm) REVERT: I 685 MET cc_start: 0.7067 (mtm) cc_final: 0.6567 (ttm) REVERT: I 760 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8521 (m-40) REVERT: I 761 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7917 (mp10) REVERT: I 955 GLN cc_start: 0.9023 (tp-100) cc_final: 0.8744 (tp-100) REVERT: I 962 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8213 (tp30) REVERT: I 1024 GLU cc_start: 0.8280 (pt0) cc_final: 0.7907 (pt0) REVERT: I 1203 ASP cc_start: 0.7615 (t0) cc_final: 0.7254 (t0) REVERT: I 1216 ARG cc_start: 0.8344 (ptp-170) cc_final: 0.7616 (ptt90) REVERT: I 1229 TYR cc_start: 0.8418 (m-10) cc_final: 0.8016 (m-10) REVERT: I 1290 MET cc_start: 0.8127 (mmt) cc_final: 0.7798 (mmp) REVERT: I 1302 THR cc_start: 0.8734 (p) cc_final: 0.8448 (t) REVERT: I 1316 GLU cc_start: 0.8032 (tp30) cc_final: 0.7526 (tm-30) REVERT: J 100 GLU cc_start: 0.7856 (pm20) cc_final: 0.7176 (pm20) REVERT: J 294 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8351 (p0) REVERT: J 303 VAL cc_start: 0.9178 (t) cc_final: 0.8923 (p) REVERT: J 339 ARG cc_start: 0.7736 (mtm110) cc_final: 0.7118 (ptp-170) REVERT: J 360 TYR cc_start: 0.6638 (OUTLIER) cc_final: 0.5767 (p90) REVERT: J 418 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7103 (tt0) REVERT: J 457 TYR cc_start: 0.8286 (m-80) cc_final: 0.7866 (m-80) REVERT: J 478 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7683 (mt) REVERT: J 508 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8035 (tp) REVERT: J 610 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7578 (ttp80) REVERT: J 697 MET cc_start: 0.8680 (ttp) cc_final: 0.8087 (ttp) REVERT: J 698 MET cc_start: 0.8151 (tpt) cc_final: 0.7845 (tpt) REVERT: J 797 THR cc_start: 0.8617 (m) cc_final: 0.7697 (p) REVERT: J 821 MET cc_start: 0.7390 (tpp) cc_final: 0.6897 (tpt) REVERT: J 913 GLU cc_start: 0.8201 (tt0) cc_final: 0.7924 (tp30) REVERT: J 1189 MET cc_start: 0.7460 (tpp) cc_final: 0.7201 (tpp) REVERT: J 1243 LEU cc_start: 0.8841 (tp) cc_final: 0.8637 (mt) REVERT: F 9 TRP cc_start: 0.7805 (m100) cc_final: 0.7324 (m100) REVERT: F 159 LEU cc_start: 0.8702 (mt) cc_final: 0.8435 (pp) REVERT: F 233 GLU cc_start: 0.8991 (mp0) cc_final: 0.8702 (mp0) REVERT: F 401 GLN cc_start: 0.8188 (tp-100) cc_final: 0.7877 (mm-40) REVERT: F 444 TYR cc_start: 0.6433 (m-10) cc_final: 0.6070 (m-80) REVERT: F 629 LEU cc_start: 0.7747 (tt) cc_final: 0.7373 (pt) REVERT: F 766 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8435 (mm-30) REVERT: F 943 ARG cc_start: 0.8153 (tmm-80) cc_final: 0.7892 (tmm-80) outliers start: 146 outliers final: 117 residues processed: 715 average time/residue: 0.2045 time to fit residues: 232.1355 Evaluate side-chains 706 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 577 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 359 ARG Chi-restraints excluded: chain I residue 397 LEU Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain I residue 486 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 760 ASN Chi-restraints excluded: chain I residue 761 GLN Chi-restraints excluded: chain I residue 807 TRP Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain I residue 856 ASN Chi-restraints excluded: chain I residue 883 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1268 GLN Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 360 TYR Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 418 GLU Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 458 ASN Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 562 GLU Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 610 ARG Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 840 LEU Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 915 ILE Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 1019 ASN Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1123 ARG Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1325 PHE Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 215 TRP Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 469 TYR Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 535 HIS Chi-restraints excluded: chain F residue 586 ASN Chi-restraints excluded: chain F residue 739 VAL Chi-restraints excluded: chain F residue 748 VAL Chi-restraints excluded: chain F residue 754 LEU Chi-restraints excluded: chain F residue 799 SER Chi-restraints excluded: chain F residue 811 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 46 optimal weight: 1.9990 chunk 311 optimal weight: 1.9990 chunk 366 optimal weight: 30.0000 chunk 290 optimal weight: 7.9990 chunk 245 optimal weight: 7.9990 chunk 365 optimal weight: 10.0000 chunk 237 optimal weight: 0.6980 chunk 356 optimal weight: 30.0000 chunk 182 optimal weight: 10.0000 chunk 380 optimal weight: 50.0000 chunk 110 optimal weight: 0.6980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS ** I1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN ** J 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 GLN ** F 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.218999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.144684 restraints weight = 55103.