Starting phenix.real_space_refine on Mon May 26 13:10:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ree_19084/05_2025/8ree_19084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ree_19084/05_2025/8ree_19084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ree_19084/05_2025/8ree_19084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ree_19084/05_2025/8ree_19084.map" model { file = "/net/cci-nas-00/data/ceres_data/8ree_19084/05_2025/8ree_19084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ree_19084/05_2025/8ree_19084.cif" } resolution = 3.8 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= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 103 5.49 5 Mg 1 5.21 5 S 96 5.16 5 C 17615 2.51 5 N 5066 2.21 5 O 5722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28605 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2365 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1735 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 10080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10080 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 619 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 22, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 338 Chain: "D" Number of atoms: 9654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 9654 Classifications: {'peptide': 1330} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 53, 'TRANS': 1276} Chain breaks: 5 Unresolved non-hydrogen bonds: 721 Unresolved non-hydrogen angles: 878 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 10, 'GLU:plan': 31, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 462 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "M" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2103 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 15, 'TRANS': 313} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 484 Unresolved non-hydrogen angles: 601 Unresolved non-hydrogen dihedrals: 387 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 19, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 280 Chain: "N" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 917 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain breaks: 1 Chain: "R" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 191 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna3p': 8} Chain: "T" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1011 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14675 SG CYS D 70 107.768 114.567 86.352 1.00 46.88 S ATOM 14804 SG CYS D 88 106.510 115.411 90.421 1.00 47.95 S ATOM 20917 SG CYS D 898 100.880 47.137 83.808 1.00 25.68 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 166 " occ=0.89 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.89 Time building chain proxies: 16.88, per 1000 atoms: 0.59 Number of scatterers: 28605 At special positions: 0 Unit cell: (141.504, 171.52, 167.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 96 16.00 P 103 15.00 Mg 1 11.99 O 5722 8.00 N 5066 7.00 C 17615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.40 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6706 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 44 sheets defined 39.3% alpha, 13.7% beta 42 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 10.80 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.780A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.588A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 263 through 274 removed outlier: 3.586A pdb=" N ASN A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.769A pdb=" N LEU A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.799A pdb=" N LEU A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 285 through 290' Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.532A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.789A pdb=" N GLY B 73 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.778A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.852A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.724A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.745A pdb=" N LYS C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 201 Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.640A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.671A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.698A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 379 through 389 Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.648A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 477 removed outlier: 4.049A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 481 Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.595A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 528 removed outlier: 3.718A pdb=" N SER C 522 " --> pdb=" O ASN C 518 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.789A pdb=" N LEU C 667 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.947A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 711 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 982 removed outlier: 3.637A pdb=" N LEU C 946 " --> pdb=" O ASP C 942 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.739A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1000 removed outlier: 3.835A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1009 Processing helix chain 'C' and resid 1009 through 1037 removed outlier: 3.563A pdb=" N ILE C1036 " --> pdb=" O LYS C1032 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C1037 " --> pdb=" O ARG C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1099 through 1101 No H-bonds generated for 'chain 'C' and resid 1099 through 1101' Processing helix chain 'C' and resid 1102 through 1107 removed outlier: 3.604A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 4.196A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.514A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1297 through 1311 removed outlier: 3.982A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.631A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.805A pdb=" N LYS D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 removed outlier: 3.541A pdb=" N ARG D 99 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.925A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.638A pdb=" N GLU D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 231 removed outlier: 4.274A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.603A pdb=" N ARG D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.863A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 599 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.586A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.213A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 738 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.732A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.621A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.784A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 914 through 925 Processing helix chain 'D' and resid 1140 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.608A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 3.906A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D1259 " --> pdb=" O VAL D1255 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1295 through 1299 removed outlier: 3.573A pdb=" N VAL D1298 " --> pdb=" O ASN D1295 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 removed outlier: 4.076A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D1315 " --> pdb=" O LYS D1311 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.768A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR D1333 " --> pdb=" O THR D1329 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 4.150A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1376 removed outlier: 4.085A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG D1371 " --> pdb=" O GLN D1367 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.634A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.663A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'M' and resid 123 through 131 removed outlier: 3.918A pdb=" N GLN M 127 " --> pdb=" O TYR M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 147 Processing helix chain 'M' and resid 157 through 166 Processing helix chain 'M' and resid 172 through 184 Processing helix chain 'M' and resid 194 through 205 removed outlier: 4.302A pdb=" N GLN M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 223 removed outlier: 3.676A pdb=" N ILE M 220 " --> pdb=" O ALA M 216 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 231 removed outlier: 3.916A pdb=" N HIS M 230 " --> pdb=" O LEU M 226 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP M 