Starting phenix.real_space_refine on Fri May 30 12:21:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t0l_40943/05_2025/8t0l_40943.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t0l_40943/05_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_40943/05_2025/8t0l_40943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t0l_40943/05_2025/8t0l_40943.map" model { file = "/net/cci-nas-00/data/ceres_data/8t0l_40943/05_2025/8t0l_40943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t0l_40943/05_2025/8t0l_40943.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.49s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'ARG:plan': 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: 18.10, per 1000 atoms: 0.54 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: 8.84 Conformation dependent library (CDL) restraints added in 4.0 seconds 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: 11.65 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: 15.52 Time building geometry restraints manager: 10.25 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: 0.940 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: 0.030 Extract box with map and model: 1.310 Check model and map are aligned: 0.270 Set scattering table: 0.310 Process input model: 87.150 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.150 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.570 ------------------------------------------------------------------------------- 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 : 9.55 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (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 TRP 0.008 0.001 TRP I 807 HIS 0.007 0.001 HIS I1070 PHE 0.019 0.002 PHE J1319 TYR 0.014 0.002 TYR J 360 ARG 0.006 0.001 ARG I 211 Details of bonding type rmsd hydrogen bonds : bond 0.14609 ( 1391) hydrogen bonds : angle 6.80573 ( 3878) metal coordination : bond 0.05402 ( 8) metal coordination : angle 49.20935 ( 12) covalent geometry : bond 0.00509 (34148) covalent geometry : angle 0.66555 (46351) *********************** 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 : 3.677 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: 0.5113 time to fit residues: 911.0238 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 : 4.065 ------------------------------------------------------------------------------- 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 352 optimal weight: 30.0000 chunk 316 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 213 optimal weight: 0.5980 chunk 168 optimal weight: 0.0040 chunk 326 optimal weight: 50.0000 chunk 126 optimal weight: 0.9990 chunk 198 optimal weight: 3.9990 chunk 243 optimal weight: 6.9990 chunk 378 optimal weight: 40.0000 overall best weight: 1.1196 ------------------------------------------------------------------------------- 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 649 GLN I 894 GLN I 952 GLN ** I1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 HIS J1023 HIS ** J1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 HIS ** F 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 745 HIS F 775 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.218510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.136105 restraints weight = 52058.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.135193 restraints weight = 29159.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.135258 restraints weight = 20623.807| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2910 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= 0.176 Angle : 0.848 48.940 46363 Z= 0.398 Chirality : 0.047 0.326 5267 Planarity : 0.005 0.070 5930 Dihedral : 13.220 112.283 5249 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.21 % Favored : 92.69 % Rotamer: Outliers : 5.16 % Allowed : 16.31 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.13), residues: 4132 helix: 0.50 (0.13), residues: 1558 sheet: -1.16 (0.23), residues: 486 loop : -1.80 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 955 HIS 0.013 0.001 HIS H 128 PHE 0.026 0.002 PHE G 35 TYR 0.037 0.002 TYR I 367 ARG 0.011 0.001 ARG I1034 Details of bonding type rmsd hydrogen bonds : bond 0.04698 ( 1391) hydrogen bonds : angle 5.59550 ( 3878) metal coordination : bond 0.01967 ( 8) metal coordination : angle 22.19156 ( 12) covalent geometry : bond 0.00403 (34148) covalent geometry : angle 0.76974 (46351) *********************** 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 942 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 760 time to evaluate : 3.458 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: 0.8370 (mtmt) cc_final: 0.8135 (pttp) REVERT: G 46 ILE cc_start: 0.8664 (tp) cc_final: 0.8229 (tp) REVERT: G 50 SER cc_start: 0.9146 (m) cc_final: 0.8717 (p) REVERT: G 103 ASN cc_start: 0.8786 (m-40) cc_final: 0.8397 (m-40) REVERT: G 152 TYR cc_start: 0.8780 (t80) cc_final: 0.8555 (t80) REVERT: G 200 LYS cc_start: 0.8855 (ttmt) cc_final: 0.8467 (ttmm) REVERT: H 41 ASN cc_start: 0.8863 (t0) cc_final: 0.8598 (t0) REVERT: H 51 MET cc_start: 0.8912 (mmp) cc_final: 0.8308 (mpp) REVERT: H 84 ASN cc_start: 0.9130 (m-40) cc_final: 0.8580 (t0) REVERT: H 121 VAL cc_start: 0.9220 (t) cc_final: 0.9016 (t) REVERT: H 125 LYS cc_start: 0.9259 (mptt) cc_final: 0.8655 (tttp) REVERT: H 145 LYS cc_start: 0.9296 (tttt) cc_final: 0.8896 (tptt) REVERT: H 146 VAL cc_start: 0.9431 (OUTLIER) cc_final: 0.8549 (p) REVERT: H 152 TYR cc_start: 0.7705 (t80) cc_final: 0.6944 (t80) REVERT: H 206 GLU cc_start: 0.8711 (tt0) cc_final: 0.8439 (tp30) REVERT: I 46 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8752 (mm-40) REVERT: I 83 GLN cc_start: 0.7104 (pm20) cc_final: 0.6903 (mp10) REVERT: I 87 ILE cc_start: 0.8998 (mm) cc_final: 0.8759 (mp) REVERT: I 158 ASP cc_start: 0.8462 (t0) cc_final: 0.8200 (t0) REVERT: I 192 ASP cc_start: 0.8558 (m-30) cc_final: 0.7840 (m-30) REVERT: I 340 ASP cc_start: 0.9167 (m-30) cc_final: 0.8709 (p0) REVERT: I 346 TYR cc_start: 0.7482 (m-10) cc_final: 0.6958 (m-80) REVERT: I 367 TYR cc_start: 0.7741 (t80) cc_final: 0.7367 (t80) REVERT: I 368 ARG cc_start: 0.9027 (mmm-85) cc_final: 0.8363 (mmm160) REVERT: I 403 MET cc_start: 0.8448 (tmm) cc_final: 0.8241 (tpp) REVERT: I 431 LYS cc_start: 0.9279 (ttmt) cc_final: 0.8881 (mtpt) REVERT: I 565 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6873 (tt0) REVERT: I 622 ASN cc_start: 0.7962 (t0) cc_final: 0.7628 (t0) REVERT: I 635 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7786 (p) REVERT: I 639 LYS cc_start: 0.8401 (mtmm) cc_final: 0.7902 (mttm) REVERT: I 649 GLN cc_start: 0.7668 (mm110) cc_final: 0.7350 (mp10) REVERT: I 687 ARG cc_start: 0.7913 (ttp-110) cc_final: 0.7399 (mtp85) REVERT: I 697 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8307 (pttm) REVERT: I 704 MET cc_start: 0.7317 (mmm) cc_final: 0.6919 (mmm) REVERT: I 737 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.7730 (m110) REVERT: I 781 ASP cc_start: 0.6972 (m-30) cc_final: 0.6762 (m-30) REVERT: I 790 ASP cc_start: 0.7772 (t70) cc_final: 0.7524 (t0) REVERT: I 930 ASP cc_start: 0.8001 (t0) cc_final: 0.7599 (t0) REVERT: I 960 LEU cc_start: 0.9236 (mp) cc_final: 0.8207 (tp) REVERT: I 1034 ARG cc_start: 0.9450 (ttp-110) cc_final: 0.9130 (ttm110) REVERT: I 1038 GLN cc_start: 0.8907 (pp30) cc_final: 0.8646 (pp30) REVERT: I 1177 ARG cc_start: 0.8554 (ptm160) cc_final: 0.7993 (ptm160) REVERT: I 1231 TYR cc_start: 0.8538 (t80) cc_final: 0.8158 (t80) REVERT: I 1316 GLU cc_start: 0.8352 (tp30) cc_final: 0.8047 (tm-30) REVERT: J 50 LYS cc_start: 0.7184 (tttp) cc_final: 0.6789 (tttp) REVERT: J 100 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7827 (pm20) REVERT: J 118 LYS cc_start: 0.9286 (mttt) cc_final: 0.9011 (mmmm) REVERT: J 195 GLU cc_start: 0.9354 (mp0) cc_final: 0.9082 (pm20) REVERT: J 265 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8076 (mm) REVERT: J 281 ARG cc_start: 0.9403 (mmm160) cc_final: 0.9144 (mmm160) REVERT: J 301 GLU cc_start: 0.9167 (tm-30) cc_final: 0.8742 (pp20) REVERT: J 303 VAL cc_start: 0.9070 (t) cc_final: 0.8796 (p) REVERT: J 330 MET cc_start: 0.9094 (mmm) cc_final: 0.8615 (mpp) REVERT: J 441 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7478 (mm) REVERT: J 458 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7430 (t0) REVERT: J 478 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7903 (mt) REVERT: J 485 MET cc_start: 0.8592 (ttt) cc_final: 0.8295 (ttt) REVERT: J 532 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7461 (tp30) REVERT: J 610 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.8078 (ttp80) REVERT: J 697 MET cc_start: 0.7635 (ppp) cc_final: 0.7387 (ttp) REVERT: J 797 THR cc_start: 0.8271 (m) cc_final: 0.7587 (p) REVERT: J 818 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6210 (pm20) REVERT: J 830 ASP cc_start: 0.8471 (t0) cc_final: 0.8047 (t70) REVERT: J 913 GLU cc_start: 0.8397 (tt0) cc_final: 0.7885 (tt0) REVERT: J 1151 LYS cc_start: 0.8696 (tppt) cc_final: 0.8439 (tppt) REVERT: J 1152 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7926 (mm-30) REVERT: J 1311 LYS cc_start: 0.9184 (mmmt) cc_final: 0.8969 (mtmm) REVERT: K 11 GLU cc_start: 0.8860 (pp20) cc_final: 0.8598 (pp20) REVERT: K 15 ASN cc_start: 0.8380 (m-40) cc_final: 0.7482 (t0) REVERT: K 26 ARG cc_start: 0.8931 (tpt170) cc_final: 0.8334 (tpm170) REVERT: K 30 MET cc_start: 0.7456 (ttm) cc_final: 0.6962 (tpp) REVERT: K 35 LYS cc_start: 0.8464 (ptpp) cc_final: 0.8257 (ptpp) REVERT: K 43 ASN cc_start: 0.8698 (t0) cc_final: 0.8387 (t0) REVERT: K 53 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7945 (mm-30) REVERT: K 58 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8285 (pp) REVERT: K 64 LEU cc_start: 0.7409 (mt) cc_final: 0.7204 (tt) REVERT: F 10 ILE cc_start: 0.9094 (pt) cc_final: 0.8834 (tp) REVERT: F 34 PHE cc_start: 0.8495 (m-80) cc_final: 0.7791 (m-10) REVERT: F 160 ASN cc_start: 0.8724 (t0) cc_final: 0.8427 (t0) REVERT: F 204 LEU cc_start: 0.9114 (mt) cc_final: 0.8862 (mt) REVERT: F 211 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8716 (mm) REVERT: F 221 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7166 (tpp80) REVERT: F 281 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8048 (mm-30) REVERT: F 376 MET cc_start: -0.1645 (mmm) cc_final: -0.1925 (mmm) REVERT: F 444 TYR cc_start: 0.8015 (m-80) cc_final: 0.7739 (m-10) REVERT: F 450 VAL cc_start: 0.8847 (t) cc_final: 0.8630 (m) REVERT: F 543 ARG cc_start: 0.8509 (mmt-90) cc_final: 0.8228 (mtt180) REVERT: F 553 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8701 (mp0) REVERT: F 558 GLN cc_start: 0.8578 (tt0) cc_final: 0.8319 (tp40) REVERT: F 723 PHE cc_start: 0.8751 (m-10) cc_final: 0.8474 (m-10) REVERT: F 766 GLU cc_start: 0.9391 (mm-30) cc_final: 0.9152 (mm-30) REVERT: F 776 PHE cc_start: 0.7909 (t80) cc_final: 0.7263 (t80) REVERT: F 820 TYR cc_start: 0.9171 (m-80) cc_final: 0.8853 (m-80) REVERT: F 941 SER cc_start: 0.9267 (m) cc_final: 0.9014 (p) REVERT: F 948 GLU cc_start: 0.9489 (tp30) cc_final: 0.9288 (pt0) REVERT: F 949 SER cc_start: 0.9416 (t) cc_final: 0.9059 (p) REVERT: F 957 LEU cc_start: 0.8677 (tp) cc_final: 0.8216 (tp) outliers start: 182 outliers final: 97 residues processed: 882 average time/residue: 0.4961 time to fit residues: 693.4816 Evaluate side-chains 755 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 641 time to evaluate : 3.717 ------------------------------------------------------------------------------- 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 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 I residue 31 GLN Chi-restraints excluded: chain I residue 46 GLN 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 384 LEU Chi-restraints excluded: chain I residue 429 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 635 THR Chi-restraints excluded: chain I residue 697 LYS 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 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 901 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 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 46 TYR Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 198 CYS 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 430 HIS Chi-restraints excluded: chain J residue 441 LEU 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 527 LEU Chi-restraints excluded: chain J residue 532 GLU 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 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 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 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 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 58 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 93 SER 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 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 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 935 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 93 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 192 optimal weight: 20.0000 chunk 403 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 391 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 214 optimal weight: 6.9990 chunk 363 optimal weight: 20.0000 chunk 234 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 46 GLN I 86 GLN ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 419 HIS ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 HIS F 194 GLN ** F 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 626 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.214413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.126694 restraints weight = 53008.