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135997 restraints weight = 38333.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.138516 restraints weight = 32782.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.138703 restraints weight = 29508.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.138995 restraints weight = 25121.540| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 34156 Z= 0.227 Angle : 0.883 23.897 46363 Z= 0.437 Chirality : 0.049 0.514 5267 Planarity : 0.005 0.088 5930 Dihedral : 12.746 119.817 5141 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.26 % Allowed : 26.41 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.13), residues: 4132 helix: 0.29 (0.13), residues: 1548 sheet: -0.88 (0.24), residues: 488 loop : -1.78 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 368 TYR 0.044 0.002 TYR I1229 PHE 0.068 0.002 PHE I 195 TRP 0.024 0.002 TRP I1276 HIS 0.012 0.001 HIS I1244 Details of bonding type rmsd covalent geometry : bond 0.00533 (34148) covalent geometry : angle 0.87713 (46351) hydrogen bonds : bond 0.04308 ( 1391) hydrogen bonds : angle 5.37078 ( 3878) metal coordination : bond 0.01466 ( 8) metal coordination : angle 6.45415 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 587 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.8514 (pttp) cc_final: 0.8236 (pttp) REVERT: G 51 MET cc_start: 0.8633 (mmm) cc_final: 0.8430 (mmm) REVERT: G 103 ASN cc_start: 0.8459 (m-40) cc_final: 0.7930 (t0) REVERT: G 152 TYR cc_start: 0.8844 (t80) cc_final: 0.8442 (t80) REVERT: G 178 SER cc_start: 0.9207 (t) cc_final: 0.8782 (m) REVERT: G 185 TYR cc_start: 0.8977 (p90) cc_final: 0.8696 (p90) REVERT: G 200 LYS cc_start: 0.8897 (ttmt) cc_final: 0.8433 (ttmm) REVERT: H 84 ASN cc_start: 0.9068 (m-40) cc_final: 0.8440 (t0) REVERT: H 125 LYS cc_start: 0.9174 (mptt) cc_final: 0.8707 (tttp) REVERT: H 212 ASP cc_start: 0.7854 (p0) cc_final: 0.7362 (p0) REVERT: I 32 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8526 (mm) REVERT: I 47 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.7458 (p90) REVERT: I 50 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7949 (tp30) REVERT: I 158 ASP cc_start: 0.8342 (t0) cc_final: 0.7801 (t70) REVERT: I 160 ASP cc_start: 0.8544 (m-30) cc_final: 0.8104 (m-30) REVERT: I 183 TRP cc_start: 0.8299 (m-10) cc_final: 0.8092 (m-10) REVERT: I 185 ASP cc_start: 0.6896 (m-30) cc_final: 0.6644 (m-30) REVERT: I 191 LYS cc_start: 0.9265 (mmmm) cc_final: 0.8669 (tptp) REVERT: I 192 ASP cc_start: 0.8491 (m-30) cc_final: 0.7699 (m-30) REVERT: I 219 GLN cc_start: 0.9446 (mt0) cc_final: 0.9190 (mt0) REVERT: I 346 TYR cc_start: 0.7476 (m-10) cc_final: 0.6606 (m-80) REVERT: I 359 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7942 (ttt-90) REVERT: I 396 ASP cc_start: 0.7307 (t0) cc_final: 0.6980 (p0) REVERT: I 472 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8369 (tm-30) REVERT: I 639 LYS cc_start: 0.8496 (mtmm) cc_final: 0.7912 (mttm) REVERT: I 685 MET cc_start: 0.7522 (mtm) cc_final: 0.7011 (ttm) REVERT: I 704 MET cc_start: 0.7363 (mmm) cc_final: 0.6784 (tpp) REVERT: I 761 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8027 (mp10) REVERT: I 955 GLN cc_start: 0.9365 (tp-100) cc_final: 0.9119 (tp-100) REVERT: I 960 LEU cc_start: 0.9275 (mm) cc_final: 0.8150 (tp) REVERT: I 962 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8411 (tp30) REVERT: I 1025 PHE cc_start: 0.8826 (t80) cc_final: 0.8329 (t80) REVERT: I 1203 ASP cc_start: 0.7867 (t0) cc_final: 0.7539 (t0) REVERT: I 1216 ARG cc_start: 0.8383 (ptp-170) cc_final: 0.7680 (ptt90) REVERT: I 1229 TYR cc_start: 0.8508 (m-10) cc_final: 0.8188 (m-10) REVERT: I 1230 MET cc_start: 0.8528 (ttm) cc_final: 0.8174 (ttt) REVERT: I 1302 THR cc_start: 0.8930 (p) cc_final: 0.8409 (t) REVERT: I 1306 LYS cc_start: 0.8677 (ptpp) cc_final: 0.8394 (pttm) REVERT: I 1316 GLU cc_start: 0.8115 (tp30) cc_final: 0.7581 (tm-30) REVERT: J 189 LEU cc_start: 0.9439 (mm) cc_final: 0.9099 (mm) REVERT: J 281 ARG cc_start: 0.9284 (mmm160) cc_final: 0.8750 (tpm170) REVERT: J 294 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8827 (p0) REVERT: J 296 LYS cc_start: 0.9569 (mttt) cc_final: 0.9342 (mtmt) REVERT: J 303 VAL cc_start: 0.9239 (t) cc_final: 0.8965 (p) REVERT: J 360 TYR cc_start: 0.6942 (OUTLIER) cc_final: 0.5910 (p90) REVERT: J 418 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7228 (tt0) REVERT: J 457 TYR cc_start: 0.8204 (m-80) cc_final: 0.7782 (m-80) REVERT: J 508 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8070 (tp) REVERT: J 610 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7770 (ttp80) REVERT: J 642 ASP cc_start: 0.8113 (m-30) cc_final: 0.7572 (t0) REVERT: J 697 MET cc_start: 0.8732 (ttp) cc_final: 0.8057 (ttp) REVERT: J 