231 " --> pdb=" O LEU M 227 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 242 through 256 removed outlier: 4.089A pdb=" N LEU M 246 " --> pdb=" O LYS M 242 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU M 248 " --> pdb=" O GLU M 244 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN M 251 " --> pdb=" O LYS M 247 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU M 256 " --> pdb=" O LEU M 252 " (cutoff:3.500A) Processing helix chain 'M' and resid 290 through 294 removed outlier: 3.895A pdb=" N SER M 293 " --> pdb=" O ASN M 290 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU M 294 " --> pdb=" O SER M 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 290 through 294' Processing helix chain 'M' and resid 341 through 355 removed outlier: 3.501A pdb=" N PHE M 354 " --> pdb=" O GLN M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 374 Processing helix chain 'M' and resid 377 through 385 removed outlier: 3.576A pdb=" N ILE M 381 " --> pdb=" O HIS M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 417 through 430 Processing helix chain 'M' and resid 438 through 450 Processing helix chain 'M' and resid 457 through 466 removed outlier: 3.820A pdb=" N LEU M 465 " --> pdb=" O TYR M 461 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER M 466 " --> pdb=" O ARG M 462 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 8.562A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 105 removed outlier: 7.320A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.626A pdb=" N GLY A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 19 removed outlier: 3.530A pdb=" N GLU B 17 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LYS B 25 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N MET B 205 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 61 removed outlier: 5.584A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.937A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.549A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.968A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.603A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.603A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 98 " --> pdb=" O VAL C 122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB7, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.065A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.699A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.699A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 633 through 637 Processing sheet with id=AC3, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.651A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 723 through 727 removed outlier: 7.016A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 4.677A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1066 through 1067 Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.627A pdb=" N THR C 830 " --> pdb=" O ARG C1058 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL C 877 " --> pdb=" O GLY C 926 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.627A pdb=" N THR C 830 " --> pdb=" O ARG C1058 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1338 Processing sheet with id=AD5, first strand: chain 'D' and resid 104 through 111 removed outlier: 8.426A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.993A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 253 through 254 removed outlier: 3.684A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 523 through 527 removed outlier: 4.407A pdb=" N GLU D 523 " --> pdb=" O ARG D 547 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LYS D 549 " --> pdb=" O GLU D 523 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N MET D 525 " --> pdb=" O LYS D 549 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ARG D 551 " --> pdb=" O MET D 525 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'D' and resid 825 through 827 removed outlier: 7.044A pdb=" N GLU D 827 " --> pdb=" O VAL D 831 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL D 831 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.805A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 966 through 967 removed outlier: 3.517A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AE6, first strand: chain 'D' and resid 1059 through 1060 removed outlier: 3.690A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1174 through 1177 removed outlier: 5.006A pdb=" N VAL D1176 " --> pdb=" O GLU D1188 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU D1188 " --> pdb=" O VAL D1176 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1265 through 1266 1100 hydrogen bonds defined for protein. 3090 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 108 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 15.04 Time building geometry restraints manager: 8.60 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: 8966 1.34 - 1.46: 4229 1.46 - 1.58: 15657 1.58 - 1.70: 205 1.70 - 1.81: 167 Bond restraints: 29224 Sorted by residual: bond pdb=" CB PRO D1185 " pdb=" CG PRO D1185 " ideal model delta sigma weight residual 1.492 1.597 -0.105 5.00e-02 4.00e+02 4.43e+00 bond pdb=" CB PRO C1317 " pdb=" CG PRO C1317 " ideal model delta sigma weight residual 1.492 1.587 -0.095 5.00e-02 4.00e+02 3.59e+00 bond pdb=" CB PRO D 41 " pdb=" CG PRO D 41 " ideal model delta sigma weight residual 1.492 1.585 -0.093 5.00e-02 4.00e+02 3.49e+00 bond pdb=" CB PRO C 205 " pdb=" CG PRO C 205 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.35e+00 bond pdb=" CG PRO C1317 " pdb=" CD PRO C1317 " ideal model delta sigma weight residual 1.503 1.562 -0.059 3.40e-02 8.65e+02 2.99e+00 ... (remaining 29219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 39856 2.89 - 5.79: 250 5.79 - 8.68: 40 8.68 - 11.58: 5 11.58 - 14.47: 3 Bond angle restraints: 40154 Sorted by residual: angle pdb=" CA PRO D1185 " pdb=" N PRO D1185 " pdb=" CD PRO D1185 " ideal model delta sigma weight residual 112.00 103.48 8.52 1.40e+00 5.10e-01 3.71e+01 angle pdb=" C LEU M 277 " pdb=" N VAL M 278 " pdb=" CA VAL M 278 " ideal model delta sigma weight residual 121.97 131.72 -9.75 1.80e+00 3.09e-01 2.93e+01 angle pdb=" CA PRO C1317 " pdb=" N PRO C1317 " pdb=" CD PRO C1317 " ideal model delta sigma weight residual 112.00 105.49 6.51 1.40e+00 5.10e-01 2.16e+01 angle pdb=" CA PRO C 205 " pdb=" N PRO C 205 " pdb=" CD PRO C 205 " ideal model delta sigma weight residual 112.00 106.10 5.90 1.40e+00 5.10e-01 1.77e+01 angle pdb=" N ASP D 751 " pdb=" CA ASP D 751 " pdb=" C ASP D 751 " ideal model delta sigma weight residual 114.75 109.49 5.26 1.26e+00 6.30e-01 1.74e+01 ... (remaining 40149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 16515 34.83 - 69.65: 977 69.65 - 104.48: 55 104.48 - 139.31: 1 139.31 - 174.14: 3 Dihedral angle restraints: 17551 sinusoidal: 7160 harmonic: 10391 Sorted by residual: dihedral pdb=" CA LEU D1138 " pdb=" C LEU D1138 " pdb=" N PRO D1139 " pdb=" CA PRO D1139 " ideal model delta harmonic sigma weight residual 180.00 142.99 37.01 0 5.00e+00 4.00e-02 5.48e+01 dihedral pdb=" CA VAL M 278 " pdb=" C VAL M 278 " pdb=" N ARG M 279 " pdb=" CA ARG M 279 " ideal model delta harmonic sigma weight residual 180.00 150.80 29.20 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA ILE D 331 " pdb=" C ILE D 331 " pdb=" N LYS D 332 " pdb=" CA LYS D 332 " ideal model delta harmonic sigma weight residual 180.00 157.90 22.10 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 17548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3334 0.036 - 0.072: 1001 0.072 - 0.109: 371 0.109 - 0.145: 77 0.145 - 0.181: 5 Chirality restraints: 4788 Sorted by residual: chirality pdb=" CB VAL M 278 " pdb=" CA VAL M 278 " pdb=" CG1 VAL M 278 " pdb=" CG2 VAL M 278 " both_signs ideal model delta sigma weight residual False -2.63 -2.81 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CB ILE M 170 " pdb=" CA ILE M 170 " pdb=" CG1 ILE M 170 " pdb=" CG2 ILE M 170 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CG LEU B 133 " pdb=" CB LEU B 133 " pdb=" CD1 LEU B 133 " pdb=" CD2 LEU B 133 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 4785 not shown) Planarity restraints: 4906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 566 " 0.080 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO C 567 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO C 567 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO C 567 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D1184 " -0.081 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PRO D1185 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO D1185 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO D1185 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 