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.125274 restraints weight = 31763.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.126523 restraints weight = 23294.449| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 34156 Z= 0.277 Angle : 0.840 43.480 46363 Z= 0.406 Chirality : 0.048 0.315 5267 Planarity : 0.006 0.087 5930 Dihedral : 13.138 119.472 5188 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.11 % Favored : 91.82 % Rotamer: Outliers : 6.52 % Allowed : 17.42 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.13), residues: 4132 helix: 0.34 (0.13), residues: 1536 sheet: -1.14 (0.23), residues: 495 loop : -1.82 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 115 HIS 0.014 0.002 HIS F 213 PHE 0.034 0.002 PHE J 62 TYR 0.031 0.002 TYR I 367 ARG 0.014 0.001 ARG F 221 Details of bonding type rmsd hydrogen bonds : bond 0.04630 ( 1391) hydrogen bonds : angle 5.53271 ( 3878) metal coordination : bond 0.02150 ( 8) metal coordination : angle 18.23289 ( 12) covalent geometry : bond 0.00646 (34148) covalent geometry : angle 0.78760 (46351) *********************** 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 915 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 685 time to evaluate : 4.134 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: G 25 LYS cc_start: 0.8479 (mtmt) cc_final: 0.8197 (pttp) REVERT: G 46 ILE cc_start: 0.8776 (tp) cc_final: 0.8369 (tp) REVERT: G 50 SER cc_start: 0.9118 (m) cc_final: 0.8747 (p) REVERT: G 51 MET cc_start: 0.8657 (mmm) cc_final: 0.8325 (mmm) REVERT: G 117 HIS cc_start: 0.8431 (t70) cc_final: 0.8089 (t-170) REVERT: G 141 SER cc_start: 0.8479 (m) cc_final: 0.8205 (p) REVERT: G 152 TYR cc_start: 0.8884 (t80) cc_final: 0.8512 (t80) REVERT: G 178 SER cc_start: 0.9355 (t) cc_final: 0.8958 (m) REVERT: G 185 TYR cc_start: 0.9079 (p90) cc_final: 0.8799 (p90) REVERT: G 200 LYS cc_start: 0.8771 (ttmt) cc_final: 0.8295 (ttmm) REVERT: H 84 ASN cc_start: 0.9234 (m-40) cc_final: 0.8642 (t0) REVERT: H 125 LYS cc_start: 0.9285 (mptt) cc_final: 0.8628 (tttp) REVERT: H 133 LEU cc_start: 0.8525 (tp) cc_final: 0.8209 (tp) REVERT: H 171 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9205 (mm) REVERT: H 174 ASP cc_start: 0.9292 (OUTLIER) cc_final: 0.9000 (m-30) REVERT: H 177 TYR cc_start: 0.8137 (m-80) cc_final: 0.7642 (m-80) REVERT: H 181 GLU cc_start: 0.8319 (tp30) cc_final: 0.7924 (tp30) REVERT: H 206 GLU cc_start: 0.8773 (tt0) cc_final: 0.8262 (tp30) REVERT: H 212 ASP cc_start: 0.8177 (p0) cc_final: 0.7630 (p0) REVERT: I 46 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8373 (mm110) REVERT: I 47 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7451 (p90) REVERT: I 87 ILE cc_start: 0.9092 (mm) cc_final: 0.8836 (mp) REVERT: I 158 ASP cc_start: 0.8495 (t0) cc_final: 0.8080 (t0) REVERT: I 160 ASP cc_start: 0.8657 (m-30) cc_final: 0.8157 (m-30) REVERT: I 185 ASP cc_start: 0.6985 (m-30) cc_final: 0.6705 (m-30) REVERT: I 192 ASP cc_start: 0.8640 (m-30) cc_final: 0.7941 (m-30) REVERT: I 340 ASP cc_start: 0.9223 (m-30) cc_final: 0.8726 (p0) REVERT: I 346 TYR cc_start: 0.7553 (m-10) cc_final: 0.6738 (m-80) REVERT: I 359 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7772 (ttm-80) REVERT: I 403 MET cc_start: 0.8355 (tmm) cc_final: 0.8134 (tpp) REVERT: I 488 MET cc_start: 0.8535 (mmm) cc_final: 0.6915 (mmm) REVERT: I 492 MET cc_start: 0.8112 (ptp) cc_final: 0.7568 (tpp) REVERT: I 565 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: I 622 ASN cc_start: 0.8197 (t0) cc_final: 0.7842 (t0) REVERT: I 623 LEU cc_start: 0.8346 (tp) cc_final: 0.8079 (tp) REVERT: I 649 GLN cc_start: 0.7946 (mm110) cc_final: 0.7717 (mp10) REVERT: I 697 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8551 (pttm) REVERT: I 704 MET cc_start: 0.7428 (mmm) cc_final: 0.6979 (mmm) REVERT: I 708 VAL cc_start: 0.8748 (t) cc_final: 0.8449 (t) REVERT: I 737 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.8007 (m110) REVERT: I 760 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8610 (m-40) REVERT: I 761 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7871 (mp10) REVERT: I 781 ASP cc_start: 0.7054 (m-30) cc_final: 0.6850 (m-30) REVERT: I 898 GLU cc_start: 0.9634 (pp20) cc_final: 0.9318 (pp20) REVERT: I 930 ASP cc_start: 0.8165 (t0) cc_final: 0.7817 (t0) REVERT: I 955 GLN cc_start: 0.9463 (tp-100) cc_final: 0.9143 (tp-100) REVERT: I 959 ASP cc_start: 0.8845 (m-30) cc_final: 0.8440 (m-30) REVERT: I 960 LEU cc_start: 0.9169 (mp) cc_final: 0.8545 (tp) REVERT: I 1038 GLN cc_start: 0.9000 (pp30) cc_final: 0.8781 (pp30) REVERT: I 1177 ARG cc_start: 0.8705 (ptm160) cc_final: 0.8343 (ptm-80) REVERT: I 1302 THR cc_start: 0.9141 (p) cc_final: 0.8700 (t) REVERT: I 1306 LYS cc_start: 0.8953 (mtmm) cc_final: 0.8721 (pttm) REVERT: I 1316 GLU cc_start: 0.8579 (tp30) cc_final: 0.7942 (tm-30) REVERT: J 62 PHE cc_start: 0.9074 (m-80) cc_final: 0.8852 (m-80) REVERT: J 100 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7854 (pm20) REVERT: J 189 LEU cc_start: 0.9548 (mm) cc_final: 0.9315 (mm) REVERT: J 237 MET cc_start: 0.8319 (mtp) cc_final: 0.8031 (mtp) REVERT: J 238 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7986 (tt) REVERT: J 265 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8155 (mm) REVERT: J 281 ARG cc_start: 0.9371 (mmm160) cc_final: 0.9103 (mmm160) REVERT: J 296 LYS cc_start: 0.9542 (mttt) cc_final: 0.9297 (mtmt) REVERT: J 301 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8587 (pp20) REVERT: J 303 VAL cc_start: 0.9080 (t) cc_final: 0.8823 (p) REVERT: J 330 MET cc_start: 0.9143 (mmm) cc_final: 0.8647 (mpp) REVERT: J 343 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6793 (mp) REVERT: J 424 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8177 (t0) REVERT: J 478 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8196 (mt) REVERT: J 485 MET cc_start: 0.8779 (ttt) cc_final: 0.8537 (ttt) REVERT: J 508 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7791 (tp) REVERT: J 610 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7882 (ttp80) REVERT: J 642 ASP cc_start: 0.8242 (m-30) cc_final: 0.7565 (t0) REVERT: J 797 THR cc_start: 0.8442 (m) cc_final: 0.7682 (p) REVERT: J 818 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6466 (pm20) REVERT: J 830 ASP cc_start: 0.8507 (t0) cc_final: 0.8036 (t70) REVERT: J 923 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8329 (tp) REVERT: J 960 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8277 (tt) REVERT: J 1023 HIS cc_start: 0.8379 (OUTLIER) cc_final: 0.8170 (t70) REVERT: J 1189 MET cc_start: 0.8225 (mtt) cc_final: 0.7836 (ttt) REVERT: J 1219 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7860 (p0) REVERT: K 11 GLU cc_start: 0.8982 (pp20) cc_final: 0.8724 (pp20) REVERT: K 12 LYS cc_start: 0.9140 (mmmt) cc_final: 0.8847 (mmmt) REVERT: K 15 ASN cc_start: 0.8360 (m-40) cc_final: 0.7423 (t0) REVERT: K 26 ARG cc_start: 0.8924 (tpt170) cc_final: 0.8297 (tpm170) REVERT: K 30 MET cc_start: 0.7344 (ttm) cc_final: 0.7114 (tpp) REVERT: K 44 ASP cc_start: 0.8254 (m-30) cc_final: 0.7970 (p0) REVERT: K 49 ILE cc_start: 0.8853 (pt) cc_final: 0.8062 (pt) REVERT: K 53 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7810 (mm-30) REVERT: F 9 TRP cc_start: 0.8623 (m100) cc_final: 0.7806 (m100) REVERT: F 10 ILE cc_start: 0.9081 (pt) cc_final: 0.8796 (tp) REVERT: F 34 PHE cc_start: 0.8468 (m-80) cc_final: 0.7716 (m-10) REVERT: F 99 GLU cc_start: 0.3413 (OUTLIER) cc_final: 0.3137 (pt0) REVERT: F 116 PHE cc_start: 0.4144 (OUTLIER) cc_final: 0.3858 (m-80) REVERT: F 130 TYR cc_start: 0.7299 (t80) cc_final: 0.6982 (t80) REVERT: F 204 LEU cc_start: 0.8993 (mt) cc_final: 0.8762 (mt) REVERT: F 211 LEU cc_start: 0.8916 (mm) cc_final: 0.8671 (mm) REVERT: F 213 HIS cc_start: 0.9384 (m170) cc_final: 0.9135 (m90) REVERT: F 214 GLN cc_start: 0.8510 (pp30) cc_final: 0.8298 (pp30) REVERT: F 252 VAL cc_start: 0.7456 (OUTLIER) cc_final: 0.7113 (p) REVERT: F 281 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8083 (mm-30) REVERT: F 358 MET cc_start: 0.7786 (ptt) cc_final: 0.7290 (ppp) REVERT: F 418 PHE cc_start: 0.8030 (m-80) cc_final: 0.7794 (m-80) REVERT: F 444 TYR cc_start: 0.8074 (m-80) cc_final: 0.7745 (m-10) REVERT: F 534 PHE cc_start: 0.7685 (m-80) cc_final: 0.6860 (m-80) REVERT: F 543 ARG cc_start: 0.8636 (mmt-90) cc_final: 0.8213 (mtt180) REVERT: F 553 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8582 (mp0) REVERT: F 580 MET cc_start: 0.8633 (tpp) cc_final: 0.8308 (tpt) REVERT: F 723 PHE cc_start: 0.8826 (m-10) cc_final: 0.8601 (m-10) REVERT: F 766 GLU cc_start: 0.9393 (mm-30) cc_final: 0.9108 (mm-30) REVERT: F 776 PHE cc_start: 0.7772 (t80) cc_final: 0.7179 (t80) REVERT: F 949 SER cc_start: 0.9414 (t) cc_final: 0.9148 (p) outliers start: 230 outliers final: 132 residues processed: 837 average time/residue: 0.4771 time to fit residues: 633.3899 Evaluate side-chains 753 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 595 time to evaluate : 3.872 ------------------------------------------------------------------------------- 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 110 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 173 VAL 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 H residue 224 LEU 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 90 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 138 ILE 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 327 GLN Chi-restraints excluded: chain I residue 336 LEU 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 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 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 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 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 1289 GLU Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS 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 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 454 CYS 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 571 ASP Chi-restraints excluded: chain J residue 574 VAL Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 596 LEU 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 843 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 918 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 1023 HIS Chi-restraints excluded: chain J residue 1046 ILE 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 1219 ASP 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 K residue 51 LEU 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 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 407 LEU 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 869 ASN Chi-restraints excluded: chain F residue 921 LEU 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 104 optimal weight: 5.9990 chunk 218 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 245 optimal weight: 4.9990 chunk 299 optimal weight: 0.6980 chunk 375 optimal weight: 40.0000 chunk 79 optimal weight: 10.0000 chunk 415 optimal weight: 30.0000 chunk 401 optimal weight: 40.0000 chunk 320 optimal weight: 30.0000 chunk 372 optimal weight: 50.0000 overall best weight: 2.6584 ------------------------------------------------------------------------------- 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 214 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 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 232 ASN ** 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** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1295 ASN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN K 70 GLN F 160 ASN F 268 HIS ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 GLN F 674 HIS F 885 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.215354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127211 restraints weight = 52772.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.129653 restraints weight = 29813.