913 GLU cc_start: 0.8307 (tt0) cc_final: 0.8025 (tp30) REVERT: J 983 LYS cc_start: 0.9191 (mmmm) cc_final: 0.8835 (tppt) REVERT: J 1243 LEU cc_start: 0.8935 (tp) cc_final: 0.8706 (mt) REVERT: F 9 TRP cc_start: 0.8641 (m100) cc_final: 0.7947 (m100) REVERT: F 233 GLU cc_start: 0.9468 (mp0) cc_final: 0.9081 (mp0) REVERT: F 240 HIS cc_start: 0.8028 (OUTLIER) cc_final: 0.7671 (p90) REVERT: F 372 MET cc_start: 0.4985 (ppp) cc_final: 0.4496 (ppp) REVERT: F 401 GLN cc_start: 0.8973 (tp-100) cc_final: 0.8216 (mm-40) REVERT: F 406 MET cc_start: 0.8499 (tmm) cc_final: 0.8047 (ppp) REVERT: F 444 TYR cc_start: 0.7696 (m-10) cc_final: 0.7140 (m-80) REVERT: F 629 LEU cc_start: 0.8721 (tt) cc_final: 0.8201 (pt) REVERT: F 681 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7765 (mm) REVERT: F 766 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8946 (mm-30) REVERT: F 943 ARG cc_start: 0.8504 (tmm-80) cc_final: 0.8237 (tmm-80) outliers start: 150 outliers final: 124 residues processed: 688 average time/residue: 0.1974 time to fit residues: 217.1898 Evaluate side-chains 704 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 568 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 359 ARG Chi-restraints excluded: chain I residue 397 LEU Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain I residue 486 THR Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 761 GLN Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 807 TRP Chi-restraints excluded: chain I residue 827 ARG Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain I residue 856 ASN Chi-restraints excluded: chain I residue 883 LEU Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1268 GLN Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 360 TYR Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 418 GLU Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 458 ASN Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 508 LEU Chi-restraints excluded: chain J residue 548 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 562 GLU Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 610 ARG Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 840 LEU Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 915 ILE Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 1019 ASN Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1123 ARG Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1325 PHE Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 215 TRP Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 469 TYR Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 535 HIS Chi-restraints excluded: chain F residue 586 ASN Chi-restraints excluded: chain F residue 681 LEU Chi-restraints excluded: chain F residue 739 VAL Chi-restraints excluded: chain F residue 748 VAL Chi-restraints excluded: chain F residue 754 LEU Chi-restraints excluded: chain F residue 792 LEU Chi-restraints excluded: chain F residue 799 SER Chi-restraints excluded: chain F residue 811 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 164 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 217 optimal weight: 0.9990 chunk 234 optimal weight: 4.9990 chunk 214 optimal weight: 7.9990 chunk 264 optimal weight: 0.0770 chunk 154 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 240 optimal weight: 0.0970 chunk 355 optimal weight: 9.9990 chunk 310 optimal weight: 7.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS ** I1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.218072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.160970 restraints weight = 55167.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.142045 restraints weight = 65640.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.139426 restraints weight = 50281.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.140040 restraints weight = 35894.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.138894 restraints weight = 37157.539| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.212 34156 Z= 0.223 Angle : 0.955 59.197 46363 Z= 0.494 Chirality : 0.048 0.474 5267 Planarity : 0.006 0.088 5930 Dihedral : 12.749 119.760 5141 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.28 % Allowed : 26.52 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.13), residues: 4132 helix: 0.29 (0.13), residues: 1548 sheet: -0.89 (0.24), residues: 488 loop : -1.77 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.056 0.001 ARG I 368 TYR 0.060 0.002 TYR I 367 PHE 0.055 0.002 PHE I 195 TRP 0.023 0.001 TRP J 115 HIS 0.011 0.001 HIS I1244 Details of bonding type rmsd covalent geometry : bond 0.00522 (34148) covalent geometry : angle 0.94932 (46351) hydrogen bonds : bond 0.04334 ( 1391) hydrogen bonds : angle 5.39167 ( 3878) metal coordination : bond 0.01208 ( 8) metal coordination : angle 6.41476 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8046.15 seconds wall clock time: 139 minutes 5.67 seconds (8345.67 seconds total)