Starting phenix.real_space_refine on Mon Aug 25 13:25:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ree_19084/08_2025/8ree_19084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ree_19084/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ree_19084/08_2025/8ree_19084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ree_19084/08_2025/8ree_19084.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ree_19084/08_2025/8ree_19084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ree_19084/08_2025/8ree_19084.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'GLU:plan': 6, 'HIS:plan': 2, 'TYR:plan': 1, 'ASP:plan': 3, 'ARG:plan': 5} 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, 'GLU:plan': 22, 'ARG:plan': 18, 'HIS:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 15, 'PHE:plan': 5, 'TYR:plan': 3, 'TRP:plan': 1} 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, 'ASN:plan1': 6, 'TYR:plan': 4, 'ARG:plan': 19, 'PHE:plan': 10, 'ASP:plan': 18, 'GLU:plan': 31, 'HIS:plan': 1, 'TRP:plan': 2} 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: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 4} 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: {'ASN:plan1': 6, 'GLU:plan': 19, 'GLN:plan1': 10, 'ASP:plan': 11, 'ARG:plan': 13, 'TYR:plan': 2, 'PHE:plan': 4, 'HIS:plan': 2} 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: 6.87, per 1000 atoms: 0.24 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: 1.99 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 4.77 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: 11.00 Time building geometry restraints manager: 2.88 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 38.700 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.400 ------------------------------------------------------------------------------- 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 : 11.01 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.013 0.000 ARG E 69 TYR 0.014 0.001 TYR C 73 PHE 0.020 0.001 PHE D 668 TRP 0.005 0.001 TRP C 183 HIS 0.010 0.001 HIS D 651 Details of bonding type rmsd covalent geometry : bond 0.00348 (29224) covalent geometry : angle 0.64355 (40154) hydrogen bonds : bond 0.18775 ( 1188) hydrogen bonds : angle 6.43340 ( 3306) metal coordination : bond 0.00202 ( 3) *********************** 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 : 1.061 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: 0.2198 time to fit residues: 257.2402 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 : 1.097 ------------------------------------------------------------------------------- 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 197 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 40.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 C 517 GLN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN C 659 GLN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1237 HIS ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 300 GLN D 335 GLN D 450 HIS ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN D 489 ASN D 921 GLN D1350 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.091859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.065326 restraints weight = 118949.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.067391 restraints weight = 57775.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.068750 restraints weight = 35575.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.069613 restraints weight = 25819.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.070171 restraints weight = 21175.784| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 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 = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 29227 Z= 0.194 Angle : 0.751 11.852 40154 Z= 0.388 Chirality : 0.045 0.281 4788 Planarity : 0.006 0.081 4906 Dihedral : 16.363 174.862 5050 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.66 % Favored : 94.26 % Rotamer: Outliers : 5.46 % Allowed : 30.32 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.14), residues: 3587 helix: 0.84 (0.15), residues: 1282 sheet: -0.06 (0.28), residues: 363 loop : -1.47 (0.14), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1211 TYR 0.040 0.002 TYR C 62 PHE 0.024 0.002 PHE C 57 TRP 0.014 0.002 TRP D 33 HIS 0.013 0.002 HIS D 469 Details of bonding type rmsd covalent geometry : bond 0.00438 (29224) covalent geometry : angle 0.75129 (40154) hydrogen bonds : bond 0.04385 ( 1188) hydrogen bonds : angle 4.94440 ( 3306) metal coordination : bond 0.00197 ( 3) *********************** 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 644 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 501 time to evaluate : 1.059 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: A 35 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.8176 (t80) REVERT: A 77 ASP cc_start: 0.6150 (OUTLIER) cc_final: 0.5526 (t0) REVERT: A 316 MET cc_start: 0.2911 (mmm) cc_final: 0.2016 (mmm) REVERT: B 92 VAL cc_start: 0.6709 (m) cc_final: 0.6297 (t) REVERT: B 118 ASP cc_start: 0.7462 (t0) cc_final: 0.7103 (t0) REVERT: C 67 GLU cc_start: 0.7325 (tt0) cc_final: 0.6937 (mm-30) REVERT: C 239 MET cc_start: 0.5952 (tpt) cc_final: 0.4917 (tpp) REVERT: C 456 VAL cc_start: 0.7274 (OUTLIER) cc_final: 0.6967 (p) REVERT: C 681 MET cc_start: 0.6369 (mtt) cc_final: 0.6097 (mtm) REVERT: C 749 ASP cc_start: 0.4387 (OUTLIER) cc_final: 0.4158 (t0) REVERT: C 825 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7611 (mt-10) REVERT: C 876 GLU cc_start: 0.4683 (pm20) cc_final: 0.4426 (pt0) REVERT: C 1066 MET cc_start: 0.7705 (mmm) cc_final: 0.6976 (mmm) REVERT: C 1143 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8573 (pp20) REVERT: C 1229 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.6448 (t80) REVERT: C 1235 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6774 (mp) REVERT: C 1273 MET cc_start: 0.4425 (ptm) cc_final: 0.1958 (mpp) REVERT: C 1337 ILE cc_start: 0.8587 (mt) cc_final: 0.8314 (mt) REVERT: D 92 VAL cc_start: 0.2348 (OUTLIER) cc_final: 0.2087 (p) REVERT: D 128 LEU cc_start: 0.5420 (OUTLIER) cc_final: 0.4898 (mt) REVERT: D 229 GLN cc_start: 0.7119 (mm-40) cc_final: 0.6916 (mm-40) REVERT: D 232 ASN cc_start: 0.3607 (OUTLIER) cc_final: 0.2947 (t0) REVERT: D 268 LEU cc_start: 0.7760 (mm) cc_final: 0.7517 (mt) REVERT: D 352 ARG cc_start: 0.6258 (tpp80) cc_final: 0.4940 (ttm-80) REVERT: D 375 GLU cc_start: 0.7493 (tp30) cc_final: 0.7067 (tp30) REVERT: D 384 LYS cc_start: 0.6187 (OUTLIER) cc_final: 0.5866 (mttt) REVERT: D 452 LEU cc_start: 0.7631 (mt) cc_final: 0.7254 (mm) REVERT: D 466 MET cc_start: 0.7240 (mtm) cc_final: 0.6164 (ttp) REVERT: D 652 GLU cc_start: 0.8178 (mp0) cc_final: 0.7865 (mp0) REVERT: D 724 MET cc_start: 0.7154 (mtp) cc_final: 0.6782 (mpp) REVERT: D 982 LEU cc_start: 0.8556 (mt) cc_final: 0.8341 (pp) REVERT: D 993 GLU cc_start: 0.0428 (mt-10) cc_final: -0.2233 (mt-10) REVERT: D 1219 ASP cc_start: 0.8076 (m-30) cc_final: 0.6973 (p0) REVERT: D 1235 ASN cc_start: 0.8157 (m-40) cc_final: 0.7865 (m-40) REVERT: D 1253 ILE cc_start: 0.7357 (mt) cc_final: 0.7156 (mt) REVERT: D 1260 MET cc_start: 0.7260 (tpp) cc_final: 0.6921 (tpp) REVERT: D 1340 LYS cc_start: 0.5002 (ptmm) cc_final: 0.4535 (ptmm) REVERT: E 16 ARG cc_start: 0.7504 (tpp80) cc_final: 0.7258 (ttp80) REVERT: E 49 ILE cc_start: 0.5846 (mt) cc_final: 0.5618 (mt) REVERT: E 59 ILE cc_start: 0.5345 (OUTLIER) cc_final: 0.4097 (mm) outliers start: 143 outliers final: 47 residues processed: 602 average time/residue: 0.1644 time to fit residues: 159.7339 Evaluate side-chains 471 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 413 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE 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 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 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 135 THR Chi-restraints excluded: chain C residue 158 ASP 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 610 GLU Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 1097 VAL 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 92 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 384 LYS Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 392 THR 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 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 D residue 1352 ILE Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 292 ASP 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 234 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 218 optimal weight: 0.9990 chunk 224 optimal weight: 0.5980 chunk 320 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 50.0000 chunk 186 optimal weight: 20.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 C1080 ASN C1256 GLN D 232 ASN D 458 ASN ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.091505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.065226 restraints weight = 120267.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.067290 restraints weight = 58563.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.068646 restraints weight = 36156.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.069518 restraints weight = 26299.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.070021 restraints weight = 21571.638| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 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 = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6269 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 29227 Z= 0.158 Angle : 0.689 13.926 40154 Z= 0.352 Chirality : 0.043 0.186 4788 Planarity : 0.005 0.081 4906 Dihedral : 16.318 175.293 5048 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.60 % Favored : 94.31 % Rotamer: Outliers : 5.12 % Allowed : 30.28 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.14), residues: 3587 helix: 0.90 (0.15), residues: 1284 sheet: -0.06 (0.27), residues: 384 loop : -1.50 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 170 TYR 0.044 0.002 TYR C 105 PHE 0.020 0.002 PHE C 828 TRP 0.013 0.001 TRP D 33 HIS 0.007 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00351 (29224) covalent geometry : angle 0.68877 (40154) hydrogen bonds : bond 0.03883 ( 1188) hydrogen bonds : angle 4.67627 ( 3306) metal coordination : bond 0.00330 ( 3) *********************** 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 608 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 474 time to evaluate : 1.005 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: A 35 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8285 (t80) REVERT: A 51 MET cc_start: 0.7775 (mmp) cc_final: 0.7465 (mmm) REVERT: A 77 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6397 (t0) REVERT: A 142 MET cc_start: 0.6440 (ttp) cc_final: 0.5801 (ttp) REVERT: A 316 MET cc_start: 0.2947 (mmm) cc_final: 0.2294 (mmm) REVERT: B 205 MET cc_start: 0.8033 (pmm) cc_final: 0.7827 (pmm) REVERT: C 239 MET cc_start: 0.6243 (tpt) cc_final: 0.4796 (tpp) REVERT: C 488 MET cc_start: 0.6077 (mtp) cc_final: 0.5431 (mtt) REVERT: C 492 MET cc_start: 0.8046 (tpp) cc_final: 0.7748 (tpp) REVERT: C 548 ARG cc_start: 0.6915 (mpt-90) cc_final: 0.6713 (mpt-90) REVERT: C 611 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6247 (mt-10) REVERT: C 681 MET cc_start: 0.6829 (mtt) cc_final: 0.6611 (mtm) REVERT: C 685 MET cc_start: 0.7541 (mmt) cc_final: 0.7187 (mmm) REVERT: C 741 MET cc_start: 0.8316 (mmm) cc_final: 0.8106 (mmm) REVERT: C 749 ASP cc_start: 0.4397 (OUTLIER) cc_final: 0.4144 (t0) REVERT: C 791 LEU cc_start: 0.8066 (mt) cc_final: 0.7752 (mt) REVERT: C 800 MET cc_start: 0.7943 (mmm) cc_final: 0.7551 (mmm) REVERT: C 921 PRO cc_start: 0.8394 (Cg_exo) cc_final: 0.8102 (Cg_endo) REVERT: C 1066 MET cc_start: 0.7915 (mmm) cc_final: 0.7312 (mmm) REVERT: C 1131 MET cc_start: 0.8766 (ptp) cc_final: 0.8312 (ptp) REVERT: C 1184 THR cc_start: 0.6799 (p) cc_final: 0.6177 (p) REVERT: C 1289 GLU cc_start: 0.6999 (tm-30) cc_final: 0.6455 (tm-30) REVERT: C 1290 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.6753 (tpt) REVERT: D 57 PHE cc_start: 0.5638 (m-10) cc_final: 0.5258 (m-10) REVERT: D 160 LEU cc_start: 0.5929 (OUTLIER) cc_final: 0.5665 (pp) REVERT: D 229 GLN cc_start: 0.7077 (mm-40) cc_final: 0.6797 (mm-40) REVERT: D 233 LYS cc_start: 0.0909 (OUTLIER) cc_final: 0.0166 (ttpt) REVERT: D 242 LEU cc_start: 