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.129333 restraints weight = 18600.031| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 34156 Z= 0.218 Angle : 0.782 34.502 46363 Z= 0.382 Chirality : 0.046 0.268 5267 Planarity : 0.005 0.073 5930 Dihedral : 13.051 119.833 5178 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.08 % Favored : 91.87 % Rotamer: Outliers : 6.07 % Allowed : 19.63 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.13), residues: 4132 helix: 0.39 (0.13), residues: 1548 sheet: -0.95 (0.24), residues: 486 loop : -1.74 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP J 115 HIS 0.011 0.001 HIS F 885 PHE 0.027 0.002 PHE F 572 TYR 0.018 0.002 TYR I1018 ARG 0.007 0.001 ARG F 900 Details of bonding type rmsd hydrogen bonds : bond 0.04280 ( 1391) hydrogen bonds : angle 5.32207 ( 3878) metal coordination : bond 0.01876 ( 8) metal coordination : angle 13.92124 ( 12) covalent geometry : bond 0.00509 (34148) covalent geometry : angle 0.74919 (46351) *********************** 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: 214 poor density : 645 time to evaluate : 4.014 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: G 25 LYS cc_start: 0.8430 (mtmt) cc_final: 0.8164 (pttp) REVERT: G 46 ILE cc_start: 0.8722 (tp) cc_final: 0.8252 (tp) REVERT: G 50 SER cc_start: 0.9076 (m) cc_final: 0.8663 (p) REVERT: G 51 MET cc_start: 0.8661 (mmm) cc_final: 0.8218 (mmm) REVERT: G 152 TYR cc_start: 0.8860 (t80) cc_final: 0.8485 (t80) REVERT: G 178 SER cc_start: 0.9273 (t) cc_final: 0.8882 (m) REVERT: G 185 TYR cc_start: 0.9078 (p90) cc_final: 0.8804 (p90) REVERT: G 200 LYS cc_start: 0.8721 (ttmt) cc_final: 0.8319 (ttmm) REVERT: H 51 MET cc_start: 0.9165 (mmm) cc_final: 0.8598 (tpp) REVERT: H 84 ASN cc_start: 0.9095 (m-40) cc_final: 0.8559 (t0) REVERT: H 125 LYS cc_start: 0.9299 (mptt) cc_final: 0.8674 (tttp) REVERT: H 133 LEU cc_start: 0.8433 (tp) cc_final: 0.8132 (tp) REVERT: H 145 LYS cc_start: 0.9420 (tttt) cc_final: 0.8906 (ttpp) REVERT: H 152 TYR cc_start: 0.7691 (t80) cc_final: 0.7123 (t80) REVERT: H 174 ASP cc_start: 0.9299 (OUTLIER) cc_final: 0.9068 (m-30) REVERT: H 181 GLU cc_start: 0.8411 (tp30) cc_final: 0.7779 (tp30) REVERT: H 186 ASN cc_start: 0.7682 (OUTLIER) cc_final: 0.7466 (p0) REVERT: H 206 GLU cc_start: 0.8659 (tt0) cc_final: 0.8363 (tp30) REVERT: H 212 ASP cc_start: 0.8101 (p0) cc_final: 0.7513 (p0) REVERT: I 46 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8440 (mm110) REVERT: I 47 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.7262 (p90) REVERT: I 87 ILE cc_start: 0.9121 (mm) cc_final: 0.8912 (mp) REVERT: I 97 ARG cc_start: 0.8593 (mtt-85) cc_final: 0.8317 (mmt90) REVERT: I 158 ASP cc_start: 0.8446 (t0) cc_final: 0.7992 (t70) REVERT: I 160 ASP cc_start: 0.8673 (m-30) cc_final: 0.8087 (m-30) REVERT: I 191 LYS cc_start: 0.9130 (mmmm) cc_final: 0.8530 (tptp) REVERT: I 192 ASP cc_start: 0.8764 (m-30) cc_final: 0.8077 (m-30) REVERT: I 340 ASP cc_start: 0.9333 (m-30) cc_final: 0.8828 (p0) REVERT: I 346 TYR cc_start: 0.7547 (m-10) cc_final: 0.7166 (m-80) REVERT: I 371 ARG cc_start: 0.8743 (tpp-160) cc_final: 0.8521 (tpp-160) REVERT: I 622 ASN cc_start: 0.8178 (t0) cc_final: 0.7806 (t0) REVERT: I 623 LEU cc_start: 0.8339 (tp) cc_final: 0.8053 (tp) REVERT: I 685 MET cc_start: 0.7499 (mtm) cc_final: 0.7161 (ttm) REVERT: I 697 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8525 (pttm) REVERT: I 704 MET cc_start: 0.7349 (mmm) cc_final: 0.7100 (mmm) REVERT: I 708 VAL cc_start: 0.8776 (t) cc_final: 0.8513 (t) REVERT: I 760 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8461 (m-40) REVERT: I 761 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: I 790 ASP cc_start: 0.8045 (t70) cc_final: 0.7749 (t0) REVERT: I 960 LEU cc_start: 0.9154 (mp) cc_final: 0.8457 (tp) REVERT: I 962 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8349 (tp30) REVERT: I 1038 GLN cc_start: 0.9042 (pp30) cc_final: 0.8813 (pp30) REVERT: I 1177 ARG cc_start: 0.8745 (ptm160) cc_final: 0.8433 (ptm-80) REVERT: I 1231 TYR cc_start: 0.8618 (t80) cc_final: 0.8282 (t80) REVERT: I 1302 THR cc_start: 0.9171 (p) cc_final: 0.8636 (t) REVERT: I 1306 LYS cc_start: 0.8833 (mtmm) cc_final: 0.8579 (pttm) REVERT: I 1316 GLU cc_start: 0.8502 (tp30) cc_final: 0.7909 (tm-30) REVERT: J 62 PHE cc_start: 0.9125 (m-80) cc_final: 0.8916 (m-80) REVERT: J 100 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: J 225 GLU cc_start: 0.9216 (tp30) cc_final: 0.8923 (tm-30) REVERT: J 238 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8187 (tt) REVERT: J 265 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8226 (mm) REVERT: J 281 ARG cc_start: 0.9428 (mmm160) cc_final: 0.9126 (mmm160) REVERT: J 298 MET cc_start: 0.9012 (mmm) cc_final: 0.7853 (tmm) REVERT: J 301 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8221 (pp20) REVERT: J 303 VAL cc_start: 0.9068 (t) cc_final: 0.8824 (p) REVERT: J 330 MET cc_start: 0.9086 (mmm) cc_final: 0.8751 (mpp) REVERT: J 478 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7791 (mt) REVERT: J 500 ILE cc_start: 0.8704 (mt) cc_final: 0.8320 (tt) REVERT: J 508 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.7962 (tp) REVERT: J 610 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7774 (ttp80) REVERT: J 702 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8107 (pt0) REVERT: J 754 ILE cc_start: 0.8945 (mm) cc_final: 0.8725 (mm) REVERT: J 797 THR cc_start: 0.8498 (m) cc_final: 0.7668 (p) REVERT: J 818 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6568 (pm20) REVERT: J 830 ASP cc_start: 0.8557 (t0) cc_final: 0.8113 (t70) REVERT: J 960 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8411 (tt) REVERT: J 983 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8472 (mppt) REVERT: J 1040 MET cc_start: 0.0950 (mmm) cc_final: 0.0420 (mmp) REVERT: J 1189 MET cc_start: 0.8017 (mtt) cc_final: 0.7493 (tpp) REVERT: J 1202 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7958 (pm20) REVERT: J 1305 ASP cc_start: 0.8316 (t0) cc_final: 0.7719 (p0) REVERT: K 15 ASN cc_start: 0.8271 (m-40) cc_final: 0.7300 (t0) REVERT: K 26 ARG cc_start: 0.8974 (tpt170) cc_final: 0.8377 (tpm170) REVERT: K 30 MET cc_start: 0.7393 (ttm) cc_final: 0.7140 (tpp) REVERT: K 53 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7785 (mm-30) REVERT: F 9 TRP cc_start: 0.8657 (m100) cc_final: 0.7781 (m100) REVERT: F 10 ILE cc_start: 0.9021 (pt) cc_final: 0.8743 (tp) REVERT: F 34 PHE cc_start: 0.8628 (m-80) cc_final: 0.7822 (m-10) REVERT: F 47 ASP cc_start: 0.6059 (OUTLIER) cc_final: 0.5389 (p0) REVERT: F 69 MET cc_start: 0.5737 (tpp) cc_final: 0.5261 (tpp) REVERT: F 116 PHE cc_start: 0.5167 (OUTLIER) cc_final: 0.4965 (m-80) REVERT: F 167 ARG cc_start: 0.8983 (mtm180) cc_final: 0.8571 (mtm110) REVERT: F 204 LEU cc_start: 0.9098 (mt) cc_final: 0.8870 (mt) REVERT: F 213 HIS cc_start: 0.9338 (m170) cc_final: 0.9052 (m-70) REVERT: F 240 HIS cc_start: 0.8256 (OUTLIER) cc_final: 0.7737 (p-80) REVERT: F 252 VAL cc_start: 0.7632 (OUTLIER) cc_final: 0.7288 (p) REVERT: F 281 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8160 (mm-30) REVERT: F 358 MET cc_start: 0.7587 (ptt) cc_final: 0.7332 (ppp) REVERT: F 407 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8654 (mt) REVERT: F 444 TYR cc_start: 0.7956 (m-80) cc_final: 0.7430 (m-80) REVERT: F 534 PHE cc_start: 0.7585 (m-80) cc_final: 0.6773 (m-80) REVERT: F 543 ARG cc_start: 0.8705 (mmt-90) cc_final: 0.8239 (mtt180) REVERT: F 553 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8670 (mp0) REVERT: F 592 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7830 (tm-30) REVERT: F 723 PHE cc_start: 0.8880 (m-10) cc_final: 0.8649 (m-10) REVERT: F 765 ARG cc_start: 0.8936 (tpt170) cc_final: 0.8599 (tpt-90) REVERT: F 766 GLU cc_start: 0.9449 (mm-30) cc_final: 0.9179 (mm-30) REVERT: F 776 PHE cc_start: 0.7776 (t80) cc_final: 0.7393 (t80) REVERT: F 949 SER cc_start: 0.9429 (t) cc_final: 0.9168 (p) outliers start: 214 outliers final: 129 residues processed: 803 average time/residue: 0.4753 time to fit residues: 605.7490 Evaluate side-chains 738 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 585 time to evaluate : 3.522 ------------------------------------------------------------------------------- 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 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 68 TYR Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 132 HIS 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 194 GLN Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 204 GLU 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 90 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 138 ILE 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 291 TYR Chi-restraints excluded: chain I residue 331 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 656 SER Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 681 MET 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 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 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1259 LEU 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 100 GLU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 242 LEU 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 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 454 CYS 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 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 571 ASP Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 596 LEU 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 702 GLN Chi-restraints excluded: chain J residue 705 THR 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 788 LEU Chi-restraints excluded: chain J residue 800 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 895 CYS Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 913 GLU 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 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 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 29 THR Chi-restraints excluded: chain F residue 30 VAL 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 237 GLU Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 248 THR 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 407 LEU 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 385 optimal weight: 50.0000 chunk 266 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 357 optimal weight: 30.0000 chunk 317 optimal weight: 30.0000 chunk 279 optimal weight: 50.0000 chunk 109 optimal weight: 0.9990 chunk 199 optimal weight: 0.7980 chunk 255 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 46 GLN ** 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 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** ** J1218 HIS ** 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 K 70 GLN ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 626 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.217719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.129799 restraints weight = 53755.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.130167 restraints weight = 30617.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.130960 restraints weight = 20801.630| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 34156 Z= 0.161 Angle : 0.747 21.950 46363 Z= 0.367 Chirality : 0.045 0.314 5267 Planarity : 0.005 0.086 5930 Dihedral : 12.922 119.174 5170 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.60 % Favored : 92.38 % Rotamer: Outliers : 5.73 % Allowed : 20.91 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.13), residues: 4132 helix: 0.54 (0.13), residues: 1539 sheet: -0.97 (0.24), residues: 499 loop : -1.63 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 115 HIS 0.006 0.001 HIS H 128 PHE 0.028 0.002 PHE I 225 TYR 0.034 0.002 TYR H 177 ARG 0.010 0.001 ARG J 99 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 1391) hydrogen bonds : angle 5.20545 ( 3878) metal coordination : bond 0.01307 ( 8) metal coordination : angle 9.10860 ( 12) covalent geometry : bond 0.00369 (34148) covalent geometry : angle 0.73268 (46351) *********************** 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 835 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 633 time to evaluate : 3.612 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: G 25 LYS cc_start: 0.8384 (mtmt) cc_final: 0.8081 (pttp) REVERT: G 46 ILE cc_start: 0.8649 (tp) cc_final: 0.8172 (tp) REVERT: G 50 SER cc_start: 0.9049 (m) cc_final: 0.8673 (p) REVERT: G 103 ASN cc_start: 0.8495 (m-40) cc_final: 0.8063 (t0) REVERT: G 142 MET cc_start: 0.8098 (ptm) cc_final: 0.7866 (ptm) REVERT: G 152 TYR cc_start: 0.8880 (t80) cc_final: 0.8498 (t80) REVERT: G 185 TYR cc_start: 0.9092 (p90) cc_final: 0.8784 (p90) REVERT: G 200 LYS cc_start: 0.8634 (ttmt) cc_final: 0.8201 (ttmm) REVERT: H 57 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8297 (p) REVERT: H 84 ASN cc_start: 0.9127 (m-40) cc_final: 0.8635 (t0) REVERT: H 125 LYS cc_start: 0.9286 (mptt) cc_final: 0.8710 (tttp) REVERT: H 145 LYS cc_start: 0.9187 (tttt) cc_final: 0.8887 (ttpp) REVERT: H 174 ASP cc_start: 0.9263 (OUTLIER) cc_final: 0.8938 (m-30) REVERT: H 181 GLU cc_start: 0.8486 (tp30) cc_final: 0.7868 (tp30) REVERT: H 186 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.7350 (p0) REVERT: H 212 ASP cc_start: 0.7927 (p0) cc_final: 0.7330 (p0) REVERT: I 32 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8430 (mm) REVERT: I 46 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8685 (mm-40) REVERT: I 87 ILE cc_start: 0.9112 (mm) cc_final: 0.8911 (mp) REVERT: I 97 ARG cc_start: 0.8564 (mtt-85) cc_final: 0.8308 (mmt90) REVERT: I 158 ASP cc_start: 0.8433 (t0) cc_final: 0.7925 (t70) REVERT: I 160 ASP cc_start: 0.8716 (m-30) cc_final: 0.8060 (m-30) REVERT: I 191 LYS cc_start: 0.9181 (mmmm) cc_final: 0.8566 (tptp) REVERT: I 192 ASP cc_start: 0.8703 (m-30) cc_final: 0.8027 (m-30) REVERT: I 340 ASP cc_start: 0.9233 (m-30) cc_final: 0.8737 (p0) REVERT: I 346 TYR cc_start: 0.7486 (m-10) cc_final: 0.7083 (m-80) REVERT: I 368 ARG cc_start: 0.9161 (mmm-85) cc_final: 0.8904 (mmt90) REVERT: I 378 ARG cc_start: 0.8951 (ttp80) cc_final: 0.8475 (ttp80) REVERT: I 488 MET cc_start: 0.8444 (mmm) cc_final: 0.8062 (mmm) REVERT: I 492 MET cc_start: 0.8321 (ptp) cc_final: 0.7313 (tpp) REVERT: I 622 ASN cc_start: 0.8167 (t0) cc_final: 0.7822 (t0) REVERT: I 623 LEU cc_start: 0.8315 (tp) cc_final: 0.8026 (tp) REVERT: I 697 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8376 (pttm) REVERT: I 737 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7819 (m110) REVERT: I 790 ASP cc_start: 0.7904 (t70) cc_final: 0.7500 (t0) REVERT: I 930 ASP cc_start: 0.7915 (t0) cc_final: 0.7677 (t0) REVERT: I 962 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8414 (tp30) REVERT: I 971 LEU cc_start: 0.7521 (tp) cc_final: 0.7217 (mt) REVERT: I 1038 GLN cc_start: 0.9034 (pp30) cc_final: 0.8819 (pp30) REVERT: I 1085 MET cc_start: 0.8799 (mmm) cc_final: 0.8535 (mmt) REVERT: I 1149 TYR cc_start: 0.7879 (m-80) cc_final: 0.7464 (m-80) REVERT: I 1177 ARG cc_start: 0.8700 (ptm160) cc_final: 0.8369 (ptm-80) REVERT: I 1203 ASP cc_start: 0.7949 (t0) cc_final: 0.7562 (t0) REVERT: I 1214 ASP cc_start: 0.8207 (t0) cc_final: 0.7742 (t0) REVERT: I 1302 THR cc_start: 0.9150 (p) cc_final: 0.8922 (t) REVERT: I 1306 LYS cc_start: 0.8858 (mtmm) cc_final: 0.8628 (ptpt) REVERT: I 1316 GLU cc_start: 0.8532 (tp30) cc_final: 0.8025 (tm-30) REVERT: J 17 PHE cc_start: 0.6674 (t80) cc_final: 0.6393 (t80) REVERT: J 44 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6777 (tp) REVERT: J 99 ARG cc_start: 0.9366 (ttm110) cc_final: 0.9075 (mtm-85) REVERT: J 115 TRP cc_start: 0.8082 (m-10) cc_final: 0.7859 (m-10) REVERT: J 118 LYS cc_start: 0.9493 (mmmm) cc_final: 0.9241 (mmmm) REVERT: J 237 MET cc_start: 0.8749 (tpp) cc_final: 0.8357 (tpp) REVERT: J 281 ARG cc_start: 0.9408 (mmm160) cc_final: 0.9108 (mmm160) REVERT: J 297 ARG cc_start: 0.9152 (ttp80) cc_final: 0.8411 (ttp80) REVERT: J 298 MET cc_start: 0.8992 (mmm) cc_final: 0.7925 (mmm) REVERT: J 301 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8758 (pt0) REVERT: J 303 VAL cc_start: 0.9057 (t) cc_final: 0.8816 (p) REVERT: J 418 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: J 441 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7510 (mm) REVERT: J 462 ASP cc_start: 0.7578 (p0) cc_final: 0.7250 (p0) REVERT: J 478 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7597 (mt) REVERT: J 500 ILE cc_start: 0.8655 (mt) cc_final: 0.8283 (tt) REVERT: J 508 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7660 (tp) REVERT: J 610 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7675 (ttp80) REVERT: J 698 MET cc_start: 0.7919 (tpt) cc_final: 0.7668 (tpt) REVERT: J 709 ARG cc_start: 0.8959 (ppt170) cc_final: 0.8629 (ppt170) REVERT: J 710 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8048 (p0) REVERT: J 797 THR cc_start: 0.8389 (m) cc_final: 0.7512 (p) REVERT: J 818 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6640 (pm20) REVERT: J 923 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8102 (tp) REVERT: J 960 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8409 (tt) REVERT: J 983 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8451 (mppt) REVERT: J 1025 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.8047 (pmm) REVERT: J 1040 MET cc_start: 0.1318 (mmm) cc_final: 0.1032 (mmp) REVERT: J 1189 MET cc_start: 0.8122 (mtt) cc_final: 0.7897 (ttt) REVERT: J 1202 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7950 (pm20) REVERT: J 1305 ASP cc_start: 0.8318 (t0) cc_final: 0.7742 (p0) REVERT: K 11 GLU cc_start: 0.8831 (pp20) cc_final: 0.8603 (pp20) REVERT: K 12 LYS cc_start: 0.9097 (mmmt) cc_final: 0.8699 (mmmt) REVERT: K 15 ASN cc_start: 0.8298 (m-40) cc_final: 0.7306 (t0) REVERT: K 26 ARG cc_start: 0.8995 (tpt170) cc_final: 0.8467 (tpm170) REVERT: F 9 TRP cc_start: 0.8637 (m100) cc_final: 0.7791 (m100) REVERT: F 10 ILE cc_start: 0.8955 (pt) cc_final: 0.8659 (tp) REVERT: F 34 PHE cc_start: 0.8569 (m-80) cc_final: 0.8316 (m-10) REVERT: F 99 GLU cc_start: 0.3105 (OUTLIER) cc_final: 0.2892 (pt0) REVERT: F 116 PHE cc_start: 0.4383 (OUTLIER) cc_final: 0.4108 (m-80) REVERT: F 175 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6444 (tp) REVERT: F 204 LEU cc_start: 0.9037 (mt) cc_final: 0.8793 (mt) REVERT: F 214 GLN cc_start: 0.9372 (tm-30) cc_final: 0.8923 (pp30) REVERT: F 233 GLU cc_start: 0.9597 (mp0) cc_final: 0.9360 (mp0) REVERT: F 240 HIS cc_start: 0.8139 (OUTLIER) cc_final: 0.7725 (p90) REVERT: F 252 VAL cc_start: 0.7481 (OUTLIER) cc_final: 0.7190 (p) REVERT: F 281 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8057 (mm-30) REVERT: F 407 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8656 (mt) REVERT: F 472 ARG cc_start: 0.8757 (tpp-160) cc_final: 0.8513 (tpp-160) REVERT: F 534 PHE cc_start: 0.7251 (m-80) cc_final: 0.6472 (m-80) REVERT: F 543 ARG cc_start: 0.8597 (mmt-90) cc_final: 0.8171 (mtt180) REVERT: F 553 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8692 (mp0) REVERT: F 592 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7763 (tm-30) REVERT: F 707 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8732 (pt0) REVERT: F 723 PHE cc_start: 0.8896 (m-10) cc_final: 0.8687 (m-10) REVERT: F 765 ARG cc_start: 0.8941 (tpt170) cc_final: 0.8729 (tpt170) REVERT: F 766 GLU cc_start: 0.9428 (mm-30) cc_final: 0.9183 (mm-30) REVERT: F 775 GLN cc_start: 0.8816 (mp10) cc_final: 0.8576 (mp10) REVERT: F 776 PHE cc_start: 0.7640 (t80) cc_final: 0.7383 (t80) REVERT: F 949 SER cc_start: 0.9378 (t) cc_final: 0.9099 (p) outliers start: 202 outliers final: 126 residues processed: 777 average time/residue: 0.4816 time to fit residues: 591.6621 Evaluate side-chains 739 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 586 time to evaluate : 3.599 ------------------------------------------------------------------------------- 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 57 THR Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 183 ILE 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 I residue 21 VAL Chi-restraints excluded: chain I residue 31 GLN Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 90 VAL 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 291 TYR Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 369 MET 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 565 GLU Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 681 MET 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 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 J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 124 ILE 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 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 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 460 ASP 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 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 574 VAL 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 710 ASP Chi-restraints excluded: chain J residue 746 LEU 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 816 THR Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 913 GLU 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 1046 ILE 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 1280 VAL 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 30 VAL 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 116 PHE 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 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 407 LEU 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 593 ARG 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 49 optimal weight: 10.0000 chunk 223 optimal weight: 0.8980 chunk 34 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 228 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 178 optimal weight: 6.9990 chunk 324 optimal weight: 9.9990 chunk 151 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 760 ASN ** 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** ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1252 HIS ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 626 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.227081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.143276 restraints weight = 53770.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142536 restraints weight = 30803.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.142991 restraints weight = 20942.653| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34156 Z= 0.135 Angle : 0.724 15.373 46363 Z= 0.357 Chirality : 0.044 0.242 5267 Planarity : 0.005 0.093 5930 Dihedral : 12.782 118.766 5160 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.75 % Favored : 93.22 % Rotamer: Outliers : 5.22 % Allowed : 22.44 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.13), residues: 4132 helix: 0.66 (0.13), residues: 1532 sheet: -0.90 (0.24), residues: 509 loop : -1.61 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 215 HIS 0.018 0.001 HIS F 626 PHE 0.026 0.002 PHE F 572 TYR 0.023 0.001 TYR H 177 ARG 0.012 0.001 ARG J1330 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 1391) hydrogen bonds : angle 5.05537 ( 3878) metal coordination : bond 0.01137 ( 8) metal coordination : angle 7.20709 ( 12) covalent geometry : bond 0.00306 (34148) covalent geometry : angle 0.71435 (46351) *********************** 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 823 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 639 time to evaluate : 3.805 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: G 25 LYS cc_start: 0.8302 (mtmt) cc_final: 0.7993 (pttp) REVERT: G 46 ILE cc_start: 0.8597 (tp) cc_final: 0.8085 (tp) REVERT: G 50 SER cc_start: 0.8963 (m) cc_final: 0.8580 (p) REVERT: G 86 LYS cc_start: 0.8157 (ttmt) cc_final: 0.7679 (ttpp) REVERT: G 95 LYS cc_start: 0.8926 (mtmt) cc_final: 0.8392 (ptmm) REVERT: G 103 ASN cc_start: 0.8520 (m-40) cc_final: 0.8072 (t0) REVERT: G 152 TYR cc_start: 0.8972 (t80) cc_final: 0.8631 (t80) REVERT: G 185 TYR cc_start: 0.9084 (p90) cc_final: 0.8734 (p90) REVERT: G 200 LYS cc_start: 0.8574 (ttmt) cc_final: 0.8136 (ttmm) REVERT: H 57 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8265 (p) REVERT: H 84 ASN cc_start: 0.9073 (m-40) cc_final: 0.8615 (t0) REVERT: H 142 MET cc_start: 0.9383 (tmm) cc_final: 0.8832 (tmm) REVERT: H 145 LYS cc_start: 0.9197 (tttt) cc_final: 0.8782 (ttpp) REVERT: H 174 ASP cc_start: 0.9319 (OUTLIER) cc_final: 0.8958 (m-30) REVERT: H 181 GLU cc_start: 0.8481 (tp30) cc_final: 0.7868 (tp30) REVERT: H 206 GLU cc_start: 0.8445 (tp30) cc_final: 0.8016 (tp30) REVERT: H 212 ASP cc_start: 0.7941 (p0) cc_final: 0.7328 (p0) REVERT: H 227 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8533 (mt0) REVERT: I 32 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8420 (mm) REVERT: I 81 ASP cc_start: 0.8111 (m-30) cc_final: 0.7697 (t0) REVERT: I 83 GLN cc_start: 0.7702 (pm20) cc_final: 0.7209 (pm20) REVERT: I 87 ILE cc_start: 0.9126 (mm) cc_final: 0.8914 (mp) REVERT: I 158 ASP cc_start: 0.8425 (t0) cc_final: 0.7948 (t70) REVERT: I 160 ASP cc_start: 0.8752 (m-30) cc_final: 0.8178 (m-30) REVERT: I 185 ASP cc_start: 0.6570 (m-30) cc_final: 0.6227 (m-30) REVERT: I 191 LYS cc_start: 0.9216 (mmmm) cc_final: 0.8603 (tptp) REVERT: I 192 ASP cc_start: 0.8695 (m-30) cc_final: 0.8050 (m-30) REVERT: I 219 GLN cc_start: 0.9571 (mt0) cc_final: 0.9195 (mt0) REVERT: I 340 ASP cc_start: 0.9238 (m-30) cc_final: 0.8757 (p0) REVERT: I 346 TYR cc_start: 0.7592 (m-10) cc_final: 0.7155 (m-80) REVERT: I 368 ARG cc_start: 0.9116 (mmm-85) cc_final: 0.8883 (mmt90) REVERT: I 378 ARG cc_start: 0.8977 (ttp80) cc_final: 0.8511 (ttp80) REVERT: I 427 ASP cc_start: 0.9079 (m-30) cc_final: 0.8671 (t0) REVERT: I 441 GLU cc_start: 0.7999 (tp30) cc_final: 0.7685 (mp0) REVERT: I 472 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8571 (tm-30) REVERT: I 565 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7119 (tt0) REVERT: I 697 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8166 (pttm) REVERT: I 704 MET cc_start: 0.7059 (mmm) cc_final: 0.6426 (tpp) REVERT: I 737 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7800 (m110) REVERT: I 761 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7819 (mp10) REVERT: I 790 ASP cc_start: 0.7840 (t70) cc_final: 0.7386 (t0) REVERT: I 960 LEU cc_start: 0.9278 (mm) cc_final: 0.8146 (tp) REVERT: I 962 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8469 (tp30) REVERT: I 1025 PHE cc_start: 0.9272 (t80) cc_final: 0.8948 (t80) REVERT: I 1038 GLN cc_start: 0.9057 (pp30) cc_final: 0.8846 (pp30) REVERT: I 1085 MET cc_start: 0.8806 (mmm) cc_final: 0.8414 (mmp) REVERT: I 1112 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8454 (mt) REVERT: I 1149 TYR cc_start: 0.7946 (m-80) cc_final: 0.7423 (m-80) REVERT: I 1177 ARG cc_start: 0.8650 (ptm160) cc_final: 0.8318 (ptm-80) REVERT: I 1203 ASP cc_start: 0.7844 (t0) cc_final: 0.7492 (t0) REVERT: I 1214 ASP cc_start: 0.8110 (t0) cc_final: 0.7847 (t0) REVERT: I 1229 TYR cc_start: 0.8803 (m-80) cc_final: 0.8565 (m-10) REVERT: I 1304 MET cc_start: 0.7829 (tpp) cc_final: 0.7567 (tpt) REVERT: I 1316 GLU cc_start: 0.8534 (tp30) cc_final: 0.8013 (tm-30) REVERT: J 17 PHE cc_start: 0.6539 (t80) cc_final: 0.6302 (t80) REVERT: J 62 PHE cc_start: 0.9085 (m-80) cc_final: 0.8809 (m-80) REVERT: J 99 ARG cc_start: 0.9361 (ttm110) cc_final: 0.9055 (mtm-85) REVERT: J 115 TRP cc_start: 0.8050 (m-10) cc_final: 0.7817 (m-10) REVERT: J 118 LYS cc_start: 0.9496 (mmmm) cc_final: 0.9228 (mmmm) REVERT: J 237 MET cc_start: 0.8696 (tpp) cc_final: 0.8470 (tpt) REVERT: J 281 ARG cc_start: 0.9406 (mmm160) cc_final: 0.9100 (mmm160) REVERT: J 297 