204 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO C 205 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO C 205 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 205 " -0.059 5.00e-02 4.00e+02 ... (remaining 4903 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 172 2.53 - 3.12: 21462 3.12 - 3.71: 44955 3.71 - 4.31: 57724 4.31 - 4.90: 97826 Nonbonded interactions: 222139 Sorted by model distance: nonbonded pdb=" O3' C R 7 " pdb="MG MG D1501 " model vdw 1.936 2.170 nonbonded pdb=" O LEU D 71 " pdb="ZN ZN D1502 " model vdw 2.127 2.230 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.147 2.170 nonbonded pdb=" OD1 ASP C 354 " pdb=" OG1 THR C 356 " model vdw 2.153 3.040 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1501 " model vdw 2.157 2.170 ... (remaining 222134 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.150 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 81.260 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.100 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3640 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 : 0.003 0.105 29227 Z= 0.149 Angle : 0.644 14.474 40154 Z= 0.337 Chirality : 0.041 0.181 4788 Planarity : 0.005 0.124 4906 Dihedral : 19.576 174.137 10845 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.66 % Favored : 94.26 % Rotamer: Outliers : 0.38 % Allowed : 31.31 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.72 (0.14), residues: 3587 helix: 0.91 (0.15), residues: 1242 sheet: -0.26 (0.28), residues: 373 loop : -1.49 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 183 HIS 0.010 0.001 HIS D 651 PHE 0.020 0.001 PHE D 668 TYR 0.014 0.001 TYR C 73 ARG 0.013 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.18775 ( 1188) hydrogen bonds : angle 6.43340 ( 3306) metal coordination : bond 0.00202 ( 3) covalent geometry : bond 0.00348 (29224) covalent geometry : angle 0.64355 (40154) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 773 time to evaluate : 3.122 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: B 92 VAL cc_start: 0.5819 (m) cc_final: 0.5579 (t) REVERT: C 239 MET cc_start: 0.3754 (tpt) cc_final: 0.3442 (tpp) REVERT: C 622 ASN cc_start: 0.5435 (OUTLIER) cc_final: 0.5213 (m110) REVERT: C 693 LEU cc_start: 0.4849 (mt) cc_final: 0.4638 (mt) REVERT: C 1225 VAL cc_start: 0.5763 (t) cc_final: 0.5547 (t) outliers start: 10 outliers final: 0 residues processed: 777 average time/residue: 0.4830 time to fit residues: 567.9704 Evaluate side-chains 454 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 453 time to evaluate : 2.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 622 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 309 optimal weight: 0.3980 chunk 278 optimal weight: 9.9990 chunk 154 optimal weight: 50.0000 chunk 95 optimal weight: 6.9990 chunk 187 optimal weight: 0.1980 chunk 148 optimal weight: 9.9990 chunk 287 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 174 optimal weight: 8.9990 chunk 214 optimal weight: 5.9990 chunk 333 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 84 ASN A 268 ASN B 227 GLN C 517 GLN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN C 965 GLN C1237 HIS ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN D 335 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN D1197 ASN D1350 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.093217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.067037 restraints weight = 116376.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.069126 restraints weight = 56475.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.070497 restraints weight = 34661.172| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5713 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29227 Z= 0.160 Angle : 0.719 11.436 40154 Z= 0.367 Chirality : 0.044 0.315 4788 Planarity : 0.005 0.088 4906 Dihedral : 16.346 174.701 5050 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.74 % Favored : 94.17 % Rotamer: Outliers : 5.31 % Allowed : 29.59 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.66 (0.14), residues: 3587 helix: 0.87 (0.15), residues: 1276 sheet: -0.02 (0.28), residues: 366 loop : -1.47 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 33 HIS 0.009 0.001 HIS D 469 PHE 0.022 0.002 PHE C 57 TYR 0.041 0.002 TYR C 62 ARG 0.007 0.001 ARG C 54 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 1188) hydrogen bonds : angle 4.86084 ( 3306) metal coordination : bond 0.00121 ( 3) covalent geometry : bond 0.00342 (29224) covalent geometry : angle 0.71852 (40154) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 498 time to evaluate : 2.896 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: A 51 MET cc_start: 0.6609 (mmm) cc_final: 0.6009 (mmm) REVERT: A 77 ASP cc_start: 0.5771 (OUTLIER) cc_final: 0.5176 (t0) REVERT: A 122 GLU cc_start: 0.6770 (pm20) cc_final: 0.6508 (pm20) REVERT: A 316 MET cc_start: 0.2743 (mmm) cc_final: 0.1903 (mmm) REVERT: B 92 VAL cc_start: 0.6582 (m) cc_final: 0.6151 (t) REVERT: B 118 ASP cc_start: 0.7278 (t0) cc_final: 0.6917 (t0) REVERT: B 197 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7956 (p0) REVERT: C 31 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7864 (tp-100) REVERT: C 239 MET cc_start: 0.5891 (tpt) cc_final: 0.4825 (tpp) REVERT: C 456 VAL cc_start: 0.7039 (OUTLIER) cc_final: 0.6731 (p) REVERT: C 685 MET cc_start: 0.6631 (mmt) cc_final: 0.6222 (mmm) REVERT: C 793 GLU cc_start: 0.6020 (tt0) cc_final: 0.5662 (tt0) REVERT: C 876 GLU cc_start: 0.3987 (pm20) cc_final: 0.3777 (pt0) REVERT: C 1066 MET cc_start: 0.7301 (mmm) cc_final: 0.6622 (mmm) REVERT: C 1098 LEU cc_start: 0.4543 (OUTLIER) cc_final: 0.4218 (mp) REVERT: C 1131 MET cc_start: 0.8294 (ptp) cc_final: 0.7933 (ptp) REVERT: C 1229 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.6672 (t80) REVERT: C 1235 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6546 (mp) REVERT: D 232 ASN cc_start: 0.3046 (m-40) cc_final: 0.2202 (t0) REVERT: D 452 LEU cc_start: 0.7126 (mt) cc_final: 0.6720 (mm) REVERT: D 652 GLU cc_start: 0.8143 (mp0) cc_final: 0.7843 (mp0) REVERT: D 747 MET cc_start: 0.6112 (mtm) cc_final: 0.5861 (mpp) REVERT: D 864 LEU cc_start: 0.7298 (tp) cc_final: 0.6985 (mt) REVERT: D 993 GLU cc_start: 0.0234 (mt-10) cc_final: -0.2379 (mt-10) REVERT: D 1260 MET cc_start: 0.6949 (tpp) cc_final: 0.6624 (tpp) REVERT: D 1340 LYS cc_start: 0.4852 (ptmm) cc_final: 0.4412 (ptmm) REVERT: E 59 ILE cc_start: 0.5150 (OUTLIER) cc_final: 0.4004 (mm) outliers start: 139 outliers final: 44 residues processed: 599 average time/residue: 0.3840 time to fit residues: 369.1774 Evaluate side-chains 474 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 422 time to evaluate : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1229 TYR Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1303 SER Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 357 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 262 optimal weight: 0.0670 chunk 102 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 276 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 321 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 274 optimal weight: 20.0000 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 2.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 186 ASN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS C1080 ASN D 229 GLN D 450 HIS ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN D 489 ASN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.092352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066229 restraints weight = 119166.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.068318 restraints weight = 58206.