0.7350 (tp) cc_final: 0.7128 (tp) REVERT: D 268 LEU cc_start: 0.7664 (mm) cc_final: 0.7444 (mt) REVERT: D 298 MET cc_start: 0.8006 (mtp) cc_final: 0.7580 (mmm) REVERT: D 352 ARG cc_start: 0.6475 (tpp80) cc_final: 0.5753 (ttm-80) REVERT: D 384 LYS cc_start: 0.6726 (OUTLIER) cc_final: 0.6412 (mttt) REVERT: D 452 LEU cc_start: 0.8172 (mt) cc_final: 0.7909 (mm) REVERT: D 466 MET cc_start: 0.7650 (mtm) cc_final: 0.6765 (ttp) REVERT: D 581 MET cc_start: 0.7745 (tpp) cc_final: 0.7453 (mmt) REVERT: D 652 GLU cc_start: 0.8209 (mp0) cc_final: 0.7785 (mp0) REVERT: D 724 MET cc_start: 0.7424 (mtp) cc_final: 0.6877 (mpp) REVERT: D 960 LEU cc_start: 0.8668 (tt) cc_final: 0.8433 (mt) REVERT: D 993 GLU cc_start: 0.0345 (mt-10) cc_final: -0.0322 (mt-10) REVERT: D 995 TYR cc_start: 0.4657 (m-80) cc_final: 0.4432 (m-10) REVERT: D 1219 ASP cc_start: 0.8070 (m-30) cc_final: 0.7415 (m-30) REVERT: D 1220 ILE cc_start: 0.8255 (mt) cc_final: 0.7634 (mt) REVERT: D 1261 LEU cc_start: 0.8188 (mt) cc_final: 0.7970 (mt) REVERT: D 1340 LYS cc_start: 0.5043 (ptmm) cc_final: 0.4639 (ptmm) outliers start: 134 outliers final: 68 residues processed: 573 average time/residue: 0.1541 time to fit residues: 146.4577 Evaluate side-chains 490 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 414 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 43 LEU 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 102 LEU Chi-restraints excluded: chain A residue 173 VAL 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 4 SER Chi-restraints excluded: chain B residue 12 ARG 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 C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 82 VAL 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 573 ASN Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 841 ARG Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1206 THR 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 D residue 8 LEU 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 233 LYS Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 384 LYS Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 434 ILE 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 839 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1238 GLN Chi-restraints excluded: chain D residue 1249 ASN 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 E residue 8 ASP Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 60 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 282 optimal weight: 1.9990 chunk 68 optimal weight: 0.0870 chunk 176 optimal weight: 0.7980 chunk 252 optimal weight: 6.9990 chunk 232 optimal weight: 0.0670 chunk 278 optimal weight: 4.9990 chunk 291 optimal weight: 50.0000 chunk 194 optimal weight: 30.0000 chunk 286 optimal weight: 0.0050 chunk 33 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 overall best weight: 0.5912 ------------------------------------------------------------------------------- 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 B 227 GLN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS D 232 ASN ** D 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.092183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.066006 restraints weight = 120136.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.068097 restraints weight = 58200.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.069472 restraints weight = 35791.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.070341 restraints weight = 25993.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.070891 restraints weight = 21329.349| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.5486 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= 0.127 Angle : 0.665 11.814 40154 Z= 0.333 Chirality : 0.043 0.251 4788 Planarity : 0.005 0.084 4906 Dihedral : 16.293 175.529 5048 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.99 % Favored : 93.95 % Rotamer: Outliers : 4.70 % Allowed : 30.93 % Favored : 64.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.14), residues: 3587 helix: 0.94 (0.15), residues: 1291 sheet: -0.01 (0.27), residues: 374 loop : -1.44 (0.14), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 137 TYR 0.029 0.002 TYR D1365 PHE 0.032 0.002 PHE C 157 TRP 0.006 0.001 TRP D 33 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00281 (29224) covalent geometry : angle 0.66474 (40154) hydrogen bonds : bond 0.03465 ( 1188) hydrogen bonds : angle 4.47837 ( 3306) metal coordination : bond 0.00189 ( 3) *********************** 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 565 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 442 time to evaluate : 1.003 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: A 35 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8217 (t80) REVERT: A 51 MET cc_start: 0.7733 (mmp) cc_final: 0.7274 (mmm) REVERT: A 77 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6630 (t0) REVERT: A 205 MET cc_start: 0.8010 (tmm) cc_final: 0.7608 (tmm) REVERT: A 316 MET cc_start: 0.2842 (mmm) cc_final: 0.2252 (mmm) REVERT: B 82 LEU cc_start: 0.9286 (mt) cc_final: 0.9063 (mm) REVERT: B 205 MET cc_start: 0.7978 (pmm) cc_final: 0.7611 (pmm) REVERT: C 239 MET cc_start: 0.6250 (tpt) cc_final: 0.4873 (tpp) REVERT: C 488 MET cc_start: 0.5911 (mtp) cc_final: 0.5496 (mtp) REVERT: C 492 MET cc_start: 0.8099 (tpp) cc_final: 0.7770 (tpp) REVERT: C 611 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6354 (mt-10) REVERT: C 685 MET cc_start: 0.7570 (mmt) cc_final: 0.7345 (mmm) REVERT: C 741 MET cc_start: 0.8306 (mmm) cc_final: 0.7878 (mmt) REVERT: C 768 MET cc_start: 0.7619 (mmm) cc_final: 0.7419 (mmm) REVERT: C 790 ASP cc_start: 0.5127 (p0) cc_final: 0.4902 (p0) REVERT: C 800 MET cc_start: 0.8014 (mmm) cc_final: 0.7319 (mmm) REVERT: C 825 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7856 (mt-10) REVERT: C 921 PRO cc_start: 0.8434 (Cg_exo) cc_final: 0.8171 (Cg_endo) REVERT: C 1131 MET cc_start: 0.8999 (ptp) cc_final: 0.8524 (ptp) REVERT: C 1134 GLN cc_start: 0.9258 (mm-40) cc_final: 0.8932 (mp10) REVERT: C 1184 THR cc_start: 0.7012 (p) cc_final: 0.6742 (p) REVERT: C 1229 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.6348 (t80) REVERT: C 1289 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6819 (tm-30) REVERT: C 1294 LYS cc_start: 0.7820 (mttt) cc_final: 0.7588 (mttp) REVERT: D 229 GLN cc_start: 0.7247 (mm-40) cc_final: 0.6945 (mm-40) REVERT: D 242 LEU cc_start: 0.7352 (tp) cc_final: 0.7103 (tp) REVERT: D 268 LEU cc_start: 0.7766 (mm) cc_final: 0.7523 (mt) REVERT: D 298 MET cc_start: 0.7974 (mtp) cc_final: 0.7580 (mmm) REVERT: D 314 ARG cc_start: 0.4953 (pmt-80) cc_final: 0.4554 (pmt-80) REVERT: D 384 LYS cc_start: 0.6626 (OUTLIER) cc_final: 0.6138 (mttt) REVERT: D 452 LEU cc_start: 0.8298 (mt) cc_final: 0.8000 (mm) REVERT: D 466 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.6299 (ttm) REVERT: D 581 MET cc_start: 0.7782 (tpp) cc_final: 0.7378 (mmt) REVERT: D 604 MET cc_start: 0.8726 (ttp) cc_final: 0.8500 (tmm) REVERT: D 724 MET cc_start: 0.7383 (mtp) cc_final: 0.6838 (mpp) REVERT: D 960 LEU cc_start: 0.8794 (tt) cc_final: 0.8503 (mt) REVERT: D 1220 ILE cc_start: 0.8044 (mt) cc_final: 0.7705 (mt) REVERT: D 1260 MET cc_start: 0.7775 (mmm) cc_final: 0.7344 (tpt) REVERT: D 1261 LEU cc_start: 0.8169 (mt) cc_final: 0.7885 (mt) REVERT: D 1340 LYS cc_start: 0.5044 (ptmm) cc_final: 0.4599 (ptmm) REVERT: D 1370 MET cc_start: 0.8289 (tpp) cc_final: 0.7905 (ptp) REVERT: E 17 PHE cc_start: 0.6068 (m-80) cc_final: 0.5851 (m-80) REVERT: E 48 VAL cc_start: 0.7293 (OUTLIER) cc_final: 0.6959 (p) outliers start: 123 outliers final: 67 residues processed: 525 average time/residue: 0.1726 time to fit residues: 153.4657 Evaluate side-chains 476 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 402 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 144 ILE 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 14 VAL 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 C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 841 ARG Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1229 TYR Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1304 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 320 ASN 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 384 LYS Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1249 ASN 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 1357 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 357 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 149 optimal weight: 20.0000 chunk 222 optimal weight: 3.9990 chunk 362 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 chunk 295 optimal weight: 30.0000 chunk 51 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 242 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS C 604 HIS ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN D 364 HIS ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.089927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.063281 restraints weight = 126538.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.065290 restraints weight = 62936.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.066600 restraints weight = 39663.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.067437 restraints weight = 29445.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.067940 restraints weight = 24520.526| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.8049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 29227 Z= 0.208 Angle : 0.762 10.990 40154 Z= 0.396 Chirality : 0.047 0.279 4788 Planarity : 0.007 0.157 4906 Dihedral : 16.409 177.260 5048 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.16 % Favored : 93.76 % Rotamer: Outliers : 5.88 % Allowed : 29.82 % Favored : 64.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.14), residues: 3587 helix: 0.63 (0.14), residues: 1293 sheet: -0.23 (0.27), residues: 374 loop : -1.59 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 219 TYR 0.065 0.003 TYR C 605 PHE 0.035 0.003 PHE B 35 TRP 0.021 0.002 TRP C 183 HIS 0.013 0.002 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00461 (29224) covalent geometry : angle 0.76190 (40154) hydrogen bonds : bond 0.04285 ( 1188) hydrogen bonds : angle 4.64737 ( 3306) metal coordination : bond 0.00422 ( 3) *********************** 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 617 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 463 time to evaluate : 1.152 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: A 35 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8628 (t80) REVERT: A 80 GLU cc_start: 0.8635 (mp0) cc_final: 0.7857 (tm-30) REVERT: A 205 MET cc_start: 0.8233 (tmm) cc_final: 0.7961 (tmm) REVERT: A 283 GLN cc_start: 0.6929 (OUTLIER) cc_final: 0.6618 (mm110) REVERT: A 316 MET cc_start: 0.3580 (mmm) cc_final: 0.3144 (mmm) REVERT: A 320 ASN cc_start: 0.7593 (OUTLIER) cc_final: 0.6967 (m-40) REVERT: B 78 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7655 (pt) REVERT: B 120 ASP cc_start: 0.8074 (t0) cc_final: 0.7637 (t70) REVERT: C 116 ASP cc_start: 0.6900 (p0) cc_final: 0.6672 (p0) REVERT: C 403 MET cc_start: 0.6828 (tmm) cc_final: 0.6383 (tmm) REVERT: C 488 MET cc_start: 0.6099 (mtp) cc_final: 0.5497 (mtt) REVERT: C 492 MET cc_start: 0.8569 (tpp) cc_final: 0.8329 (tpp) REVERT: C 577 VAL cc_start: 0.9358 (OUTLIER) cc_final: 0.9083 (m) REVERT: C 589 THR cc_start: 0.7646 (m) cc_final: 0.7214 (p) REVERT: C 611 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.8010 (pt0) REVERT: C 672 GLU cc_start: 0.8648 (pm20) cc_final: 0.8262 (pm20) REVERT: C 715 THR cc_start: 0.8219 (p) cc_final: 0.7959 (t) REVERT: C 773 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6358 (mt) REVERT: C 800 MET cc_start: 0.8582 (mmm) cc_final: 0.8322 (mmm) REVERT: C 815 SER cc_start: 0.8825 (m) cc_final: 0.8463 (p) REVERT: C 876 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.7047 (pt0) REVERT: C 921 PRO cc_start: 0.8989 (Cg_exo) cc_final: 0.8733 (Cg_endo) REVERT: C 930 ASP cc_start: 0.7350 (t0) cc_final: 0.7132 (t0) REVERT: C 1080 ASN cc_start: 0.9048 (m-40) cc_final: 0.8762 (m110) REVERT: C 1107 MET cc_start: 0.8600 (mpp) cc_final: 0.8178 (mpp) REVERT: C 1109 ILE cc_start: 0.8041 (mm) cc_final: 0.7204 (mm) REVERT: C 1113 LEU cc_start: 0.8898 (mt) cc_final: 0.8579 (mt) REVERT: C 1273 MET cc_start: 0.4864 (ptp) cc_final: 0.4638 (ptp) REVERT: C 1289 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7519 (tm-30) REVERT: C 1290 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7743 (ttt) REVERT: C 1295 SER cc_start: 0.8077 (OUTLIER) cc_final: 0.7727 (p) REVERT: C 1329 GLU cc_start: 0.7894 (tt0) cc_final: 0.7226 (tt0) REVERT: C 1330 ILE cc_start: 0.8516 (mt) cc_final: 0.8300 (mt) REVERT: C 1333 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8166 (mp) REVERT: D 22 ILE cc_start: 0.7340 (tt) cc_final: 0.6889 (pt) REVERT: D 130 MET cc_start: 0.2939 (mpp) cc_final: 0.2602 (mpp) REVERT: D 229 GLN cc_start: 0.7820 (mm-40) cc_final: 0.7478 (mm-40) REVERT: D 233 LYS cc_start: 0.2282 (OUTLIER) cc_final: 0.2016 (mtmt) REVERT: D 268 LEU cc_start: 0.7913 (mm) cc_final: 0.7624 (mt) REVERT: D 298 MET cc_start: 0.8360 (mtp) cc_final: 0.7950 (mmp) REVERT: D 350 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.9110 (p) REVERT: D 384 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7523 (mmmt) REVERT: D 390 LEU cc_start: 0.8591 (tp) cc_final: 0.8247 (mm) REVERT: D 466 MET cc_start: 0.8243 (mtm) cc_final: 0.7949 (ttm) REVERT: D 484 MET cc_start: 0.8025 (mtp) cc_final: 0.7659 (mpp) REVERT: D 495 ASN cc_start: 0.8642 (p0) cc_final: 0.8083 (p0) REVERT: D 497 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8512 (mm-30) REVERT: D 603 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8683 (mmmm) REVERT: D 604 MET cc_start: 0.9047 (ttp) cc_final: 0.8670 (ppp) REVERT: D 627 THR cc_start: 0.8585 (m) cc_final: 0.8339 (p) REVERT: D 803 VAL cc_start: 0.7023 (t) cc_final: 0.6697 (t) REVERT: D 960 LEU cc_start: 0.8838 (tt) cc_final: 0.8559 (tp) REVERT: D 993 GLU cc_start: 0.2677 (mt-10) cc_final: 0.0834 (mt-10) REVERT: D 1219 ASP cc_start: 0.8253 (m-30) cc_final: 0.7904 (m-30) REVERT: D 1220 ILE cc_start: 0.8954 (mt) cc_final: 0.8436 (mt) REVERT: E 8 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7690 (m-30) REVERT: E 18 ASP cc_start: 0.9076 (m-30) cc_final: 0.8866 (m-30) REVERT: E 48 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7627 (p) outliers start: 154 outliers final: 77 residues processed: 569 average time/residue: 0.1672 time to fit residues: 161.0723 Evaluate side-chains 495 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 401 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 PHE 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 178 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 78 ILE 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 203 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 611 GLU 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 734 ILE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 876 GLU Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 932 GLN Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 233 LYS Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 384 LYS Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 997 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 1334 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 406 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 264 optimal weight: 6.9990 chunk 181 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 281 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 271 optimal weight: 20.0000 chunk 186 optimal weight: 2.9990 chunk 261 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 229 optimal weight: 7.9990 chunk 213 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN B 194 GLN C 573 ASN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 113 HIS E 31 GLN M 121 GLN M 262 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.087454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.060494 restraints weight = 126419.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.062446 restraints weight = 63089.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.063705 restraints weight = 40059.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.064515 restraints weight = 29956.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.065016 restraints weight = 25092.812| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 1.0606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.167 29227 Z= 0.245 Angle : 0.807 15.346 40154 Z= 0.415 Chirality : 0.047 0.345 4788 Planarity : 0.006 0.072 4906 Dihedral : 16.545 175.810 5048 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.33 % Favored : 93.62 % Rotamer: Outliers : 5.23 % Allowed : 31.42 % Favored : 63.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.14), residues: 3587 helix: 0.42 (0.14), residues: 1304 sheet: -0.47 (0.27), residues: 371 loop : -1.64 (0.13), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 352 TYR 0.039 0.002 TYR D 626 PHE 0.039 0.003 PHE D 620 TRP 0.024 0.002 TRP C 183 HIS 0.014 0.002 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00551 (29224) covalent geometry : angle 0.80746 (40154) hydrogen bonds : bond 0.04224 ( 1188) hydrogen bonds : angle 4.80266 ( 3306) metal coordination : bond 0.00443 ( 3) *********************** 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 533 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 396 time to evaluate : 0.703 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: A 47 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9292 (mm) REVERT: A 51 MET cc_start: 0.8956 (mmm) cc_final: 0.8610 (mmm) REVERT: A 61 ILE cc_start: 0.9618 (tp) cc_final: 0.9033 (tp) REVERT: A 75 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8240 (tp-100) REVERT: A 199 ASP cc_start: 0.8518 (t0) cc_final: 0.8311 (t0) REVERT: A 205 MET cc_start: 0.8560 (tmm) cc_final: 0.8223 (tmm) REVERT: A 224 LEU cc_start: 0.9270 (tp) cc_final: 0.9056 (tp) REVERT: A 316 MET cc_start: 0.4370 (mmm) cc_final: 0.3640 (mtt) REVERT: B 18 GLN cc_start: 0.8268 (pm20) cc_final: 0.7310 (tm-30) REVERT: B 177 TYR cc_start: 0.7129 (m-80) cc_final: 0.6882 (m-80) REVERT: C 53 PHE cc_start: 0.7858 (m-10) cc_final: 0.7456 (m-80) REVERT: C 57 PHE cc_start: 0.6381 (m-80) cc_final: 0.5135 (m-80) REVERT: C 177 ILE cc_start: 0.8434 (mt) cc_final: 0.8057 (mm) REVERT: C 241 LEU cc_start: 0.4982 (OUTLIER) cc_final: 0.4511 (tt) REVERT: C 403 MET cc_start: 0.7178 (tmm) cc_final: 