ARG cc_start: 0.9150 (ttp80) cc_final: 0.8421 (ttp80) REVERT: J 298 MET cc_start: 0.9040 (mmm) cc_final: 0.7915 (mmm) REVERT: J 301 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8829 (pt0) REVERT: J 303 VAL cc_start: 0.9024 (t) cc_final: 0.8774 (p) REVERT: J 330 MET cc_start: 0.9072 (mmm) cc_final: 0.8729 (mpp) REVERT: J 441 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7386 (mm) REVERT: J 457 TYR cc_start: 0.7873 (m-80) cc_final: 0.7620 (m-80) REVERT: J 462 ASP cc_start: 0.7287 (p0) cc_final: 0.7079 (p0) REVERT: J 478 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7579 (mt) REVERT: J 500 ILE cc_start: 0.8545 (mt) cc_final: 0.8280 (tt) REVERT: J 508 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7513 (tp) REVERT: J 554 GLU cc_start: 0.8054 (pt0) cc_final: 0.7820 (pt0) REVERT: J 610 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7914 (ttp80) REVERT: J 697 MET cc_start: 0.8412 (ttp) cc_final: 0.7933 (ttp) REVERT: J 710 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8099 (p0) REVERT: J 797 THR cc_start: 0.8255 (m) cc_final: 0.7469 (p) REVERT: J 818 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6738 (pm20) REVERT: J 830 ASP cc_start: 0.8564 (t0) cc_final: 0.8064 (t0) REVERT: J 960 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8514 (tt) REVERT: J 1305 ASP cc_start: 0.8287 (t0) cc_final: 0.7754 (p0) REVERT: K 11 GLU cc_start: 0.8877 (pp20) cc_final: 0.8634 (pp20) REVERT: K 12 LYS cc_start: 0.9101 (mmmt) cc_final: 0.8749 (mmmt) REVERT: K 15 ASN cc_start: 0.8255 (m-40) cc_final: 0.7201 (t0) REVERT: K 26 ARG cc_start: 0.9006 (tpt170) cc_final: 0.8391 (tpm170) REVERT: K 44 ASP cc_start: 0.7963 (p0) cc_final: 0.7562 (p0) REVERT: F 9 TRP cc_start: 0.8648 (m100) cc_final: 0.7877 (m100) REVERT: F 10 ILE cc_start: 0.8883 (pt) cc_final: 0.8641 (tp) REVERT: F 34 PHE cc_start: 0.8892 (m-80) cc_final: 0.8438 (m-80) REVERT: F 116 PHE cc_start: 0.4886 (OUTLIER) cc_final: 0.4622 (m-80) REVERT: F 175 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6402 (tp) REVERT: F 204 LEU cc_start: 0.9021 (mt) cc_final: 0.8781 (mt) REVERT: F 213 HIS cc_start: 0.9345 (m-70) cc_final: 0.9071 (m-70) REVERT: F 233 GLU cc_start: 0.9594 (mp0) cc_final: 0.9374 (mp0) REVERT: F 240 HIS cc_start: 0.8254 (OUTLIER) cc_final: 0.7903 (p90) REVERT: F 252 VAL cc_start: 0.7410 (OUTLIER) cc_final: 0.7115 (p) REVERT: F 281 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7983 (mm-30) REVERT: F 407 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8654 (mt) REVERT: F 444 TYR cc_start: 0.8004 (m-10) cc_final: 0.7564 (m-10) REVERT: F 472 ARG cc_start: 0.8800 (tpp-160) cc_final: 0.8572 (tpp-160) REVERT: F 534 PHE cc_start: 0.7113 (m-80) cc_final: 0.6298 (m-80) REVERT: F 543 ARG cc_start: 0.8535 (mmm-85) cc_final: 0.8075 (mtt180) REVERT: F 553 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8643 (mp0) REVERT: F 629 LEU cc_start: 0.8942 (tt) cc_final: 0.8484 (pt) REVERT: F 765 ARG cc_start: 0.8999 (tpt170) cc_final: 0.8248 (tpt-90) REVERT: F 766 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9214 (mm-30) REVERT: F 775 GLN cc_start: 0.8813 (mp10) cc_final: 0.8571 (mp10) REVERT: F 776 PHE cc_start: 0.7512 (t80) cc_final: 0.7258 (t80) REVERT: F 888 LEU cc_start: 0.8900 (mt) cc_final: 0.8541 (pp) REVERT: F 943 ARG cc_start: 0.8489 (tmm-80) cc_final: 0.8287 (tmm-80) outliers start: 184 outliers final: 115 residues processed: 767 average time/residue: 0.4786 time to fit residues: 579.2517 Evaluate side-chains 729 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 593 time to evaluate : 3.792 ------------------------------------------------------------------------------- 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 147 GLN 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 95 LYS Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 174 ASP 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 224 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 31 GLN Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 146 VAL 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 431 LYS 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 666 SER 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 737 ASN 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 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 1112 ILE 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 1289 GLU 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 242 LEU 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 425 ARG 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 460 ASP 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 710 ASP Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 803 VAL 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 857 LEU Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 960 LEU 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 1209 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1280 VAL 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 F residue 30 VAL Chi-restraints excluded: chain F residue 33 LEU 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 218 GLU Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 248 THR 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 345 GLU Chi-restraints excluded: chain F residue 407 LEU 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 593 ARG Chi-restraints excluded: chain F residue 739 VAL Chi-restraints excluded: chain F residue 869 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 6 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 410 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 382 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 411 optimal weight: 10.0000 chunk 252 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 239 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 I1244 HIS ** 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 ** J1218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 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 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 700 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.215400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.125917 restraints weight = 53549.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.125965 restraints weight = 32308.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.128270 restraints weight = 22965.317| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 34156 Z= 0.233 Angle : 0.774 19.892 46363 Z= 0.384 Chirality : 0.046 0.345 5267 Planarity : 0.005 0.092 5930 Dihedral : 12.784 118.587 5155 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.79 % Favored : 92.18 % Rotamer: Outliers : 5.59 % Allowed : 23.46 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.13), residues: 4132 helix: 0.59 (0.13), residues: 1536 sheet: -0.73 (0.24), residues: 489 loop : -1.70 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 115 HIS 0.006 0.001 HIS J 469 PHE 0.027 0.002 PHE G 35 TYR 0.022 0.002 TYR H 177 ARG 0.013 0.001 ARG J 214 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 1391) hydrogen bonds : angle 5.18315 ( 3878) metal coordination : bond 0.01405 ( 8) metal coordination : angle 6.05315 ( 12) covalent geometry : bond 0.00544 (34148) covalent geometry : angle 0.76765 (46351) *********************** 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 809 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 612 time to evaluate : 4.053 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: G 25 LYS cc_start: 0.8316 (mtmt) cc_final: 0.8007 (pttp) REVERT: G 46 ILE cc_start: 0.8614 (tp) cc_final: 0.8414 (mt) REVERT: G 86 LYS cc_start: 0.8212 (ttmt) cc_final: 0.7717 (ttpp) REVERT: G 95 LYS cc_start: 0.8930 (mtmt) cc_final: 0.8522 (ptmm) REVERT: G 103 ASN cc_start: 0.8610 (m-40) cc_final: 0.8137 (t0) REVERT: G 152 TYR cc_start: 0.9040 (t80) cc_final: 0.8671 (t80) REVERT: G 178 SER cc_start: 0.9272 (t) cc_final: 0.8919 (m) REVERT: G 185 TYR cc_start: 0.9160 (p90) cc_final: 0.8864 (p90) REVERT: G 200 LYS cc_start: 0.8513 (ttmt) cc_final: 0.8164 (ttmm) REVERT: H 57 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8279 (p) REVERT: H 84 ASN cc_start: 0.9059 (m-40) cc_final: 0.8578 (t0) REVERT: H 142 MET cc_start: 0.9438 (tmm) cc_final: 0.9064 (tmm) REVERT: H 145 LYS cc_start: 0.9230 (tttt) cc_final: 0.8700 (ttpp) REVERT: H 147 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8205 (mm-40) REVERT: H 174 ASP cc_start: 0.9294 (OUTLIER) cc_final: 0.8831 (m-30) REVERT: H 181 GLU cc_start: 0.8562 (tp30) cc_final: 0.7924 (tp30) REVERT: H 186 ASN cc_start: 0.7596 (OUTLIER) cc_final: 0.7354 (p0) REVERT: H 206 GLU cc_start: 0.8512 (tp30) cc_final: 0.7929 (mm-30) REVERT: H 212 ASP cc_start: 0.7995 (p0) cc_final: 0.7409 (p0) REVERT: I 32 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8448 (mm) REVERT: I 158 ASP cc_start: 0.8452 (t0) cc_final: 0.7912 (t70) REVERT: I 160 ASP cc_start: 0.8719 (m-30) cc_final: 0.8072 (m-30) REVERT: I 191 LYS cc_start: 0.9226 (mmmm) cc_final: 0.8619 (tptp) REVERT: I 192 ASP cc_start: 0.8752 (m-30) cc_final: 0.8154 (m-30) REVERT: I 219 GLN cc_start: 0.9587 (mt0) cc_final: 0.9229 (mt0) REVERT: I 340 ASP cc_start: 0.9274 (m-30) cc_final: 0.8768 (p0) REVERT: I 346 TYR cc_start: 0.7614 (m-10) cc_final: 0.7183 (m-80) REVERT: I 359 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7665 (ttt-90) REVERT: I 368 ARG cc_start: 0.9109 (mmm-85) cc_final: 0.8854 (mmt90) REVERT: I 369 MET cc_start: 0.8823 (tpp) cc_final: 0.8172 (tpt) REVERT: I 427 ASP cc_start: 0.9102 (m-30) cc_final: 0.8768 (t0) REVERT: I 441 GLU cc_start: 0.8096 (tp30) cc_final: 0.7575 (mp0) REVERT: I 488 MET cc_start: 0.8747 (mmm) cc_final: 0.8421 (mmm) REVERT: I 492 MET cc_start: 0.8909 (pmm) cc_final: 0.8478 (pmm) REVERT: I 549 ASP cc_start: 0.7938 (t0) cc_final: 0.7481 (m-30) REVERT: I 622 ASN cc_start: 0.8167 (t0) cc_final: 0.7811 (t0) REVERT: I 697 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8374 (pttm) REVERT: I 708 VAL cc_start: 0.8648 (t) cc_final: 0.8404 (t) REVERT: I 737 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7178 (t0) REVERT: I 761 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7886 (mp10) REVERT: I 790 ASP cc_start: 0.7958 (t70) cc_final: 0.7562 (t0) REVERT: I 955 GLN cc_start: 0.9551 (tp-100) cc_final: 0.9323 (tp-100) REVERT: I 960 LEU cc_start: 0.9214 (mm) cc_final: 0.8053 (tp) REVERT: I 962 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8467 (tp30) REVERT: I 1025 PHE cc_start: 0.9307 (t80) cc_final: 0.8940 (t80) REVERT: I 1038 GLN cc_start: 0.9108 (pp30) cc_final: 0.8874 (pp30) REVERT: I 1085 MET cc_start: 0.9014 (mmm) cc_final: 0.8800 (mmt) REVERT: I 1203 ASP cc_start: 0.8043 (t0) cc_final: 0.7706 (t0) REVERT: I 1302 THR cc_start: 0.9248 (p) cc_final: 0.8852 (t) REVERT: I 1316 GLU cc_start: 0.8535 (tp30) cc_final: 0.8036 (tm-30) REVERT: J 62 PHE cc_start: 0.9074 (m-80) cc_final: 0.8724 (m-80) REVERT: J 99 ARG cc_start: 0.9384 (ttm110) cc_final: 0.9088 (mtm-85) REVERT: J 100 GLU cc_start: 0.7640 (pm20) cc_final: 0.6940 (pm20) REVERT: J 118 LYS cc_start: 0.9504 (mmmm) cc_final: 0.9207 (mmmm) REVERT: J 222 LYS cc_start: 0.9451 (ptpp) cc_final: 0.9044 (ptpp) REVERT: J 281 ARG cc_start: 0.9434 (mmm160) cc_final: 0.9118 (mmm160) REVERT: J 297 ARG cc_start: 0.9112 (ttp80) cc_final: 0.8089 (ttp80) REVERT: J 298 MET cc_start: 0.9084 (mmm) cc_final: 0.7823 (tpp) REVERT: J 301 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8976 (pt0) REVERT: J 330 MET cc_start: 0.9173 (mmm) cc_final: 0.8713 (mpp) REVERT: J 339 ARG cc_start: 0.7917 (mtm110) cc_final: 0.7579 (mtm110) REVERT: J 343 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6749 (mp) REVERT: J 457 TYR cc_start: 0.8074 (m-80) cc_final: 0.7791 (m-80) REVERT: J 478 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7624 (mt) REVERT: J 500 ILE cc_start: 0.8566 (mt) cc_final: 0.8235 (tt) REVERT: J 508 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7789 (tp) REVERT: J 554 GLU cc_start: 0.8135 (pt0) cc_final: 0.7908 (pt0) REVERT: J 610 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7692 (ttp80) REVERT: J 697 MET cc_start: 0.8488 (ttp) cc_final: 0.7887 (ttp) REVERT: J 746 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7908 (pp) REVERT: J 797 THR cc_start: 0.8462 (m) cc_final: 0.7582 (p) REVERT: J 818 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6821 (pm20) REVERT: J 960 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8592 (tt) REVERT: J 1189 MET cc_start: 0.7999 (mtt) cc_final: 0.7471 (tpp) REVERT: J 1243 LEU cc_start: 0.8943 (tp) cc_final: 0.8538 (mt) REVERT: J 1268 ASN cc_start: 0.8776 (OUTLIER) cc_final: 0.8565 (p0) REVERT: J 1278 GLU cc_start: 0.7056 (tm-30) cc_final: 0.6853 (tm-30) REVERT: K 11 GLU cc_start: 0.8837 (pp20) cc_final: 0.8523 (pp20) REVERT: K 12 LYS cc_start: 0.9100 (mmmt) cc_final: 0.8771 (mmmt) REVERT: K 15 ASN cc_start: 0.8254 (m-40) cc_final: 0.7178 (t0) REVERT: K 26 ARG cc_start: 0.9041 (tpt170) cc_final: 0.8687 (tpm170) REVERT: K 30 MET cc_start: 0.7420 (tpp) cc_final: 0.6994 (tpp) REVERT: F 9 TRP cc_start: 0.8665 (m100) cc_final: 0.7937 (m100) REVERT: F 10 ILE cc_start: 0.8984 (pt) cc_final: 0.8676 (tp) REVERT: F 34 PHE cc_start: 0.8972 (m-80) cc_final: 0.8323 (m-80) REVERT: F 116 PHE cc_start: 0.5250 (OUTLIER) cc_final: 0.5049 (m-80) REVERT: F 175 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6490 (tp) REVERT: F 204 LEU cc_start: 0.9069 (mt) cc_final: 0.8838 (mt) REVERT: F 233 GLU cc_start: 0.9612 (mp0) cc_final: 0.9310 (mp0) REVERT: F 240 HIS cc_start: 0.8261 (OUTLIER) cc_final: 0.7909 (p90) REVERT: F 252 VAL cc_start: 0.7581 (OUTLIER) cc_final: 0.7328 (p) REVERT: F 281 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8168 (mm-30) REVERT: F 321 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7335 (ptp) REVERT: F 407 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8621 (mt) REVERT: F 444 TYR cc_start: 0.8149 (m-10) cc_final: 0.7797 (m-10) REVERT: F 472 ARG cc_start: 0.8864 (tpp-160) cc_final: 0.8641 (tpp-160) REVERT: F 629 LEU cc_start: 0.8962 (tt) cc_final: 0.8508 (pt) REVERT: F 746 MET cc_start: 0.2405 (mmt) cc_final: 0.2201 (mmt) REVERT: F 765 ARG cc_start: 0.9050 (tpt170) cc_final: 0.8357 (tpt-90) REVERT: F 766 GLU cc_start: 0.9473 (mm-30) cc_final: 0.9260 (mm-30) REVERT: F 776 PHE cc_start: 0.7564 (t80) cc_final: 0.7262 (t80) REVERT: F 888 LEU cc_start: 0.9032 (mt) cc_final: 0.8557 (pp) outliers start: 197 outliers final: 137 residues processed: 751 average time/residue: 0.4820 time to fit residues: 575.9638 Evaluate side-chains 735 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 576 time to evaluate : 3.592 ------------------------------------------------------------------------------- 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 79 LEU 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 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 95 LYS Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 174 ASP 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 24 VAL Chi-restraints excluded: chain I residue 31 GLN Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 90 VAL 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 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 420 LEU Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain I residue 468 LEU 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 657 THR Chi-restraints excluded: chain I residue 666 SER Chi-restraints excluded: chain I residue 697 LYS 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 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 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 1289 GLU 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 223 LEU Chi-restraints excluded: chain J residue 241 VAL 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 343 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 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 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 574 VAL Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 596 LEU 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 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 788 LEU 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 857 LEU Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 960 LEU 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 1257 VAL Chi-restraints excluded: chain J residue 1268 ASN 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 F residue 11 SER 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 102 LEU Chi-restraints excluded: chain F residue 116 PHE Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 163 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 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 407 LEU Chi-restraints excluded: chain F residue 469 TYR Chi-restraints excluded: chain F residue 593 ARG Chi-restraints excluded: chain F residue 739 VAL Chi-restraints excluded: chain F residue 792 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 299 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 chunk 392 optimal weight: 30.0000 chunk 264 optimal weight: 6.9990 chunk 267 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 91 optimal weight: 0.0670 chunk 243 optimal weight: 9.9990 chunk 246 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 23 HIS ** H 128 HIS ** 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 I1244 HIS ** I1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN ** J 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 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 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 745 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.217871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.133174 restraints weight = 53896.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.132420 restraints weight = 30004.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.133680 restraints weight = 20584.191| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 34156 Z= 0.157 Angle : 0.764 14.026 46363 Z= 0.376 Chirality : 0.045 0.282 5267 Planarity : 0.005 0.095 5930 Dihedral : 12.662 118.620 5146 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.07 % Favored : 92.91 % Rotamer: Outliers : 4.94 % Allowed : 24.65 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.13), residues: 4132 helix: 0.64 (0.13), residues: 1523 sheet: -0.79 (0.24), residues: 492 loop : -1.60 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 215 HIS 0.018 0.001 HIS F 692 PHE 0.027 0.002 PHE J 35 TYR 0.022 0.002 TYR H 177 ARG 0.011 0.001 ARG F 920 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 1391) hydrogen bonds : angle 5.09636 ( 3878) metal coordination : bond 0.01210 ( 8) metal coordination : angle 5.21707 ( 12) covalent geometry : bond 0.00363 (34148) covalent geometry : angle 0.75901 (46351) *********************** 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 790 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 616 time to evaluate : 3.780 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: G 25 LYS cc_start: 0.8237 (mtmt) cc_final: 0.7912 (pttp) REVERT: G 86 LYS cc_start: 0.8161 (ttmt) cc_final: 0.7677 (ttpp) REVERT: G 95 LYS cc_start: 0.8932 (mtmt) cc_final: 0.8512 (ptmm) REVERT: G 103 ASN cc_start: 0.8609 (m-40) cc_final: 0.8119 (t0) REVERT: G 152 TYR cc_start: 0.9005 (t80) cc_final: 0.8597 (t80) REVERT: G 178 SER cc_start: 0.9256 (t) cc_final: 0.8949 (m) REVERT: G 185 TYR cc_start: 0.9121 (p90) cc_final: 0.8798 (p90) REVERT: G 200 LYS cc_start: 0.8520 (ttmt) cc_final: 0.8163 (ttmm) REVERT: H 15 ASP cc_start: 0.7563 (m-30) cc_final: 0.6948 (m-30) REVERT: H 47 LEU cc_start: 0.8652 (mt) cc_final: 0.7971 (mt) REVERT: H 51 MET cc_start: 0.9208 (mmm) cc_final: 0.8383 (tpp) REVERT: H 57 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8278 (p) REVERT: H 84 ASN cc_start: 0.9046 (m-40) cc_final: 0.8623 (t0) REVERT: H 125 LYS cc_start: 0.9268 (mptt) cc_final: 0.8691 (tttp) REVERT: H 142 MET cc_start: 0.9395 (tmm) cc_final: 0.8922 (tmm) REVERT: H 145 LYS cc_start: 0.9225 (tttt) cc_final: 0.8684 (ttpp) REVERT: H 147 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8140 (mm-40) REVERT: H 152 TYR cc_start: 0.7775 (t80) cc_final: 0.7522 (t80) REVERT: H 174 ASP cc_start: 0.9281 (OUTLIER) cc_final: 0.8828 (m-30) REVERT: H 181 GLU cc_start: 0.8473 (tp30) cc_final: 0.7862 (tp30) REVERT: H 186 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.7377 (p0) REVERT: H 206 GLU cc_start: 0.8505 (tp30) cc_final: 0.7996 (mm-30) REVERT: H 212 ASP cc_start: 0.7936 (p0) cc_final: 0.7312 (p0) REVERT: I 32 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8457 (mm) REVERT: I 158 ASP cc_start: 0.8410 (t0) cc_final: 0.7902 (t70) REVERT: I 160 ASP cc_start: 0.8751 (m-30) cc_final: 0.8130 (m-30) REVERT: I 185 ASP cc_start: 0.6814 (m-30) cc_final: 0.6523 (m-30) REVERT: I 191 LYS cc_start: 0.9305 (mmmm) cc_final: 0.8673 (tptp) REVERT: I 192 ASP cc_start: 0.8700 (m-30) cc_final: 0.8102 (m-30) REVERT: I 239 MET cc_start: 0.8364 (tpt) cc_final: 0.7936 (tpt) REVERT: I 340 ASP cc_start: 0.9189 (m-30) cc_final: 0.8697 (p0) REVERT: I 346 TYR cc_start: 0.7611 (m-10) cc_final: 0.7115 (m-80) REVERT: I 359 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7680 (ttt-90) REVERT: I 370 MET cc_start: 0.8617 (mmt) cc_final: 0.8121 (mmm) REVERT: I 427 ASP cc_start: 0.9051 (m-30) cc_final: 0.8660 (t0) REVERT: I 441 GLU cc_start: 0.8066 (tp30) cc_final: 0.7515 (mp0) REVERT: I 488 MET cc_start: 0.8669 (mmm) cc_final: 0.8086 (mmm) REVERT: I 549 ASP cc_start: 0.7923 (t0) cc_final: 0.7522 (m-30) REVERT: I 622 ASN cc_start: 0.8150 (t0) cc_final: 0.7774 (t0) REVERT: I 697 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8170 (pttm) REVERT: I 704 MET cc_start: 0.7151 (mmm) cc_final: 0.6531 (tpp) REVERT: I 737 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7961 (m110) REVERT: I 761 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7895 (mp10) REVERT: I 790 ASP cc_start: 0.7864 (t70) cc_final: 0.7381 (t0) REVERT: I 955 GLN cc_start: 0.9558 (tp-100) cc_final: 0.9324 (tp-100) REVERT: I 960 LEU cc_start: 0.9218 (mm) cc_final: 0.8025 (tp) REVERT: I 962 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8450 (tp30) REVERT: I 1025 PHE cc_start: 0.9251 (t80) cc_final: 0.8894 (t80) REVERT: I 1038 GLN cc_start: 0.9158 (pp30) cc_final: 0.8892 (pp30) REVERT: I 1085 MET cc_start: 0.8815 (mmm) cc_final: 0.8447 (mmp) REVERT: I 1149 TYR cc_start: 0.7842 (m-80) cc_final: 0.7418 (m-80) REVERT: I 1177 ARG cc_start: 0.8658 (ptm160) cc_final: 0.8259 (ptm160) REVERT: I 1203 ASP cc_start: 0.7887 (t0) cc_final: 0.7533 (t0) REVERT: I 1243 MET cc_start: 0.7999 (ttp) cc_final: 0.7784 (ttp) REVERT: I 1302 THR cc_start: 0.9144 (p) cc_final: 0.8806 (t) REVERT: I 1316 GLU cc_start: 0.8483 (tp30) cc_final: 0.7999 (tm-30) REVERT: J 62 PHE cc_start: 0.9036 (m-80) cc_final: 0.8707 (m-80) REVERT: J 99 ARG cc_start: 0.9374 (ttm110) cc_final: 0.9103 (mtm-85) REVERT: J 115 TRP cc_start: 0.7913 (m-10) cc_final: 0.7567 (m-10) REVERT: J 118 LYS cc_start: 0.9521 (mmmm) cc_final: 0.9217 (mmmm) REVERT: J 140 TYR cc_start: 0.7208 (m-10) cc_final: 0.6618 (m-80) REVERT: J 160 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7876 (tp) REVERT: J 265 LEU cc_start: 0.9108 (tp) cc_final: 0.8823 (tp) REVERT: J 281 ARG cc_start: 0.9417 (mmm160) cc_final: 0.9105 (mmm160) REVERT: J 296 LYS cc_start: 0.9550 (mttt) cc_final: 0.9279 (mtmt) REVERT: J 297 ARG cc_start: 0.9115 (ttp80) cc_final: 0.8457 (ttp80) REVERT: J 298 MET cc_start: 0.9086 (mmm) cc_final: 0.8010 (mmm) REVERT: J 301 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8854 (pt0) REVERT: J 330 MET cc_start: 0.9114 (mmm) cc_final: 0.8588 (mpp) REVERT: J 418 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: J 457 TYR cc_start: 0.7940 (m-80) cc_final: 0.7704 (m-80) REVERT: J 478 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7438 (mt) REVERT: J 500 ILE cc_start: 0.8528 (mt) cc_final: 0.8233 (tt) REVERT: J 508 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7654 (tp) REVERT: J 554 GLU cc_start: 0.8173 (pt0) cc_final: 0.7935 (pt0) REVERT: J 610 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7624 (ttp80) REVERT: J 697 MET cc_start: 0.8438 (ttp) cc_final: 0.7802 (ttp) REVERT: J 746 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7820 (pp) REVERT: J 818 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6901 (pm20) REVERT: J 960 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8565 (tt) REVERT: J 1189 MET cc_start: 0.7982 (mtt) cc_final: 0.7416 (tpp) REVERT: J 1243 LEU cc_start: 0.8987 (tp) cc_final: 0.8635 (mt) REVERT: J 1305 ASP cc_start: 0.8363 (t0) cc_final: 0.7773 (p0) REVERT: K 15 ASN cc_start: 0.8223 (m-40) cc_final: 0.7133 (t0) REVERT: K 26 ARG cc_start: 0.9039 (tpt170) cc_final: 0.8770 (tpm170) REVERT: K 30 MET cc_start: 0.7395 (tpp) cc_final: 0.7092 (tpp) REVERT: F 9 TRP cc_start: 0.8654 (m100) cc_final: 0.7890 (m100) REVERT: F 10 ILE cc_start: 0.8950 (pt) cc_final: 0.8569 (tp) REVERT: F 34 PHE cc_start: 0.8906 (m-80) cc_final: 0.8219 (m-10) REVERT: F 152 THR cc_start: 0.8942 (p) cc_final: 0.8034 (t) REVERT: F 159 LEU cc_start: 0.9317 (mt) cc_final: 0.9031 (pp) REVERT: F 175 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6376 (tp) REVERT: F 204 LEU cc_start: 0.9033 (mt) cc_final: 0.8799 (mt) REVERT: F 212 GLN cc_start: 0.9212 (pt0) cc_final: 0.8942 (pm20) REVERT: F 233 GLU cc_start: 0.9586 (mp0) cc_final: 0.9351 (mp0) REVERT: F 240 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7866 (p90) REVERT: F 281 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8051 (mm-30) REVERT: F 321 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7287 (ptp) REVERT: F 407 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8558 (mt) REVERT: F 444 TYR cc_start: 0.8059 (m-10) cc_final: 0.7648 (m-10) REVERT: F 472 ARG cc_start: 0.8817 (tpp-160) cc_final: 0.8584 (tpp-160) REVERT: F 553 GLU cc_start: 0.9250 (pm20) cc_final: 0.8898 (mp0) REVERT: F 561 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8893 (tp) REVERT: F 765 ARG cc_start: 0.9004 (tpt170) cc_final: 0.8049 (tpt170) REVERT: F 766 GLU cc_start: 0.9435 (mm-30) cc_final: 0.9216 (mm-30) REVERT: F 776 PHE cc_start: 0.7452 (t80) cc_final: 0.6995 (t80) REVERT: F 888 LEU cc_start: 0.8971 (mt) cc_final: 0.8527 (pp) outliers start: 174 outliers final: 127 residues processed: 734 average time/residue: 0.4672 time to fit residues: 544.5101 Evaluate side-chains 736 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 588 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 SER 