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.069687 restraints weight = 35900.737| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 29227 Z= 0.164 Angle : 0.707 13.516 40154 Z= 0.359 Chirality : 0.044 0.255 4788 Planarity : 0.005 0.081 4906 Dihedral : 16.312 175.583 5048 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.49 % Favored : 94.42 % Rotamer: Outliers : 4.77 % Allowed : 29.40 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.63 (0.14), residues: 3587 helix: 0.90 (0.15), residues: 1286 sheet: 0.11 (0.28), residues: 377 loop : -1.50 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 686 HIS 0.009 0.001 HIS D 113 PHE 0.021 0.002 PHE D 719 TYR 0.028 0.002 TYR C 756 ARG 0.016 0.001 ARG D1231 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 1188) hydrogen bonds : angle 4.63257 ( 3306) metal coordination : bond 0.00389 ( 3) covalent geometry : bond 0.00361 (29224) covalent geometry : angle 0.70683 (40154) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 465 time to evaluate : 3.074 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: A 39 LEU cc_start: 0.7622 (mt) cc_final: 0.7020 (mt) REVERT: A 77 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6271 (t0) REVERT: A 107 ILE cc_start: 0.7008 (OUTLIER) cc_final: 0.6074 (tp) REVERT: A 142 MET cc_start: 0.6057 (ttp) cc_final: 0.5807 (ttp) REVERT: A 176 CYS cc_start: 0.7702 (m) cc_final: 0.7495 (p) REVERT: A 316 MET cc_start: 0.2899 (mmm) cc_final: 0.2199 (mmm) REVERT: B 177 TYR cc_start: 0.7429 (m-80) cc_final: 0.7095 (m-80) REVERT: B 205 MET cc_start: 0.8013 (pmm) cc_final: 0.7735 (pmm) REVERT: C 239 MET cc_start: 0.6147 (tpt) cc_final: 0.4647 (tpp) REVERT: C 488 MET cc_start: 0.6131 (mtp) cc_final: 0.5565 (mtp) REVERT: C 592 ARG cc_start: 0.5896 (mtp85) cc_final: 0.5107 (mtp85) REVERT: C 611 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6157 (mt-10) REVERT: C 685 MET cc_start: 0.7303 (mmt) cc_final: 0.6956 (mmm) REVERT: C 741 MET cc_start: 0.8428 (mmm) cc_final: 0.8161 (mmm) REVERT: C 756 TYR cc_start: 0.3535 (m-80) cc_final: 0.3223 (m-80) REVERT: C 791 LEU cc_start: 0.7667 (mt) cc_final: 0.7368 (mt) REVERT: C 800 MET cc_start: 0.7704 (mmm) cc_final: 0.7284 (mmm) REVERT: C 921 PRO cc_start: 0.8511 (Cg_exo) cc_final: 0.8250 (Cg_endo) REVERT: C 1066 MET cc_start: 0.7536 (mmm) cc_final: 0.7052 (mmm) REVERT: C 1098 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.5684 (mp) REVERT: C 1235 LEU cc_start: 0.7690 (mp) cc_final: 0.7467 (mp) REVERT: C 1289 GLU cc_start: 0.6792 (tm-30) cc_final: 0.5975 (tm-30) REVERT: D 160 LEU cc_start: 0.5861 (OUTLIER) cc_final: 0.5581 (pp) REVERT: D 242 LEU cc_start: 0.7170 (tp) cc_final: 0.6823 (tp) REVERT: D 298 MET cc_start: 0.7997 (mtp) cc_final: 0.7481 (mmm) REVERT: D 352 ARG cc_start: 0.6961 (tpt170) cc_final: 0.5395 (ttm-80) REVERT: D 375 GLU cc_start: 0.7856 (tp30) cc_final: 0.7509 (tp30) REVERT: D 452 LEU cc_start: 0.7765 (mt) cc_final: 0.7364 (mm) REVERT: D 466 MET cc_start: 0.7329 (ttp) cc_final: 0.5746 (ttm) REVERT: D 513 MET cc_start: 0.7071 (ptm) cc_final: 0.6823 (ptm) REVERT: D 581 MET cc_start: 0.7516 (tpp) cc_final: 0.7145 (mmt) REVERT: D 643 ASP cc_start: 0.7893 (m-30) cc_final: 0.7124 (t0) REVERT: D 652 GLU cc_start: 0.8214 (mp0) cc_final: 0.7791 (mp0) REVERT: D 699 ASP cc_start: 0.8579 (m-30) cc_final: 0.8099 (t0) REVERT: D 724 MET cc_start: 0.6474 (OUTLIER) cc_final: 0.5875 (mpp) REVERT: D 960 LEU cc_start: 0.8714 (tt) cc_final: 0.8438 (mt) REVERT: D 993 GLU cc_start: 0.0703 (mt-10) cc_final: -0.0399 (mt-10) REVERT: D 1261 LEU cc_start: 0.8155 (mt) cc_final: 0.7951 (mt) REVERT: D 1340 LYS cc_start: 0.4959 (ptmm) cc_final: 0.4549 (ptmm) REVERT: E 17 PHE cc_start: 0.6358 (m-80) cc_final: 0.6122 (m-80) outliers start: 125 outliers final: 67 residues processed: 552 average time/residue: 0.3616 time to fit residues: 328.8591 Evaluate side-chains 485 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 412 time to evaluate : 2.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 841 ARG Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1182 ILE Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1278 LEU Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1304 MET Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1303 SER Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1352 ILE Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 357 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 126 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 204 optimal weight: 30.0000 chunk 26 optimal weight: 50.0000 chunk 219 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 364 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 139 optimal weight: 30.0000 chunk 245 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 37 HIS A 41 ASN A 186 ASN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN C 832 HIS ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN D 232 ASN D 276 ASN D 419 HIS ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 127 GLN M 262 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.089511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.063044 restraints weight = 128289.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.065054 restraints weight = 64489.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.066367 restraints weight = 40936.915| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.8984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.179 29227 Z= 0.282 Angle : 0.909 13.860 40154 Z= 0.477 Chirality : 0.050 0.398 4788 Planarity : 0.008 0.109 4906 Dihedral : 16.626 177.390 5048 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.28 % Favored : 92.64 % Rotamer: Outliers : 7.48 % Allowed : 27.80 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: 3587 helix: 0.12 (0.14), residues: 1287 sheet: -0.24 (0.27), residues: 360 loop : -1.80 (0.13), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 33 HIS 0.014 0.002 HIS D1252 PHE 0.047 0.004 PHE C 934 TYR 0.057 0.003 TYR D 795 ARG 0.034 0.002 ARG D 799 Details of bonding type rmsd hydrogen bonds : bond 0.05068 ( 1188) hydrogen bonds : angle 5.20404 ( 3306) metal coordination : bond 0.02615 ( 3) covalent geometry : bond 0.00635 (29224) covalent geometry : angle 0.90891 (40154) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 462 time to evaluate : 3.043 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: A 61 ILE cc_start: 0.8514 (tp) cc_final: 0.8298 (tp) REVERT: A 205 MET cc_start: 0.8650 (tmm) cc_final: 0.8103 (tmm) REVERT: A 316 MET cc_start: 0.4112 (mmm) cc_final: 0.3226 (mtt) REVERT: A 320 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.7226 (m-40) REVERT: B 18 GLN cc_start: 0.8063 (pm20) cc_final: 0.7170 (tm-30) REVERT: B 26 VAL cc_start: 0.9432 (t) cc_final: 0.9203 (p) REVERT: B 51 MET cc_start: 0.7378 (tpp) cc_final: 0.6982 (tpp) REVERT: B 177 TYR cc_start: 0.8473 (m-80) cc_final: 0.7846 (m-80) REVERT: C 7 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7690 (pt0) REVERT: C 130 MET cc_start: 0.7692 (ttp) cc_final: 0.7384 (ttp) REVERT: C 144 VAL cc_start: 0.7947 (p) cc_final: 0.7662 (m) REVERT: C 488 MET cc_start: 0.6033 (mtp) cc_final: 0.5400 (mtt) REVERT: C 492 MET cc_start: 0.8799 (tpp) cc_final: 0.8578 (tpp) REVERT: C 513 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8107 (mp10) REVERT: C 522 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.8623 (p) REVERT: C 605 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.6963 (t80) REVERT: C 672 GLU cc_start: 0.8759 (pm20) cc_final: 0.8446 (pm20) REVERT: C 791 LEU cc_start: 0.9186 (mt) cc_final: 0.8946 (mt) REVERT: C 800 MET cc_start: 0.8703 (mmm) cc_final: 0.8374 (mmm) REVERT: C 815 SER cc_start: 0.9443 (m) cc_final: 0.9165 (p) REVERT: C 866 ASP cc_start: 0.4686 (OUTLIER) cc_final: 0.4330 (p0) REVERT: C 921 PRO cc_start: 0.9036 (Cg_exo) cc_final: 0.8810 (Cg_endo) REVERT: C 1107 MET cc_start: 0.8798 (mpp) cc_final: 0.8492 (mpp) REVERT: C 1176 LEU cc_start: 0.9152 (mp) cc_final: 0.8730 (tt) REVERT: C 1180 MET cc_start: 0.9281 (tpp) cc_final: 0.9053 (tpt) REVERT: C 1265 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8313 (t80) REVERT: C 1273 MET cc_start: 0.5420 (ptm) cc_final: 0.4883 (mmm) REVERT: C 1289 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7823 (tm-30) REVERT: C 1319 MET cc_start: 0.7505 (ttp) cc_final: 0.7237 (ttp) REVERT: C 1329 GLU cc_start: 0.8217 (tt0) cc_final: 0.7737 (tt0) REVERT: C 1330 ILE cc_start: 0.8673 (mt) cc_final: 0.8461 (mt) REVERT: D 102 MET cc_start: 0.2062 (mmt) cc_final: 0.1825 (mmt) REVERT: D 130 MET cc_start: 0.3793 (mpp) cc_final: 0.3470 (mpp) REVERT: D 298 MET cc_start: 0.8568 (mtp) cc_final: 0.8303 (mmm) REVERT: D 330 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6227 (ptm) REVERT: D 377 PHE cc_start: 0.9002 (m-80) cc_final: 0.8460 (m-80) REVERT: D 384 LYS cc_start: 0.7717 (mttt) cc_final: 0.7383 (mmmm) REVERT: D 390 LEU cc_start: 0.8946 (tp) cc_final: 0.8598 (mm) REVERT: D 454 CYS cc_start: 0.8842 (m) cc_final: 0.8485 (m) REVERT: D 466 MET cc_start: 0.8366 (ttp) cc_final: 0.7492 (ttm) REVERT: D 603 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8884 (mmmm) REVERT: D 604 MET cc_start: 0.9136 (tmm) cc_final: 0.8863 (ppp) REVERT: D 698 MET cc_start: 0.9492 (mmm) cc_final: 0.9227 (mpp) REVERT: D 724 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8048 (mtm) REVERT: D 743 MET cc_start: 0.8720 (tmm) cc_final: 0.8250 (tmm) REVERT: D 747 MET cc_start: 0.6061 (OUTLIER) cc_final: 0.5793 (mpp) REVERT: D 822 MET cc_start: 0.8651 (mmm) cc_final: 0.8074 (mmm) REVERT: D 1344 LEU cc_start: 0.8573 (mp) cc_final: 0.8329 (mp) REVERT: D 1361 THR cc_start: 0.9017 (t) cc_final: 0.8231 (t) REVERT: E 8 