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 57 THR Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 183 ILE 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 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 75 LEU Chi-restraints excluded: chain I residue 90 VAL 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 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 468 LEU 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 666 SER Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain I residue 681 MET 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 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 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 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 1289 GLU 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 124 ILE Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 279 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 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 574 VAL 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 683 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 803 VAL 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 857 LEU Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 913 GLU 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 1219 ASP 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 F residue 11 SER Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 163 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 321 MET Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain F residue 407 LEU 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 754 LEU Chi-restraints excluded: chain F residue 811 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 81 optimal weight: 5.9990 chunk 366 optimal weight: 50.0000 chunk 157 optimal weight: 3.9990 chunk 327 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 215 optimal weight: 5.9990 chunk 384 optimal weight: 30.0000 chunk 144 optimal weight: 9.9990 chunk 338 optimal weight: 8.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 23 HIS ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1017 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 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** ** 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 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 692 HIS F 745 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.215745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.129501 restraints weight = 53486.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.129995 restraints weight = 29913.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.129931 restraints weight = 19597.620| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 34156 Z= 0.212 Angle : 0.799 14.592 46363 Z= 0.396 Chirality : 0.046 0.290 5267 Planarity : 0.005 0.107 5930 Dihedral : 12.619 118.013 5143 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.01 % Favored : 91.97 % Rotamer: Outliers : 4.88 % Allowed : 25.25 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 4132 helix: 0.60 (0.13), residues: 1527 sheet: -0.82 (0.24), residues: 506 loop : -1.63 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 115 HIS 0.017 0.001 HIS F 692 PHE 0.028 0.002 PHE F 572 TYR 0.034 0.002 TYR I1229 ARG 0.024 0.001 ARG J 312 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 1391) hydrogen bonds : angle 5.17309 ( 3878) metal coordination : bond 0.01401 ( 8) metal coordination : angle 6.13288 ( 12) covalent geometry : bond 0.00497 (34148) covalent geometry : angle 0.79278 (46351) *********************** 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 769 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 597 time to evaluate : 4.159 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: 0.8257 (mtmt) cc_final: 0.7955 (pttp) REVERT: G 86 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7749 (ttpp) REVERT: G 95 LYS cc_start: 0.8962 (mtmt) cc_final: 0.8550 (ptmm) REVERT: G 103 ASN cc_start: 0.8616 (m-40) cc_final: 0.8126 (t0) REVERT: G 152 TYR cc_start: 0.9038 (t80) cc_final: 0.8663 (t80) REVERT: G 178 SER cc_start: 0.9297 (t) cc_final: 0.8919 (m) REVERT: G 185 TYR cc_start: 0.9148 (p90) cc_final: 0.8827 (p90) REVERT: G 200 LYS cc_start: 0.8522 (ttmt) cc_final: 0.8096 (ttmm) REVERT: H 15 ASP cc_start: 0.7721 (m-30) cc_final: 0.7081 (m-30) REVERT: H 57 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8409 (p) REVERT: H 84 ASN cc_start: 0.9089 (m-40) cc_final: 0.8650 (t0) REVERT: H 125 LYS cc_start: 0.9286 (mptt) cc_final: 0.8710 (tttp) REVERT: H 142 MET cc_start: 0.9425 (tmm) cc_final: 0.8950 (tmm) REVERT: H 145 LYS cc_start: 0.9231 (tttt) cc_final: 0.8837 (ttpp) REVERT: H 152 TYR cc_start: 0.7875 (t80) cc_final: 0.7614 (t80) REVERT: H 174 ASP cc_start: 0.9296 (OUTLIER) cc_final: 0.8830 (m-30) REVERT: H 181 GLU cc_start: 0.8518 (tp30) cc_final: 0.7865 (tp30) REVERT: H 186 ASN cc_start: 0.7640 (OUTLIER) cc_final: 0.7372 (p0) REVERT: H 206 GLU cc_start: 0.8550 (tp30) cc_final: 0.8001 (mm-30) REVERT: H 212 ASP cc_start: 0.7954 (p0) cc_final: 0.7374 (p0) REVERT: I 32 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8482 (mm) REVERT: I 97 ARG cc_start: 0.8715 (mtt-85) cc_final: 0.7950 (ttm-80) REVERT: I 132 ASP cc_start: 0.8035 (m-30) cc_final: 0.7740 (t0) REVERT: I 158 ASP cc_start: 0.8429 (t0) cc_final: 0.7893 (t70) REVERT: I 160 ASP cc_start: 0.8762 (m-30) cc_final: 0.8136 (m-30) REVERT: I 185 ASP cc_start: 0.6946 (m-30) cc_final: 0.6657 (m-30) REVERT: I 191 LYS cc_start: 0.9320 (mmmm) cc_final: 0.8680 (tptp) REVERT: I 192 ASP cc_start: 0.8729 (m-30) cc_final: 0.8147 (m-30) REVERT: I 195 PHE cc_start: 0.6908 (m-80) cc_final: 0.6693 (t80) REVERT: I 219 GLN cc_start: 0.9589 (mt0) cc_final: 0.9234 (mt0) REVERT: I 239 MET cc_start: 0.8450 (tpt) cc_final: 0.7989 (tpt) REVERT: I 340 ASP cc_start: 0.9255 (m-30) cc_final: 0.8774 (p0) REVERT: I 346 TYR cc_start: 0.7611 (m-10) cc_final: 0.7103 (m-80) REVERT: I 359 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7663 (ttt-90) REVERT: I 370 MET cc_start: 0.8522 (mmt) cc_final: 0.7996 (mmm) REVERT: I 427 ASP cc_start: 0.9037 (m-30) cc_final: 0.8712 (t0) REVERT: I 431 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9047 (ttpt) REVERT: I 441 GLU cc_start: 0.8117 (tp30) cc_final: 0.7441 (mp0) REVERT: I 488 MET cc_start: 0.8576 (mmm) cc_final: 0.8248 (mmm) REVERT: I 549 ASP cc_start: 0.7975 (t0) cc_final: 0.7562 (m-30) REVERT: I 622 ASN cc_start: 0.8156 (t0) cc_final: 0.7789 (t0) REVERT: I 761 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7946 (mp10) REVERT: I 790 ASP cc_start: 0.7940 (t70) cc_final: 0.7515 (t0) REVERT: I 955 GLN cc_start: 0.9565 (tp-100) cc_final: 0.9324 (tp-100) REVERT: I 962 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8468 (tp30) REVERT: I 1025 PHE cc_start: 0.9273 (t80) cc_final: 0.9069 (t80) REVERT: I 1038 GLN cc_start: 0.9182 (pp30) cc_final: 0.8921 (pp30) REVERT: I 1085 MET cc_start: 0.8897 (mmm) cc_final: 0.8669 (mmt) REVERT: I 1177 ARG cc_start: 0.8687 (ptm160) cc_final: 0.8262 (ptm160) REVERT: I 1203 ASP cc_start: 0.8006 (t0) cc_final: 0.7644 (t0) REVERT: I 1216 ARG cc_start: 0.8561 (ptp-170) cc_final: 0.7647 (ptt90) REVERT: I 1229 TYR cc_start: 0.8933 (m-10) cc_final: 0.8680 (m-10) REVERT: I 1302 THR cc_start: 0.9168 (p) cc_final: 0.8900 (t) REVERT: I 1316 GLU cc_start: 0.8451 (tp30) cc_final: 0.7984 (tm-30) REVERT: J 62 PHE cc_start: 0.9029 (m-80) cc_final: 0.8692 (m-80) REVERT: J 99 ARG cc_start: 0.9376 (ttm110) cc_final: 0.9112 (mtm-85) REVERT: J 115 TRP cc_start: 0.8011 (m-10) cc_final: 0.7739 (m-10) REVERT: J 118 LYS cc_start: 0.9546 (mmmm) cc_final: 0.9293 (mmmm) REVERT: J 160 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7847 (tp) REVERT: J 189 LEU cc_start: 0.9551 (mm) cc_final: 0.9299 (mm) REVERT: J 281 ARG cc_start: 0.9424 (mmm160) cc_final: 0.9110 (mmm160) REVERT: J 296 LYS cc_start: 0.9552 (mttt) cc_final: 0.9289 (mtmt) REVERT: J 297 ARG cc_start: 0.9095 (ttp80) cc_final: 0.8448 (ttp80) REVERT: J 298 MET cc_start: 0.9080 (mmm) cc_final: 0.8042 (mmm) REVERT: J 301 GLU cc_start: 0.9333 (tm-30) cc_final: 0.8819 (pt0) REVERT: J 330 MET cc_start: 0.9158 (mmm) cc_final: 0.8668 (mpp) REVERT: J 457 TYR cc_start: 0.8099 (m-80) cc_final: 0.7877 (m-80) REVERT: J 500 ILE cc_start: 0.8584 (mt) cc_final: 0.8274 (tt) REVERT: J 508 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7808 (tp) REVERT: J 554 GLU cc_start: 0.8210 (pt0) cc_final: 0.7989 (pt0) REVERT: J 610 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7708 (ttp80) REVERT: J 697 MET cc_start: 0.8509 (ttp) cc_final: 0.7904 (ttp) REVERT: J 746 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7903 (pp) REVERT: J 818 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6934 (pm20) REVERT: J 960 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8564 (tt) REVERT: J 1189 MET cc_start: 0.8005 (mtt) cc_final: 0.7393 (tpp) REVERT: J 1243 LEU cc_start: 0.8958 (tp) cc_final: 0.8718 (tt) REVERT: K 26 ARG cc_start: 0.9028 (tpt170) cc_final: 0.8754 (tpm170) REVERT: K 30 MET cc_start: 0.7428 (tpp) cc_final: 0.7165 (tpp) REVERT: K 67 ARG cc_start: 0.9155 (mmp80) cc_final: 0.8819 (mmp80) REVERT: F 9 TRP cc_start: 0.8596 (m100) cc_final: 0.7829 (m100) REVERT: F 10 ILE cc_start: 0.8965 (pt) cc_final: 0.8651 (tp) REVERT: F 34 PHE cc_start: 0.8855 (m-80) cc_final: 0.8162 (m-10) REVERT: F 152 THR cc_start: 0.8872 (p) cc_final: 0.7918 (t) REVERT: F 159 LEU cc_start: 0.9296 (mt) cc_final: 0.9021 (pp) REVERT: F 175 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6637 (tp) REVERT: F 204 LEU cc_start: 0.9074 (mt) cc_final: 0.8839 (mt) REVERT: F 212 GLN cc_start: 0.9259 (pt0) cc_final: 0.8956 (pm20) REVERT: F 233 GLU cc_start: 0.9591 (mp0) cc_final: 0.9286 (mp0) REVERT: F 240 HIS cc_start: 0.8223 (OUTLIER) cc_final: 0.7902 (p90) REVERT: F 321 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7311 (ptp) REVERT: F 407 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8586 (mt) REVERT: F 444 TYR cc_start: 0.8116 (m-10) cc_final: 0.7705 (m-10) REVERT: F 472 ARG cc_start: 0.8840 (tpp-160) cc_final: 0.8597 (tpp-160) REVERT: F 561 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8915 (tp) REVERT: F 690 GLU cc_start: 0.9034 (tp30) cc_final: 0.8419 (mm-30) REVERT: F 765 ARG cc_start: 0.8983 (tpt170) cc_final: 0.8100 (tpt170) REVERT: F 766 GLU cc_start: 0.9453 (mm-30) cc_final: 0.9226 (mm-30) outliers start: 172 outliers final: 134 residues processed: 713 average time/residue: 0.4773 time to fit residues: 540.4671 Evaluate side-chains 735 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 583 time to evaluate : 3.732 ------------------------------------------------------------------------------- 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 98 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 205 MET 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 95 LYS Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 174 ASP 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 24 VAL Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 90 VAL 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 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 468 LEU Chi-restraints excluded: chain I residue 486 THR Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 547 VAL 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 666 SER 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 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 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 160 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 279 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 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 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 574 VAL 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 683 ILE 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 717 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 803 VAL 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 898 CYS Chi-restraints excluded: chain J residue 913 GLU 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 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 F residue 11 SER 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 157 HIS Chi-restraints excluded: chain F residue 163 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 276 LEU Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 321 MET Chi-restraints excluded: chain F residue 407 LEU 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 593 ARG Chi-restraints excluded: chain F residue 692 HIS Chi-restraints excluded: chain F residue 754 LEU 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 400 optimal weight: 40.0000 chunk 138 optimal weight: 0.9990 chunk 74 optimal weight: 0.3980 chunk 200 optimal weight: 0.0270 chunk 193 optimal weight: 8.9990 chunk 204 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 183 optimal weight: 5.9990 chunk 157 optimal weight: 0.6980 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 23 HIS ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 580 GLN ** I 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1017 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 364 HIS J 450 HIS J 910 ASN ** J1218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 745 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.220257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.133381 restraints weight = 53939.