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.7951 (m-30) REVERT: E 17 PHE cc_start: 0.7940 (m-80) cc_final: 0.7519 (m-80) REVERT: E 41 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: E 59 ILE cc_start: 0.6537 (OUTLIER) cc_final: 0.6203 (tp) REVERT: M 158 ILE cc_start: 0.5336 (OUTLIER) cc_final: 0.4738 (tt) outliers start: 196 outliers final: 81 residues processed: 607 average time/residue: 0.3563 time to fit residues: 358.0950 Evaluate side-chains 471 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 375 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 605 TYR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1182 ILE Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1259 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 765 GLU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1253 ILE Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1303 SER Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1352 ILE Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 406 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 346 optimal weight: 40.0000 chunk 148 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 187 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 249 optimal weight: 6.9990 chunk 107 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 365 optimal weight: 10.0000 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN C 824 GLN C 832 HIS ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 HIS ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 GLN ** M 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.089600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.063038 restraints weight = 125114.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.065065 restraints weight = 62153.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.066384 restraints weight = 39195.428| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.9493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29227 Z= 0.144 Angle : 0.695 12.750 40154 Z= 0.353 Chirality : 0.044 0.240 4788 Planarity : 0.005 0.062 4906 Dihedral : 16.486 175.759 5048 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.13 % Favored : 94.79 % Rotamer: Outliers : 4.12 % Allowed : 31.84 % Favored : 64.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.96 (0.14), residues: 3587 helix: 0.61 (0.14), residues: 1278 sheet: -0.22 (0.26), residues: 386 loop : -1.64 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 236 HIS 0.009 0.001 HIS D1366 PHE 0.017 0.002 PHE C 390 TYR 0.030 0.002 TYR D1363 ARG 0.009 0.001 ARG B 33 Details of bonding type rmsd hydrogen bonds : bond 0.03576 ( 1188) hydrogen bonds : angle 4.63811 ( 3306) metal coordination : bond 0.00159 ( 3) covalent geometry : bond 0.00323 (29224) covalent geometry : angle 0.69520 (40154) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 406 time to evaluate : 2.898 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: A 61 ILE cc_start: 0.8966 (tp) cc_final: 0.7952 (pt) REVERT: A 316 MET cc_start: 0.4104 (mmm) cc_final: 0.3594 (mtt) REVERT: B 18 GLN cc_start: 0.8115 (pm20) cc_final: 0.7218 (tm-30) REVERT: B 26 VAL cc_start: 0.9511 (t) cc_final: 0.9300 (p) REVERT: B 177 TYR cc_start: 0.8368 (m-80) cc_final: 0.7831 (m-80) REVERT: C 40 GLU cc_start: 0.8553 (tp30) cc_final: 0.8195 (tp30) REVERT: C 130 MET cc_start: 0.7820 (ttp) cc_final: 0.7390 (ttp) REVERT: C 403 MET cc_start: 0.7206 (tmm) cc_final: 0.6793 (tmm) REVERT: C 488 MET cc_start: 0.6404 (OUTLIER) cc_final: 0.5909 (mtt) REVERT: C 492 MET cc_start: 0.8620 (tpp) cc_final: 0.8400 (tpp) REVERT: C 605 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.7130 (t80) REVERT: C 672 GLU cc_start: 0.8786 (pm20) cc_final: 0.8468 (pm20) REVERT: C 685 MET cc_start: 0.8867 (mmm) cc_final: 0.8612 (mmm) REVERT: C 791 LEU cc_start: 0.8965 (mt) cc_final: 0.8697 (mt) REVERT: C 800 MET cc_start: 0.8777 (mmm) cc_final: 0.8383 (mmm) REVERT: C 815 SER cc_start: 0.9340 (m) cc_final: 0.9106 (p) REVERT: C 828 PHE cc_start: 0.7915 (m-80) cc_final: 0.7542 (t80) REVERT: C 921 PRO cc_start: 0.9064 (Cg_exo) cc_final: 0.8838 (Cg_endo) REVERT: C 1107 MET cc_start: 0.8807 (mpp) cc_final: 0.8484 (mpp) REVERT: C 1243 MET cc_start: 0.8562 (tmm) cc_final: 0.7942 (tmm) REVERT: C 1273 MET cc_start: 0.5573 (ptm) cc_final: 0.4523 (mpp) REVERT: C 1297 ASP cc_start: 0.6441 (t0) cc_final: 0.6214 (m-30) REVERT: C 1304 MET cc_start: 0.8587 (mmm) cc_final: 0.8141 (mmm) REVERT: D 57 PHE cc_start: 0.7952 (m-80) cc_final: 0.7516 (m-80) REVERT: D 130 MET cc_start: 0.3234 (mpp) cc_final: 0.2645 (mpp) REVERT: D 229 GLN cc_start: 0.7844 (mm110) cc_final: 0.7499 (mm-40) REVERT: D 246 PRO cc_start: 0.6729 (Cg_exo) cc_final: 0.6363 (Cg_endo) REVERT: D 264 ASP cc_start: 0.8675 (m-30) cc_final: 0.8357 (t70) REVERT: D 298 MET cc_start: 0.8475 (mtp) cc_final: 0.8137 (mmp) REVERT: D 390 LEU cc_start: 0.8881 (tp) cc_final: 0.8613 (mm) REVERT: D 428 THR cc_start: 0.7755 (m) cc_final: 0.7412 (p) REVERT: D 644 MET cc_start: 0.8394 (mpp) cc_final: 0.7855 (mtm) REVERT: D 697 MET cc_start: 0.9286 (ppp) cc_final: 0.9070 (ppp) REVERT: D 724 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8032 (mpp) REVERT: D 743 MET cc_start: 0.8825 (tmm) cc_final: 0.8512 (tmm) REVERT: D 747 MET cc_start: 0.6129 (OUTLIER) cc_final: 0.5819 (mpp) REVERT: D 822 MET cc_start: 0.8603 (mmm) cc_final: 0.8122 (mmm) REVERT: D 1361 THR cc_start: 0.8937 (t) cc_final: 0.8352 (t) REVERT: E 7 GLN cc_start: 0.8530 (tp40) cc_final: 0.7968 (tp40) REVERT: E 8 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8053 (m-30) REVERT: E 17 PHE cc_start: 0.7986 (m-80) cc_final: 0.7579 (m-80) REVERT: E 59 ILE cc_start: 0.6858 (OUTLIER) cc_final: 0.6437 (tp) REVERT: M 278 VAL cc_start: 0.1612 (t) cc_final: 0.0566 (t) REVERT: M 280 LYS cc_start: 0.5866 (pptt) cc_final: 0.5346 (mttt) outliers start: 108 outliers final: 52 residues processed: 486 average time/residue: 0.3607 time to fit residues: 300.7607 Evaluate side-chains 417 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 359 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 605 TYR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1303 SER Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 60 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 201 optimal weight: 40.0000 chunk 15 optimal weight: 0.9980 chunk 324 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 229 optimal weight: 5.9990 chunk 359 optimal weight: 40.0000 chunk 233 optimal weight: 2.9990 chunk 45 optimal weight: 30.0000 chunk 184 optimal weight: 9.9990 chunk 294 optimal weight: 50.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 75 GLN A 132 HIS ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1299 ASN D 80 HIS D 232 ASN ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.087730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.060703 restraints weight = 127861.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.062653 restraints weight = 64690.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.063913 restraints weight = 41450.907| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 1.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 29227 Z= 0.191 Angle : 0.723 15.639 40154 Z= 0.372 Chirality : 0.045 0.299 4788 Planarity : 0.005 0.059 4906 Dihedral : 16.468 177.019 5048 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.72 % Favored : 93.23 % Rotamer: Outliers : 5.00 % Allowed : 31.46 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.93 (0.14), residues: 3587 helix: 0.64 (0.14), residues: 1299 sheet: -0.24 (0.27), residues: 378 loop : -1.65 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 183 HIS 0.005 0.001 HIS C 150 PHE 0.032 0.002 PHE C1270 TYR 0.029 0.002 TYR C1281 ARG 0.015 0.001 ARG C1269 Details of bonding type rmsd hydrogen bonds : bond 0.03892 ( 1188) hydrogen bonds : angle 4.61740 ( 3306) metal coordination : bond 0.00235 ( 3) covalent geometry : bond 0.00432 (29224) covalent geometry : angle 0.72313 (40154) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 363 time to evaluate : 2.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 SER cc_start: 0.6916 (OUTLIER) cc_final: 0.6647 (p) REVERT: A 199 ASP cc_start: 0.8565 (t0) cc_final: 0.8291 (t0) REVERT: A 316 MET cc_start: 0.4790 (mmm) cc_final: 0.3934 (mtt) REVERT: B 18 GLN cc_start: 0.8360 (pm20) cc_final: 0.7333 (tm-30) REVERT: B 51 MET cc_start: 0.8253 (mmm) cc_final: 0.7708 (mmm) REVERT: B 177 TYR cc_start: 0.8735 (m-80) cc_final: 0.8002 (m-80) REVERT: B 227 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8908 (tp-100) REVERT: C 40 GLU cc_start: 0.8841 (tp30) cc_final: 0.8602 (tp30) REVERT: C 55 SER cc_start: 0.7056 (OUTLIER) cc_final: 0.6800 (p) REVERT: C 142 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7577 (mm-30) REVERT: C 403 MET cc_start: 0.7417 (tmm) cc_final: 0.6976 (tmm) REVERT: C 431 LYS cc_start: 0.8878 (pttt) cc_final: 0.8673 (tmmt) REVERT: C 488 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6583 (mtt) REVERT: C 674 ASP cc_start: 0.8655 (p0) cc_final: 0.8401 (m-30) REVERT: C 685 MET cc_start: 0.8936 (mmm) cc_final: 0.8670 (mmm) REVERT: C 791 LEU cc_start: 0.9076 (mt) cc_final: 0.8812 (mt) REVERT: C 800 MET cc_start: 0.8810 (mmm) cc_final: 0.8347 (mmm) REVERT: C 815 SER cc_start: 0.9360 (m) cc_final: 0.9027 (p) REVERT: C 948 ILE cc_start: 0.8411 (pp) cc_final: 0.7762 (pp) REVERT: C 951 MET cc_start: 0.8992 (ptp) cc_final: 0.8782 (mpp) REVERT: C 1066 MET cc_start: 0.8718 (mmm) cc_final: 0.8418 (mmm) REVERT: C 1107 MET cc_start: 0.8990 (mpp) cc_final: 0.8614 (mpp) REVERT: C 1119 MET cc_start: 0.8822 (mmm) cc_final: 0.8389 (tpp) REVERT: C 1170 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8200 (tmm) REVERT: C 1243 MET cc_start: 0.8788 (tmm) cc_final: 0.8507 (tmm) REVERT: C 1246 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6545 (ttt180) REVERT: C 1273 MET cc_start: 0.6320 (ptm) cc_final: 0.5510 (mpp) REVERT: C 1274 GLU cc_start: 0.7841 (mp0) cc_final: 0.7633 (mp0) REVERT: C 1281 TYR cc_start: 0.7799 (m-80) cc_final: 0.7518 (m-80) REVERT: C 1297 ASP cc_start: 0.7216 (t0) cc_final: 0.6763 (m-30) REVERT: C 1304 MET cc_start: 0.9261 (mmm) cc_final: 0.8739 (tpp) REVERT: D 57 PHE cc_start: 0.8031 (m-80) cc_final: 0.7777 (m-10) REVERT: D 130 MET cc_start: 0.4193 (mpp) cc_final: 0.3189 (mpp) REVERT: D 211 GLU cc_start: 0.8781 (tp30) cc_final: 0.8384 (mt-10) REVERT: D 229 GLN cc_start: 0.8219 (mm110) cc_final: 0.7844 (mm110) REVERT: D 264 ASP cc_start: 0.8869 (m-30) cc_final: 0.8385 (t70) REVERT: D 298 MET cc_start: 0.8515 (mtp) cc_final: 0.8306 (mmp) REVERT: D 322 ARG cc_start: 0.7153 (ptp-170) cc_final: 0.6919 (mtt180) REVERT: D 390 LEU cc_start: 0.9128 (tp) cc_final: 0.8836 (mm) REVERT: D 428 THR cc_start: 0.8905 (m) cc_final: 0.8592 (p) REVERT: D 466 MET cc_start: 0.8629 (tpp) cc_final: 0.8270 (tpt) REVERT: D 485 MET cc_start: 0.9135 (mmt) cc_final: 0.8893 (mmm) REVERT: D 497 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8622 (mp0) REVERT: D 581 MET cc_start: 0.9268 (tpp) cc_final: 0.8965 (mmt) REVERT: D 603 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8948 (mmmm) REVERT: D 644 MET cc_start: 0.8388 (mpp) cc_final: 0.7778 (mtm) REVERT: D 724 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8356 (mtm) REVERT: D 747 MET cc_start: 0.6168 (mpp) cc_final: 0.5888 (mpp) REVERT: D 822 MET cc_start: 0.8739 (mmm) cc_final: 0.8187 (mmm) REVERT: D 993 GLU cc_start: 0.2860 (mt-10) cc_final: -0.0526 (mt-10) REVERT: D 1334 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: D 1347 LEU cc_start: 0.8968 (mt) cc_final: 0.8614 (mt) REVERT: D 1361 THR cc_start: 0.9166 (t) cc_final: 0.8731 (t) REVERT: E 7 GLN cc_start: 0.8693 (tp40) cc_final: 0.8019 (tp40) REVERT: E 8 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8274 (m-30) REVERT: E 17 PHE cc_start: 0.8447 (m-80) cc_final: 0.8070 (m-80) REVERT: E 42 GLU cc_start: 0.8690 (mp0) cc_final: 0.8437 (mp0) REVERT: E 59 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.6945 (tp) outliers start: 131 outliers final: 72 residues processed: 454 average time/residue: 0.3466 time to fit residues: 266.5825 Evaluate side-chains 414 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 332 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1246 ARG Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain C residue 1259 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1303 SER Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1352 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 287 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 145 optimal weight: 9.9990 chunk 282 optimal weight: 10.0000 chunk 229 optimal weight: 0.9980 chunk 284 optimal weight: 30.0000 chunk 46 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 chunk 198 optimal weight: 0.3980 chunk 213 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 chunk 191 optimal weight: 3.9990 chunk 94 optimal weight: 0.0020 overall best weight: 2.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN C 568 ASN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 276 ASN D 469 HIS ** M 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.087749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.060772 restraints weight = 127734.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.062745 restraints weight = 63880.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.064026 restraints weight = 40576.878| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 1.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29227 Z= 0.155 Angle : 0.673 10.693 40154 Z= 0.344 Chirality : 0.043 0.328 4788 Planarity : 0.005 0.063 4906 Dihedral : 16.425 175.956 5048 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.52 % Favored : 94.40 % Rotamer: Outliers : 3.86 % Allowed : 32.61 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.80 (0.14), residues: 3587 helix: 0.79 (0.15), residues: 1293 sheet: -0.17 (0.27), residues: 374 loop : -1.60 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 183 HIS 0.018 0.001 HIS D1366 PHE 0.014 0.001 PHE C 390 TYR 0.021 0.001 TYR C 179 ARG 0.008 0.001 ARG D1369 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 1188) hydrogen bonds : angle 4.41473 ( 3306) metal coordination : bond 0.00076 ( 3) covalent geometry : bond 0.00344 (29224) covalent geometry : angle 0.67300 (40154) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 351 time to evaluate : 3.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8931 (m-80) cc_final: 0.8655 (m-80) REVERT: A 95 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7964 (mtpp) REVERT: A 199 ASP cc_start: 0.8542 (t0) cc_final: 0.8238 (t0) REVERT: A 262 LEU cc_start: 0.4859 (OUTLIER) cc_final: 0.4542 (mm) REVERT: A 316 MET cc_start: 0.4936 (mmm) cc_final: 0.4202 (mtt) REVERT: B 13 LEU cc_start: 0.7361 (tt) cc_final: 0.6895 (mm) REVERT: B 51 MET cc_start: 0.8321 (mmm) cc_final: 0.7673 (mmm) REVERT: B 177 TYR cc_start: 0.8698 (m-80) cc_final: 0.8274 (m-80) REVERT: B 227 GLN cc_start: 0.9339 (mm-40) cc_final: 0.9069 (tp-100) REVERT: C 40 GLU cc_start: 0.8849 (tp30) cc_final: 0.8622 (tp30) REVERT: C 57 PHE cc_start: 0.6609 (m-80) cc_final: 0.5708 (m-80) REVERT: C 142 GLU cc_start: 0.8020 (mm-30) cc_final: 0.6996 (mm-30) REVERT: C 403 MET cc_start: 0.7551 (tmm) cc_final: 0.7033 (tmm) REVERT: C 431 LYS cc_start: 0.8901 (pttt) cc_final: 0.8697 (tmmt) REVERT: C 468 LEU cc_start: 0.8490 (mt) cc_final: 0.8085 (mt) REVERT: C 488 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6762 (mtt) REVERT: C 685 MET cc_start: 0.9004 (mmm) cc_final: 0.8747 (mmm) REVERT: C 791 LEU cc_start: 0.9064 (mt) cc_final: 0.8797 (mt) REVERT: C 800 MET cc_start: 0.8826 (mmm) cc_final: 0.8406 (mmm) REVERT: C 815 SER cc_start: 0.9367 (m) cc_final: 0.9048 (p) REVERT: C 1066 MET cc_start: 0.8661 (mmm) cc_final: 0.8447 (mmm) REVERT: C 1098 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8924 (mm) REVERT: C 1119 MET cc_start: 0.8831 (mmm) cc_final: 0.8598 (tpp) REVERT: C 1170 MET cc_start: 0.8470 (tmm) cc_final: 0.8140 (tmm) REVERT: C 1273 MET cc_start: 0.6426 (ptm) cc_final: 0.5861 (mpp) REVERT: C 1297 ASP cc_start: 0.7357 (t0) cc_final: 0.6544 (m-30) REVERT: D 57 PHE cc_start: 0.8280 (m-80) cc_final: 0.8054 (m-80) REVERT: D 130 MET cc_start: 0.4413 (mpp) cc_final: 0.3908 (mpp) REVERT: D 201 LEU cc_start: 0.8249 (mt) cc_final: 0.7543 (tp) REVERT: D 211 GLU cc_start: 0.8854 (tp30) cc_final: 0.8425 (mt-10) REVERT: D 229 GLN cc_start: 0.8326 (mm110) cc_final: 0.7907 (mm-40) REVERT: D 264 ASP cc_start: 0.8946 (m-30) cc_final: 0.8578 (t70) REVERT: D 314 ARG cc_start: 0.6014 (pmt-80) cc_final: 0.5700 (ptm160) REVERT: D 322 ARG cc_start: 0.7011 (ptp-170) cc_final: 0.6695 (mtt180) REVERT: D 381 ILE cc_start: 0.9632 (mm) cc_final: 0.9425 (mt) REVERT: D 394 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7943 (pt) REVERT: D 428 THR cc_start: 0.9075 (m) cc_final: 0.8505 (p) REVERT: D 497 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8498 (mp0) REVERT: D 644 MET cc_start: 0.8458 (mpp) cc_final: 0.8101 (mtm) REVERT: D 724 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8385 (mtm) REVERT: D 725 MET cc_start: 0.9308 (tpp) cc_final: 0.8995 (mmm) REVERT: D 747 MET cc_start: 0.6062 (mpp) cc_final: 0.5749 (mpp) REVERT: D 822 MET cc_start: 0.8670 (mmm) cc_final: 0.8028 (mmm) REVERT: D 837 ASP cc_start: 0.8909 (t0) cc_final: 0.8677 (t70) REVERT: D 993 GLU cc_start: 0.3241 (mt-10) cc_final: 0.3031 (mt-10) REVERT: D 1334 