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.132589 restraints weight = 30886.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.134379 restraints weight = 23411.221| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34156 Z= 0.141 Angle : 0.795 14.486 46363 Z= 0.392 Chirality : 0.045 0.264 5267 Planarity : 0.005 0.088 5930 Dihedral : 12.532 115.756 5143 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.51 % Favored : 93.47 % Rotamer: Outliers : 4.00 % Allowed : 26.10 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.13), residues: 4132 helix: 0.54 (0.13), residues: 1543 sheet: -0.86 (0.24), residues: 495 loop : -1.59 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I1276 HIS 0.019 0.001 HIS F 692 PHE 0.034 0.002 PHE F 572 TYR 0.026 0.002 TYR I1229 ARG 0.014 0.001 ARG F 900 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 1391) hydrogen bonds : angle 5.07791 ( 3878) metal coordination : bond 0.00919 ( 8) metal coordination : angle 5.49552 ( 12) covalent geometry : bond 0.00318 (34148) covalent geometry : angle 0.79050 (46351) ********************** 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 773 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 632 time to evaluate : 4.202 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: G 25 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7873 (pttp) REVERT: G 51 MET cc_start: 0.8749 (mmm) cc_final: 0.8148 (mmm) REVERT: G 86 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7709 (ttpp) REVERT: G 95 LYS cc_start: 0.8965 (mtmt) cc_final: 0.8560 (ptmm) REVERT: G 103 ASN cc_start: 0.8597 (m-40) cc_final: 0.8096 (t0) REVERT: G 142 MET cc_start: 0.8119 (ptm) cc_final: 0.7864 (ptm) REVERT: G 152 TYR cc_start: 0.8989 (t80) cc_final: 0.8600 (t80) REVERT: G 185 TYR cc_start: 0.9075 (p90) cc_final: 0.8717 (p90) REVERT: G 200 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8155 (ttmm) REVERT: H 15 ASP cc_start: 0.7526 (m-30) cc_final: 0.6931 (m-30) REVERT: H 47 LEU cc_start: 0.8644 (mt) cc_final: 0.8048 (mt) REVERT: H 51 MET cc_start: 0.9170 (mmm) cc_final: 0.8681 (tpp) REVERT: H 57 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8155 (p) REVERT: H 84 ASN cc_start: 0.9018 (m-40) cc_final: 0.8307 (t0) REVERT: H 125 LYS cc_start: 0.9251 (mptt) cc_final: 0.8634 (tttp) REVERT: H 142 MET cc_start: 0.9436 (tmm) cc_final: 0.8979 (tmm) REVERT: H 145 LYS cc_start: 0.9206 (tttt) cc_final: 0.8741 (ttpp) REVERT: H 147 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8312 (mm-40) REVERT: H 174 ASP cc_start: 0.9295 (OUTLIER) cc_final: 0.8833 (m-30) REVERT: H 181 GLU cc_start: 0.8504 (tp30) cc_final: 0.7846 (tp30) REVERT: H 186 ASN cc_start: 0.7717 (OUTLIER) cc_final: 0.7209 (p0) REVERT: H 206 GLU cc_start: 0.8482 (tp30) cc_final: 0.7907 (tp30) REVERT: H 212 ASP cc_start: 0.7813 (p0) cc_final: 0.7194 (p0) REVERT: I 32 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8443 (mm) REVERT: I 97 ARG cc_start: 0.8619 (mtt-85) cc_final: 0.7885 (ttm-80) REVERT: I 132 ASP cc_start: 0.7938 (m-30) cc_final: 0.7729 (t0) REVERT: I 158 ASP cc_start: 0.8322 (t0) cc_final: 0.7831 (t0) REVERT: I 160 ASP cc_start: 0.8848 (m-30) cc_final: 0.8248 (m-30) REVERT: I 185 ASP cc_start: 0.6639 (m-30) cc_final: 0.6344 (m-30) REVERT: I 191 LYS cc_start: 0.9307 (mmmm) cc_final: 0.8645 (tptp) REVERT: I 192 ASP cc_start: 0.8625 (m-30) cc_final: 0.8024 (m-30) REVERT: I 239 MET cc_start: 0.8712 (tpt) cc_final: 0.8265 (tpt) REVERT: I 340 ASP cc_start: 0.9327 (m-30) cc_final: 0.8866 (p0) REVERT: I 346 TYR cc_start: 0.7486 (m-10) cc_final: 0.6955 (m-80) REVERT: I 359 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7628 (ttt-90) REVERT: I 370 MET cc_start: 0.8381 (mmt) cc_final: 0.8092 (mmm) REVERT: I 427 ASP cc_start: 0.9021 (m-30) cc_final: 0.8617 (t0) REVERT: I 431 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9045 (ttpt) REVERT: I 441 GLU cc_start: 0.8043 (tp30) cc_final: 0.7392 (mp0) REVERT: I 488 MET cc_start: 0.8600 (mmm) cc_final: 0.8217 (mmm) REVERT: I 515 MET cc_start: 0.7779 (mtp) cc_final: 0.7417 (mtp) REVERT: I 549 ASP cc_start: 0.7841 (t0) cc_final: 0.7473 (m-30) REVERT: I 551 HIS cc_start: 0.8870 (t-90) cc_final: 0.8587 (t-90) REVERT: I 622 ASN cc_start: 0.8140 (t0) cc_final: 0.7740 (t0) REVERT: I 639 LYS cc_start: 0.8404 (mtmm) cc_final: 0.7921 (mttm) REVERT: I 687 ARG cc_start: 0.7962 (ttp-110) cc_final: 0.7694 (mtp85) REVERT: I 704 MET cc_start: 0.7099 (mmm) cc_final: 0.6355 (tpp) REVERT: I 761 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7802 (mp10) REVERT: I 790 ASP cc_start: 0.7769 (t70) cc_final: 0.7330 (t0) REVERT: I 955 GLN cc_start: 0.9590 (tp-100) cc_final: 0.9361 (tp-100) REVERT: I 960 LEU cc_start: 0.9254 (mm) cc_final: 0.8039 (tp) REVERT: I 962 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8478 (tp30) REVERT: I 1025 PHE cc_start: 0.9325 (t80) cc_final: 0.8943 (t80) REVERT: I 1085 MET cc_start: 0.8768 (mmm) cc_final: 0.8343 (mmp) REVERT: I 1149 TYR cc_start: 0.7753 (m-80) cc_final: 0.7377 (m-80) REVERT: I 1177 ARG cc_start: 0.8620 (ptm160) cc_final: 0.8165 (ptm160) REVERT: I 1203 ASP cc_start: 0.7843 (t0) cc_final: 0.7480 (t0) REVERT: I 1216 ARG cc_start: 0.8500 (ptp-170) cc_final: 0.7560 (ptt90) REVERT: I 1229 TYR cc_start: 0.8618 (m-10) cc_final: 0.8124 (m-10) REVERT: I 1279 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7297 (mt-10) REVERT: I 1302 THR cc_start: 0.9155 (p) cc_final: 0.8950 (t) REVERT: I 1316 GLU cc_start: 0.8405 (tp30) cc_final: 0.7984 (tm-30) REVERT: J 62 PHE cc_start: 0.9008 (m-80) cc_final: 0.8664 (m-80) REVERT: J 99 ARG cc_start: 0.9384 (ttm110) cc_final: 0.9095 (mtm-85) REVERT: J 115 TRP cc_start: 0.7915 (m-10) cc_final: 0.7446 (m-10) REVERT: J 118 LYS cc_start: 0.9573 (mmmm) cc_final: 0.9285 (mmmm) REVERT: J 160 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7810 (tp) REVERT: J 189 LEU cc_start: 0.9574 (mm) cc_final: 0.9323 (mm) REVERT: J 222 LYS cc_start: 0.9338 (ptpp) cc_final: 0.8897 (mmtp) REVERT: J 281 ARG cc_start: 0.9416 (mmm160) cc_final: 0.9101 (mmm160) REVERT: J 296 LYS cc_start: 0.9545 (mttt) cc_final: 0.9292 (mtmt) REVERT: J 297 ARG cc_start: 0.9129 (ttp80) cc_final: 0.8417 (ttp80) REVERT: J 298 MET cc_start: 0.9081 (mmm) cc_final: 0.8081 (mmm) REVERT: J 301 GLU cc_start: 0.9278 (tm-30) cc_final: 0.8776 (pt0) REVERT: J 322 ARG cc_start: 0.9259 (pmt-80) cc_final: 0.8863 (tpp-160) REVERT: J 330 MET cc_start: 0.9127 (mmm) cc_final: 0.8641 (mpp) REVERT: J 418 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: J 457 TYR cc_start: 0.7940 (m-80) cc_final: 0.7709 (m-80) REVERT: J 508 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7547 (tp) REVERT: J 554 GLU cc_start: 0.8167 (pt0) cc_final: 0.7913 (pt0) REVERT: J 610 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7860 (ttp80) REVERT: J 697 MET cc_start: 0.8400 (ttp) cc_final: 0.7862 (ttp) REVERT: J 709 ARG cc_start: 0.9045 (ppt170) cc_final: 0.8845 (ttp80) REVERT: J 725 MET cc_start: 0.8438 (mtm) cc_final: 0.8236 (mtm) REVERT: J 746 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7705 (pp) REVERT: J 818 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6920 (pm20) REVERT: J 923 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7576 (tp) REVERT: J 960 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8598 (tt) REVERT: J 1189 MET cc_start: 0.7968 (mtt) cc_final: 0.7507 (tpp) REVERT: J 1243 LEU cc_start: 0.8914 (tp) cc_final: 0.8482 (mt) REVERT: J 1244 GLN cc_start: 0.7410 (tm-30) cc_final: 0.6968 (tm-30) REVERT: J 1305 ASP cc_start: 0.8393 (t0) cc_final: 0.7793 (p0) REVERT: K 11 GLU cc_start: 0.8959 (pp20) cc_final: 0.8720 (pm20) REVERT: K 26 ARG cc_start: 0.9043 (tpt170) cc_final: 0.8774 (tpm170) REVERT: K 30 MET cc_start: 0.7410 (tpp) cc_final: 0.7183 (tpp) REVERT: F 9 TRP cc_start: 0.8516 (m100) cc_final: 0.7698 (m100) REVERT: F 10 ILE cc_start: 0.8999 (pt) cc_final: 0.8695 (tp) REVERT: F 34 PHE cc_start: 0.8880 (m-80) cc_final: 0.8164 (m-10) REVERT: F 159 LEU cc_start: 0.9283 (mt) cc_final: 0.9033 (pp) REVERT: F 175 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6620 (tp) REVERT: F 204 LEU cc_start: 0.9079 (mt) cc_final: 0.8842 (mt) REVERT: F 212 GLN cc_start: 0.9158 (pt0) cc_final: 0.8916 (pm20) REVERT: F 233 GLU cc_start: 0.9595 (mp0) cc_final: 0.9372 (mp0) REVERT: F 240 HIS cc_start: 0.8227 (OUTLIER) cc_final: 0.7904 (p90) REVERT: F 407 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8557 (mt) REVERT: F 444 TYR cc_start: 0.8183 (m-10) cc_final: 0.7662 (m-80) REVERT: F 472 ARG cc_start: 0.8924 (tpp-160) cc_final: 0.8639 (tpp-160) REVERT: F 485 TRP cc_start: 0.7694 (p90) cc_final: 0.7355 (p90) REVERT: F 561 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8919 (tp) REVERT: F 621 LEU cc_start: 0.7653 (tp) cc_final: 0.6756 (pp) REVERT: F 690 GLU cc_start: 0.9017 (tp30) cc_final: 0.8436 (tp30) REVERT: F 766 GLU cc_start: 0.9467 (mm-30) cc_final: 0.9202 (mm-30) REVERT: F 888 LEU cc_start: 0.8955 (mt) cc_final: 0.8602 (pp) outliers start: 141 outliers final: 109 residues processed: 725 average time/residue: 0.4621 time to fit residues: 532.2661 Evaluate side-chains 713 residues out of total 3531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 585 time to evaluate : 3.765 ------------------------------------------------------------------------------- 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 124 VAL Chi-restraints excluded: chain G residue 205 MET 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 57 THR Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 174 ASP 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 I residue 32 LEU Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 81 ASP 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 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 493 ILE Chi-restraints excluded: chain I residue 547 VAL 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 667 LEU Chi-restraints excluded: chain I residue 690 VAL 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 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 1289 GLU 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 160 LEU Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 279 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 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 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 610 ARG 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 706 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 803 VAL 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 898 CYS Chi-restraints excluded: chain J residue 913 GLU 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 1019 ASN Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1123 ARG Chi-restraints excluded: chain J residue 1219 ASP 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 F residue 11 SER 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 163 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 276 LEU Chi-restraints excluded: chain F residue 407 LEU 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 593 ARG Chi-restraints excluded: chain F residue 754 LEU 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 90 optimal weight: 4.9990 chunk 290 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 219 optimal weight: 0.9980 chunk 226 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 140 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 322 optimal weight: 50.0000 chunk 84 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 23 HIS ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 GLN ** I 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS ** I1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 HIS ** J1218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN ** 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 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 GLN F 692 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.217685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.130336 restraints weight = 53602.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129697 restraints weight = 31456.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.132116 restraints weight = 20700.358| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34156 Z= 0.161 Angle : 0.802 14.090 46363 Z= 0.395 Chirality : 0.046 0.276 5267 Planarity : 0.005 0.086 5930 Dihedral : 12.434 107.350 5139 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.14 % Favored : 92.84 % Rotamer: Outliers : 4.28 % Allowed : 26.44 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 4132 helix: 0.57 (0.13), residues: 1544 sheet: -0.90 (0.23), residues: 513 loop : -1.57 (0.14), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 287 HIS 0.012 0.001 HIS I1244 PHE 0.058 0.002 PHE I 195 TYR 0.029 0.002 TYR I1229 ARG 0.013 0.001 ARG F 900 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 1391) hydrogen bonds : angle 5.07330 ( 3878) metal coordination : bond 0.01101 ( 8) metal coordination : angle 5.64019 ( 12) covalent geometry : bond 0.00375 (34148) covalent geometry : angle 0.79671 (46351) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15511.98 seconds wall clock time: 269 minutes 45.11 seconds (16185.11 seconds total)