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: D 1361 THR cc_start: 0.9163 (t) cc_final: 0.8727 (t) REVERT: E 7 GLN cc_start: 0.8680 (tp40) cc_final: 0.8170 (tp40) REVERT: E 8 ASP cc_start: 0.8735 (p0) cc_final: 0.8305 (m-30) REVERT: E 17 PHE cc_start: 0.8663 (m-80) cc_final: 0.8274 (m-80) REVERT: E 40 PRO cc_start: 0.8651 (Cg_exo) cc_final: 0.8361 (Cg_endo) REVERT: E 44 ASP cc_start: 0.7746 (p0) cc_final: 0.7476 (p0) outliers start: 101 outliers final: 63 residues processed: 422 average time/residue: 0.3442 time to fit residues: 245.3364 Evaluate side-chains 390 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 320 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain C residue 1259 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1303 SER Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1352 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 406 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 280 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 176 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 299 optimal weight: 50.0000 chunk 38 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 chunk 329 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 75 GLN C 462 ASN C 832 HIS ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS D 469 HIS ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN ** M 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.087154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.060254 restraints weight = 130565.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.062139 restraints weight = 66378.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.063364 restraints weight = 42798.680| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 1.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 29227 Z= 0.161 Angle : 0.692 13.850 40154 Z= 0.355 Chirality : 0.043 0.245 4788 Planarity : 0.005 0.058 4906 Dihedral : 16.439 177.326 5048 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.89 % Favored : 93.06 % Rotamer: Outliers : 3.40 % Allowed : 32.76 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.75 (0.14), residues: 3587 helix: 0.80 (0.15), residues: 1305 sheet: -0.15 (0.27), residues: 377 loop : -1.56 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 236 HIS 0.017 0.001 HIS D1366 PHE 0.023 0.002 PHE C 464 TYR 0.029 0.001 TYR C1281 ARG 0.009 0.001 ARG D 431 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 1188) hydrogen bonds : angle 4.42746 ( 3306) metal coordination : bond 0.00180 ( 3) covalent geometry : bond 0.00364 (29224) covalent geometry : angle 0.69239 (40154) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 335 time to evaluate : 3.063 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: A 95 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8025 (mtpp) REVERT: A 199 ASP cc_start: 0.8569 (t0) cc_final: 0.8327 (t0) REVERT: A 316 MET cc_start: 0.5222 (mmm) cc_final: 0.4444 (mtt) REVERT: B 13 LEU cc_start: 0.7247 (tt) cc_final: 0.6809 (mt) REVERT: B 51 MET cc_start: 0.8429 (mmm) cc_final: 0.7803 (tmm) REVERT: B 177 TYR cc_start: 0.8691 (m-80) cc_final: 0.8370 (m-80) REVERT: B 227 GLN cc_start: 0.9472 (mm-40) cc_final: 0.9267 (mm-40) REVERT: C 57 PHE cc_start: 0.6534 (m-80) cc_final: 0.5913 (m-80) REVERT: C 142 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7159 (mm-30) REVERT: C 239 MET cc_start: 0.4896 (OUTLIER) cc_final: 0.4138 (mmp) REVERT: C 403 MET cc_start: 0.7738 (tmm) cc_final: 0.7287 (tmm) REVERT: C 431 LYS cc_start: 0.8949 (pttt) cc_final: 0.8718 (tmmt) REVERT: C 468 LEU cc_start: 0.8613 (mt) cc_final: 0.8016 (mt) REVERT: C 488 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6885 (mtt) REVERT: C 492 MET cc_start: 0.8808 (tpp) cc_final: 0.8413 (tpp) REVERT: C 494 ASN cc_start: 0.7389 (t0) cc_final: 0.6934 (t0) REVERT: C 515 MET cc_start: 0.7260 (ptt) cc_final: 0.6633 (ptt) REVERT: C 791 LEU cc_start: 0.9154 (mt) cc_final: 0.8918 (mt) REVERT: C 800 MET cc_start: 0.8837 (mmm) cc_final: 0.8449 (mmm) REVERT: C 815 SER cc_start: 0.9258 (m) cc_final: 0.9056 (p) REVERT: C 872 TYR cc_start: 0.8098 (m-10) cc_final: 0.7649 (m-10) REVERT: C 1066 MET cc_start: 0.8613 (mmm) cc_final: 0.8251 (mmm) REVERT: C 1170 MET cc_start: 0.8453 (tmm) cc_final: 0.8152 (tmm) REVERT: C 1281 TYR cc_start: 0.8010 (m-80) cc_final: 0.7689 (m-80) REVERT: C 1297 ASP cc_start: 0.7790 (t0) cc_final: 0.7459 (t0) REVERT: C 1304 MET cc_start: 0.9448 (mmm) cc_final: 0.9224 (tpp) REVERT: C 1329 GLU cc_start: 0.8923 (tt0) cc_final: 0.8416 (tt0) REVERT: D 130 MET cc_start: 0.5388 (mpp) cc_final: 0.4763 (mpp) REVERT: D 201 LEU cc_start: 0.8353 (mt) cc_final: 0.7588 (tp) REVERT: D 229 GLN cc_start: 0.8442 (mm110) cc_final: 0.8044 (mm110) REVERT: D 322 ARG cc_start: 0.7204 (ptp-170) cc_final: 0.6966 (mtt180) REVERT: D 330 MET cc_start: 0.7900 (ppp) cc_final: 0.7222 (ppp) REVERT: D 428 THR cc_start: 0.9266 (m) cc_final: 0.8737 (p) REVERT: D 497 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8589 (mp0) REVERT: D 581 MET cc_start: 0.9367 (tpp) cc_final: 0.9154 (mmt) REVERT: D 644 MET cc_start: 0.8399 (mpp) cc_final: 0.8192 (mtm) REVERT: D 724 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8522 (mtm) REVERT: D 725 MET cc_start: 0.9271 (tpp) cc_final: 0.9059 (mmm) REVERT: D 747 MET cc_start: 0.6037 (mpp) cc_final: 0.5719 (mpp) REVERT: D 822 MET cc_start: 0.8749 (mmm) cc_final: 0.8304 (mmm) REVERT: D 1215 GLU cc_start: 0.6992 (tp30) cc_final: 0.6773 (tp30) REVERT: E 7 GLN cc_start: 0.8736 (tp40) cc_final: 0.7993 (tm-30) REVERT: E 8 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8266 (m-30) REVERT: E 40 PRO cc_start: 0.8742 (Cg_exo) cc_final: 0.8480 (Cg_endo) outliers start: 89 outliers final: 63 residues processed: 398 average time/residue: 0.3561 time to fit residues: 240.2839 Evaluate side-chains 380 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 312 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain C residue 1259 LEU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1303 SER Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain D residue 1352 ILE Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 406 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 305 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 236 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 144 optimal weight: 7.9990 chunk 130 optimal weight: 0.0370 chunk 318 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN C 462 ASN C 832 HIS ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.088201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.061206 restraints weight = 129727.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.063111 restraints weight = 65859.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.064335 restraints weight = 42495.419| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 1.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29227 Z= 0.126 Angle : 0.683 13.285 40154 Z= 0.342 Chirality : 0.042 0.188 4788 Planarity : 0.004 0.055 4906 Dihedral : 16.382 176.578 5048 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.46 % Favored : 94.48 % Rotamer: Outliers : 2.44 % Allowed : 34.33 % Favored : 63.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.61 (0.14), residues: 3587 helix: 0.93 (0.15), residues: 1298 sheet: 0.04 (0.28), residues: 366 loop : -1.49 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 285 HIS 0.007 0.001 HIS D1366 PHE 0.020 0.001 PHE C 157 TYR 0.023 0.001 TYR C1281 ARG 0.005 0.000 ARG M 284 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 1188) hydrogen bonds : angle 4.29727 ( 3306) metal coordination : bond 0.00097 ( 3) covalent geometry : bond 0.00282 (29224) covalent geometry : angle 0.68322 (40154) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 324 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASP cc_start: 0.8502 (t0) cc_final: 0.8241 (t0) REVERT: A 316 MET cc_start: 0.5429 (mmm) cc_final: 0.4747 (mtt) REVERT: B 13 LEU cc_start: 0.7228 (tt) cc_final: 0.6846 (mt) REVERT: B 51 MET cc_start: 0.8472 (mmm) cc_final: 0.7830 (tmm) REVERT: B 177 TYR cc_start: 0.8657 (m-80) cc_final: 0.8385 (m-80) REVERT: C 40 GLU cc_start: 0.8500 (tp30) cc_final: 0.8194 (tp30) REVERT: C 57 PHE cc_start: 0.6586 (m-80) cc_final: 0.6001 (m-80) REVERT: C 403 MET cc_start: 0.7812 (tmm) cc_final: 0.7319 (tmm) REVERT: C 431 LYS cc_start: 0.8941 (pttt) cc_final: 0.8727 (tmmt) REVERT: C 488 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6909 (mtt) REVERT: C 492 MET cc_start: 0.8747 (tpp) cc_final: 0.8194 (tpp) REVERT: C 494 ASN cc_start: 0.7248 (t0) cc_final: 0.6511 (m-40) REVERT: C 696 ASP cc_start: 0.6703 (t0) cc_final: 0.6463 (t0) REVERT: C 741 MET cc_start: 0.8486 (mmm) cc_final: 0.8244 (mmm) REVERT: C 791 LEU cc_start: 0.9090 (mt) cc_final: 0.8772 (mt) REVERT: C 800 MET cc_start: 0.8760 (mmm) cc_final: 0.8428 (mmm) REVERT: C 815 SER cc_start: 0.9250 (m) cc_final: 0.9023 (p) REVERT: C 1066 MET cc_start: 0.8629 (mmm) cc_final: 0.8415 (mmm) REVERT: C 1170 MET cc_start: 0.8430 (tmm) cc_final: 0.8129 (tmm) REVERT: C 1273 MET cc_start: 0.7520 (mpp) cc_final: 0.6953 (mpp) REVERT: C 1281 TYR cc_start: 0.7912 (m-80) cc_final: 0.7538 (m-80) REVERT: C 1297 ASP cc_start: 0.7829 (t0) cc_final: 0.7120 (t70) REVERT: C 1304 MET cc_start: 0.9383 (mmm) cc_final: 0.9003 (tpp) REVERT: C 1329 GLU cc_start: 0.8937 (tt0) cc_final: 0.8453 (tt0) REVERT: D 132 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8944 (pt) REVERT: D 201 LEU cc_start: 0.8375 (mt) cc_final: 0.7649 (tp) REVERT: D 229 GLN cc_start: 0.8429 (mm110) cc_final: 0.8052 (mm-40) REVERT: D 297 ARG cc_start: 0.8426 (mtt180) cc_final: 0.8048 (mtm110) REVERT: D 322 ARG cc_start: 0.6980 (ptp-170) cc_final: 0.6729 (mtt180) REVERT: D 330 MET cc_start: 0.7817 (ppp) cc_final: 0.7138 (ppp) REVERT: D 497 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8801 (mm-30) REVERT: D 581 MET cc_start: 0.9368 (tpp) cc_final: 0.8982 (mmt) REVERT: D 697 MET cc_start: 0.9392 (ppp) cc_final: 0.9124 (ppp) REVERT: D 724 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8509 (mtm) REVERT: D 725 MET cc_start: 0.9280 (tpp) cc_final: 0.9075 (mmm) REVERT: D 747 MET cc_start: 0.5907 (mpp) cc_final: 0.5624 (mpp) REVERT: D 822 MET cc_start: 0.8684 (mmm) cc_final: 0.8150 (mmm) REVERT: E 7 GLN cc_start: 0.8710 (tp40) cc_final: 0.8094 (tm-30) REVERT: E 8 ASP cc_start: 0.8706 (p0) cc_final: 0.8312 (m-30) REVERT: E 40 PRO cc_start: 0.8918 (Cg_exo) cc_final: 0.8667 (Cg_endo) REVERT: M 279 ARG cc_start: 0.6418 (tpp-160) cc_final: 0.3845 (mpt180) REVERT: M 280 LYS cc_start: 0.6366 (pptt) cc_final: 0.4915 (tptp) outliers start: 64 outliers final: 48 residues processed: 372 average time/residue: 0.3572 time to fit residues: 226.0135 Evaluate side-chains 355 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 304 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain C residue 1259 LEU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1303 SER Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 85 optimal weight: 10.0000 chunk 88 optimal weight: 30.0000 chunk 181 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 284 optimal weight: 40.0000 chunk 3 optimal weight: 20.0000 chunk 77 optimal weight: 30.0000 chunk 269 optimal weight: 0.3980 chunk 217 optimal weight: 0.9980 chunk 362 optimal weight: 10.0000 overall best weight: 6.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS C 462 ASN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 HIS ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 419 HIS ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 127 GLN ** M 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.083302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.056241 restraints weight = 126882.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.057922 restraints weight = 66190.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.058997 restraints weight = 43448.643| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 1.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 29227 Z= 0.248 Angle : 0.818 14.070 40154 Z= 0.420 Chirality : 0.048 0.290 4788 Planarity : 0.006 0.080 4906 Dihedral : 16.628 179.096 5048 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.78 % Favored : 92.14 % Rotamer: Outliers : 2.60 % Allowed : 34.56 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -1.07 (0.14), residues: 3587 helix: 0.45 (0.14), residues: 1293 sheet: -0.46 (0.26), residues: 405 loop : -1.63 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 33 HIS 0.007 0.001 HIS D1252 PHE 0.050 0.003 PHE C1270 TYR 0.028 0.002 TYR D 269 ARG 0.011 0.001 ARG D1258 Details of bonding type rmsd hydrogen bonds : bond 0.04745 ( 1188) hydrogen bonds : angle 4.82984 ( 3306) metal coordination : bond 0.00650 ( 3) covalent geometry : bond 0.00563 (29224) covalent geometry : angle 0.81772 (40154) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 275 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASP cc_start: 0.8651 (t0) cc_final: 0.8431 (t0) REVERT: A 316 MET cc_start: 0.5637 (mmm) cc_final: 0.4845 (mtt) REVERT: B 13 LEU cc_start: 0.7618 (tt) cc_final: 0.7342 (mt) REVERT: B 51 MET cc_start: 0.8586 (mmm) cc_final: 0.8056 (mmm) REVERT: B 205 MET cc_start: 0.9182 (ptp) cc_final: 0.8969 (ptp) REVERT: C 14 ASP cc_start: 0.8835 (t0) cc_final: 0.8601 (t0) REVERT: C 403 MET cc_start: 0.8285 (tmm) cc_final: 0.7903 (tmm) REVERT: C 407 ARG cc_start: 0.8753 (ttp-170) cc_final: 0.8486 (tpp80) REVERT: C 446 ASP cc_start: 0.8572 (m-30) cc_final: 0.8219 (t0) REVERT: C 488 MET cc_start: 0.7177 (mtp) cc_final: 0.6968 (mtt) REVERT: C 800 MET cc_start: 0.8807 (mmm) cc_final: 0.8463 (mmm) REVERT: C 815 SER cc_start: 0.9377 (m) cc_final: 0.9153 (p) REVERT: C 834 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8481 (tm-30) REVERT: C 838 CYS cc_start: 0.7590 (t) cc_final: 0.7153 (t) REVERT: C 951 MET cc_start: 0.8927 (ptp) cc_final: 0.8706 (mpp) REVERT: C 1066 MET cc_start: 0.8670 (mmm) cc_final: 0.7755 (mmm) REVERT: C 1243 MET cc_start: 0.9034 (tmm) cc_final: 0.8616 (tmm) REVERT: C 1304 MET cc_start: 0.9451 (mmm) cc_final: 0.9174 (tpp) REVERT: C 1305 TYR cc_start: 0.9216 (t80) cc_final: 0.8881 (t80) REVERT: C 1321 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8671 (tp30) REVERT: C 1329 GLU cc_start: 0.9146 (tt0) cc_final: 0.8583 (tt0) REVERT: D 29 MET cc_start: 0.8689 (ttt) cc_final: 0.8319 (tmm) REVERT: D 330 MET cc_start: 0.8547 (ppp) cc_final: 0.8049 (ppp) REVERT: D 497 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8669 (mp0) REVERT: D 581 MET cc_start: 0.9440 (tpp) cc_final: 0.9188 (mmt) REVERT: D 603 LYS cc_start: 0.9520 (OUTLIER) cc_final: 0.9211 (ttmm) REVERT: D 698 MET cc_start: 0.9462 (mmm) cc_final: 0.9146 (mmm) REVERT: D 724 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8684 (mtt) REVERT: E 7 GLN cc_start: 0.8770 (tp40) cc_final: 0.8232 (tm-30) REVERT: E 66 VAL cc_start: 0.9427 (t) cc_final: 0.9204 (m) REVERT: M 184 ARG cc_start: 0.7666 (mpt180) cc_final: 0.7325 (mmt-90) REVERT: M 280 LYS cc_start: 0.6642 (pptt) cc_final: 0.6321 (tttm) outliers start: 68 outliers final: 46 residues processed: 333 average time/residue: 0.3526 time to fit residues: 197.4019 Evaluate side-chains 290 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 242 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain C residue 1259 LEU Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain M residue 406 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 83 optimal weight: 40.0000 chunk 89 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 359 optimal weight: 40.0000 chunk 185 optimal weight: 0.9980 chunk 258 optimal weight: 10.0000 chunk 277 optimal weight: 0.9980 chunk 291 optimal weight: 30.0000 chunk 82 optimal weight: 3.9990 chunk 364 optimal weight: 10.0000 chunk 330 optimal weight: 40.0000 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS C 219 GLN C 462 ASN C 824 GLN C 832 HIS ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN M 127 GLN M 202 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.084239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.056480 restraints weight = 130344.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.058227 restraints weight = 67673.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.059354 restraints weight = 44651.866| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 1.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29227 Z= 0.184 Angle : 0.739 14.009 40154 Z= 0.380 Chirality : 0.045 0.220 4788 Planarity : 0.005 0.059 4906 Dihedral : 16.575 177.381 5048 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.02 % Favored : 93.92 % Rotamer: Outliers : 2.18 % Allowed : 35.40 % Favored : 62.43 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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 (0.14), residues: 3587 helix: 0.56 (0.15), residues: 1294 sheet: -0.60 (0.26), residues: 396 loop : -1.55 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 126 HIS 0.012 0.001 HIS A 23 PHE 0.043 0.002 PHE C 157 TYR 0.036 0.002 TYR C1281 ARG 0.006 0.001 ARG C1069 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 1188) hydrogen bonds : angle 4.64667 ( 3306) metal coordination : bond 0.00291 ( 3) covalent geometry : bond 0.00415 (29224) covalent geometry : angle 0.73925 (40154) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11679.21 seconds wall clock time: 203 minutes 37.28 seconds (12217.28 seconds total)