0.6728 (tmm) REVERT: C 488 MET cc_start: 0.6748 (mtp) cc_final: 0.6267 (mtt) REVERT: C 611 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8664 (pt0) REVERT: C 800 MET cc_start: 0.8853 (mmm) cc_final: 0.8519 (mmm) REVERT: C 825 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8454 (mt-10) REVERT: C 930 ASP cc_start: 0.7727 (t0) cc_final: 0.7487 (t0) REVERT: C 1066 MET cc_start: 0.8557 (mmm) cc_final: 0.8135 (mmm) REVERT: C 1080 ASN cc_start: 0.9201 (m-40) cc_final: 0.8947 (m110) REVERT: C 1107 MET cc_start: 0.8860 (mpp) cc_final: 0.8517 (mpp) REVERT: C 1109 ILE cc_start: 0.8779 (mm) cc_final: 0.8384 (mm) REVERT: C 1273 MET cc_start: 0.6742 (ptp) cc_final: 0.4893 (mpp) REVERT: C 1329 GLU cc_start: 0.8646 (tt0) cc_final: 0.7835 (tt0) REVERT: D 211 GLU cc_start: 0.8582 (tp30) cc_final: 0.8269 (mt-10) REVERT: D 229 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7773 (mm-40) REVERT: D 264 ASP cc_start: 0.8738 (m-30) cc_final: 0.8424 (t70) REVERT: D 298 MET cc_start: 0.8494 (mtp) cc_final: 0.8254 (mmp) REVERT: D 330 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7313 (ppp) REVERT: D 370 LYS cc_start: 0.8307 (pttm) cc_final: 0.8009 (ptpp) REVERT: D 390 LEU cc_start: 0.9180 (tp) cc_final: 0.8888 (mm) REVERT: D 485 MET cc_start: 0.9227 (mmt) cc_final: 0.8976 (mmm) REVERT: D 581 MET cc_start: 0.9303 (tpp) cc_final: 0.8849 (mmt) REVERT: D 603 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8921 (mmmm) REVERT: D 644 MET cc_start: 0.8755 (mpp) cc_final: 0.8408 (mpp) REVERT: D 822 MET cc_start: 0.8820 (mmm) cc_final: 0.8453 (mmm) REVERT: D 982 LEU cc_start: 0.8851 (mm) cc_final: 0.8623 (pp) REVERT: D 993 GLU cc_start: 0.2881 (mt-10) cc_final: 0.1423 (mt-10) REVERT: D 995 TYR cc_start: 0.5469 (m-10) cc_final: 0.5063 (m-10) REVERT: D 1334 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: E 7 GLN cc_start: 0.8501 (tp40) cc_final: 0.8182 (tp40) REVERT: E 8 ASP cc_start: 0.8595 (p0) cc_final: 0.8074 (m-30) REVERT: E 17 PHE cc_start: 0.8171 (m-80) cc_final: 0.7930 (m-80) REVERT: E 18 ASP cc_start: 0.9152 (m-30) cc_final: 0.8857 (m-30) REVERT: E 19 LEU cc_start: 0.8968 (tp) cc_final: 0.8714 (tp) REVERT: E 59 ILE cc_start: 0.6995 (OUTLIER) cc_final: 0.6769 (tp) REVERT: M 278 VAL cc_start: 0.2196 (OUTLIER) cc_final: 0.1826 (t) outliers start: 137 outliers final: 67 residues processed: 492 average time/residue: 0.1568 time to fit residues: 130.1972 Evaluate side-chains 419 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 344 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain B residue 10 LYS 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 192 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 446 ASP Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 833 ILE Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1182 ILE Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 701 LEU 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 1163 VAL 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 1361 THR Chi-restraints excluded: chain E residue 4 VAL 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 63 ILE Chi-restraints excluded: chain M residue 278 VAL 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 65 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 78 optimal weight: 0.0070 chunk 87 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 157 optimal weight: 20.0000 overall best weight: 4.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1299 ASN D1197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.086814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.059641 restraints weight = 129135.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.061507 restraints weight = 65799.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.062736 restraints weight = 42542.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.063491 restraints weight = 32281.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.063932 restraints weight = 27425.912| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 1.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29227 Z= 0.189 Angle : 0.733 14.114 40154 Z= 0.375 Chirality : 0.045 0.334 4788 Planarity : 0.005 0.074 4906 Dihedral : 16.479 177.334 5048 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.08 % Favored : 93.87 % Rotamer: Outliers : 4.51 % Allowed : 33.49 % Favored : 62.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.14), residues: 3587 helix: 0.62 (0.14), residues: 1284 sheet: -0.40 (0.27), residues: 364 loop : -1.59 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D1369 TYR 0.017 0.002 TYR C1281 PHE 0.020 0.002 PHE C 157 TRP 0.011 0.001 TRP C1276 HIS 0.005 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00428 (29224) covalent geometry : angle 0.73265 (40154) hydrogen bonds : bond 0.04014 ( 1188) hydrogen bonds : angle 4.55800 ( 3306) metal coordination : bond 0.00252 ( 3) *********************** 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 480 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 362 time to evaluate : 1.124 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 47 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9375 (mm) REVERT: A 75 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8204 (tp-100) REVERT: A 80 GLU cc_start: 0.8809 (mt-10) cc_final: 0.7821 (tm-30) REVERT: A 95 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8066 (mtpp) REVERT: A 199 ASP cc_start: 0.8546 (t0) cc_final: 0.8315 (t0) REVERT: A 316 MET cc_start: 0.4845 (mmm) cc_final: 0.4132 (mtt) REVERT: B 49 SER cc_start: 0.8954 (m) cc_final: 0.8734 (p) REVERT: B 177 TYR cc_start: 0.7679 (m-80) cc_final: 0.6997 (m-80) REVERT: C 57 PHE cc_start: 0.6647 (m-80) cc_final: 0.5914 (m-80) REVERT: C 183 TRP cc_start: 0.8517 (OUTLIER) cc_final: 0.7677 (m-10) REVERT: C 403 MET cc_start: 0.7520 (tmm) cc_final: 0.7121 (tmm) REVERT: C 468 LEU cc_start: 0.8423 (mt) cc_final: 0.7860 (mt) REVERT: C 488 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6781 (mtt) REVERT: C 504 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8615 (mt-10) REVERT: C 561 ILE cc_start: 0.9678 (mm) cc_final: 0.9342 (tp) REVERT: C 611 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8772 (pt0) REVERT: C 685 MET cc_start: 0.9272 (mtt) cc_final: 0.9063 (mtt) REVERT: C 749 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.6578 (t70) REVERT: C 791 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9085 (mt) REVERT: C 800 MET cc_start: 0.8791 (mmm) cc_final: 0.8538 (mmm) REVERT: C 929 ILE cc_start: 0.8934 (mp) cc_final: 0.8732 (mp) REVERT: C 1098 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9052 (mm) REVERT: C 1107 MET cc_start: 0.8953 (mpp) cc_final: 0.8604 (mpp) REVERT: C 1119 MET cc_start: 0.8817 (mmm) cc_final: 0.8597 (mmm) REVERT: C 1230 MET cc_start: 0.8926 (tmm) cc_final: 0.8687 (ttt) REVERT: C 1273 MET cc_start: 0.6806 (ptp) cc_final: 0.5642 (mpp) REVERT: C 1304 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8902 (tpp) REVERT: C 1329 GLU cc_start: 0.8859 (tt0) cc_final: 0.8077 (tt0) REVERT: D 130 MET cc_start: 0.5558 (mpp) cc_final: 0.4679 (mpp) REVERT: D 201 LEU cc_start: 0.8236 (mt) cc_final: 0.7521 (tp) REVERT: D 229 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7867 (mm-40) REVERT: D 275 ARG cc_start: 0.8419 (mmt-90) cc_final: 0.7976 (tpp80) REVERT: D 314 ARG cc_start: 0.6006 (pmt-80) cc_final: 0.5275 (ptm160) REVERT: D 330 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7134 (ppp) REVERT: D 390 LEU cc_start: 0.9134 (tp) cc_final: 0.8888 (mm) REVERT: D 485 MET cc_start: 0.9156 (mmt) cc_final: 0.8887 (mmm) REVERT: D 486 SER cc_start: 0.9284 (m) cc_final: 0.8964 (p) REVERT: D 497 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8492 (mp0) REVERT: D 603 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.9062 (mmmm) REVERT: D 644 MET cc_start: 0.8912 (mpp) cc_final: 0.8600 (mpp) REVERT: D 743 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8573 (ppp) REVERT: D 822 MET cc_start: 0.8756 (mmm) cc_final: 0.8379 (mmm) REVERT: D 837 ASP cc_start: 0.8905 (t0) cc_final: 0.8702 (t70) REVERT: D 993 GLU cc_start: 0.2980 (mt-10) cc_final: 0.2251 (mt-10) REVERT: D 995 TYR cc_start: 0.6017 (m-10) cc_final: 0.5410 (m-10) REVERT: D 1334 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: E 7 GLN cc_start: 0.8689 (tp40) cc_final: 0.8289 (tp40) REVERT: E 8 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8255 (m-30) REVERT: E 17 PHE cc_start: 0.8410 (m-80) cc_final: 0.8052 (m-80) REVERT: E 19 LEU cc_start: 0.8995 (tp) cc_final: 0.8694 (tp) REVERT: E 30 MET cc_start: 0.8440 (tpt) cc_final: 0.8206 (tpt) REVERT: E 44 ASP cc_start: 0.7825 (p0) cc_final: 0.7471 (p0) REVERT: M 283 ASP cc_start: 0.8863 (t0) cc_final: 0.8648 (m-30) outliers start: 118 outliers final: 62 residues processed: 442 average time/residue: 0.1694 time to fit residues: 127.1366 Evaluate side-chains 407 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 331 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 47 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 183 TRP 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 511 LEU Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 605 TYR Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 611 GLU 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 723 VAL Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 870 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 1251 TYR Chi-restraints excluded: chain C residue 1304 MET Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 233 LYS Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 432 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 724 MET Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 801 VAL 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 871 LEU Chi-restraints excluded: chain D residue 997 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 D residue 1361 THR Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 172 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 7 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 296 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 272 optimal weight: 0.4980 chunk 213 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 119 optimal weight: 0.4980 chunk 261 optimal weight: 20.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS C 462 ASN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1268 GLN ** D 450 HIS ** 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 = 0.3726 r_free = 0.3726 target = 0.087641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.060467 restraints weight = 128503.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.062349 restraints weight = 64974.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.063562 restraints weight = 41960.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.064313 restraints weight = 31904.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.064787 restraints weight = 27090.255| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 1.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29227 Z= 0.137 Angle : 0.695 12.416 40154 Z= 0.346 Chirality : 0.043 0.282 4788 Planarity : 0.004 0.071 4906 Dihedral : 16.421 176.065 5048 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.05 % Favored : 93.89 % Rotamer: Outliers : 2.86 % Allowed : 35.24 % Favored : 61.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.14), residues: 3587 helix: 0.84 (0.15), residues: 1292 sheet: -0.25 (0.28), residues: 353 loop : -1.54 (0.14), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 322 TYR 0.019 0.001 TYR C 605 PHE 0.017 0.001 PHE C 38 TRP 0.012 0.001 TRP D 409 HIS 0.003 0.001 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00314 (29224) covalent geometry : angle 0.69494 (40154) hydrogen bonds : bond 0.03487 ( 1188) hydrogen bonds : angle 4.37642 ( 3306) metal coordination : bond 0.00115 ( 3) *********************** 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 416 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 341 time to evaluate : 0.763 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 47 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9345 (mm) REVERT: A 51 MET cc_start: 0.8521 (mmm) cc_final: 0.8244 (mmm) REVERT: A 75 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8131 (tp-100) REVERT: A 80 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8035 (tm-30) REVERT: A 199 ASP cc_start: 0.8485 (t0) cc_final: 0.8257 (t0) REVERT: A 283 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6828 (mm110) REVERT: A 316 MET cc_start: 0.5068 (mmm) cc_final: 0.4585 (mtt) REVERT: B 51 MET cc_start: 0.8233 (mmm) cc_final: 0.8017 (mmm) REVERT: C 57 PHE cc_start: 0.6517 (m-80) cc_final: 0.6212 (m-80) REVERT: C 143 ARG cc_start: 0.8041 (mmp-170) cc_final: 0.7786 (mmm160) REVERT: C 403 MET cc_start: 0.7533 (tmm) cc_final: 0.7048 (tmm) REVERT: C 468 LEU cc_start: 0.8525 (mt) cc_final: 0.7883 (mt) REVERT: C 488 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6554 (mtt) REVERT: C 561 ILE cc_start: 0.9608 (mm) cc_final: 0.9290 (tp) REVERT: C 696 ASP cc_start: 0.6291 (t0) cc_final: 0.5997 (t0) REVERT: C 791 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9033 (mt) REVERT: C 800 MET cc_start: 0.8743 (mmm) cc_final: 0.8492 (mmm) REVERT: C 929 ILE cc_start: 0.8904 (mp) cc_final: 0.8695 (mp) REVERT: C 1107 MET cc_start: 0.8904 (mpp) cc_final: 0.8651 (mpp) REVERT: C 1273 MET cc_start: 0.6919 (ptp) cc_final: 0.5879 (mpp) REVERT: D 29 MET cc_start: 0.8192 (ttp) cc_final: 0.7341 (tmm) REVERT: D 130 MET cc_start: 0.5532 (mpp) cc_final: 0.4622 (mpp) REVERT: D 201 LEU cc_start: 0.8249 (mt) cc_final: 0.7531 (tp) REVERT: D 229 GLN cc_start: 0.8320 (mm-40) cc_final: 0.7884 (mm-40) REVERT: D 275 ARG cc_start: 0.8409 (mmt-90) cc_final: 0.8191 (tpp-160) REVERT: D 314 ARG cc_start: 0.5946 (pmt-80) cc_final: 0.5491 (ptm160) REVERT: D 390 LEU cc_start: 0.9152 (tp) cc_final: 0.8929 (mm) REVERT: D 485 MET cc_start: 0.9022 (mmt) cc_final: 0.8788 (mmm) REVERT: D 581 MET cc_start: 0.9321 (tpp) cc_final: 0.9017 (mmt) REVERT: D 604 MET cc_start: 0.9068 (ptm) cc_final: 0.8790 (ptm) REVERT: D 644 MET cc_start: 0.8879 (mpp) cc_final: 0.8595 (mpp) REVERT: D 698 MET cc_start: 0.9581 (mmm) cc_final: 0.9199 (mmm) REVERT: D 822 MET cc_start: 0.8716 (mmm) cc_final: 0.8250 (mmm) REVERT: D 993 GLU cc_start: 0.2920 (mt-10) cc_final: 0.1931 (mt-10) REVERT: D 995 TYR cc_start: 0.5825 (m-10) cc_final: 0.5153 (m-10) REVERT: E 7 GLN cc_start: 0.8708 (tp40) cc_final: 0.8340 (tp40) REVERT: E 8 ASP cc_start: 0.8698 (p0) cc_final: 0.8331 (m-30) REVERT: E 17 PHE cc_start: 0.8505 (m-80) cc_final: 0.7998 (m-80) REVERT: E 19 LEU cc_start: 0.8967 (tp) cc_final: 0.8658 (tp) outliers start: 75 outliers final: 47 residues processed: 400 average time/residue: 0.1693 time to fit residues: 114.2230 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 : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 30 ILE 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 599 VAL Chi-restraints excluded: chain C residue 605 TYR Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 65 VAL 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 400 MET Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1253 ILE 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 1361 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 357 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 37 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 360 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 330 optimal weight: 30.0000 chunk 155 optimal weight: 30.0000 chunk 78 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 15 optimal weight: 0.0010 chunk 29 optimal weight: 7.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 132 HIS C 462 ASN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.086076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.058955 restraints weight = 128014.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.060708 restraints weight = 65830.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.061841 restraints weight = 43097.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.062555 restraints weight = 33093.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.062944 restraints weight = 28293.837| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- 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: 0.7953 moved from start: 1.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 29227 Z= 0.173 Angle : 0.743 13.689 40154 Z= 0.372 Chirality : 0.045 0.639 4788 Planarity : 0.005 0.070 4906 Dihedral : 16.435 176.960 5048 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.58 % Favored : 93.36 % Rotamer: Outliers : 3.02 % Allowed : 35.05 % Favored : 61.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.14), residues: 3587 helix: 0.79 (0.15), residues: 1290 sheet: -0.38 (0.27), residues: 367 loop : -1.55 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 279 TYR 0.017 0.001 TYR C 605 PHE 0.024 0.002 PHE C 505 TRP 0.025 0.002 TRP M 285 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00396 (29224) covalent geometry : angle 0.74251 (40154) hydrogen bonds : bond 0.03863 ( 1188) hydrogen bonds : angle 4.46097 ( 3306) metal coordination : bond 0.00169 ( 3) *********************** 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 374 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 295 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8102 (tp-100) REVERT: A 80 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8199 (tm-30) REVERT: A 141 SER cc_start: 0.6811 (OUTLIER) cc_final: 0.6583 (p) REVERT: A 199 ASP cc_start: 0.8567 (t0) cc_final: 0.8365 (t0) REVERT: A 283 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6775 (mm110) REVERT: A 316 MET cc_start: 0.5316 (mmm) cc_final: 0.4766 (mtt) REVERT: B 51 MET cc_start: 0.8397 (mmm) cc_final: 0.8195 (mmm) REVERT: B 147 GLN cc_start: 0.8066 (pm20) cc_final: 0.7787 (pm20) REVERT: C 403 MET cc_start: 0.7816 (tmm) cc_final: 0.7427 (tmm) REVERT: C 468 LEU cc_start: 0.8778 (mt) cc_final: 0.8008 (mt) REVERT: C 488 MET cc_start: 0.7327 (mtp) cc_final: 0.7061 (mtt) REVERT: C 561 ILE cc_start: 0.9620 (mm) cc_final: 0.9267 (tp) REVERT: C 791 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9325 (mt) REVERT: C 800 MET cc_start: 0.8833 (mmm) cc_final: 0.8539 (mmm) REVERT: C 948 ILE cc_start: 0.8279 (pp) cc_final: 0.7643 (pp) REVERT: C 1107 MET cc_start: 0.9175 (mpp) cc_final: 0.8866 (mpp) REVERT: C 1273 MET cc_start: 0.6968 (ptp) cc_final: 0.6622 (mtm) REVERT: C 1290 MET cc_start: 0.8861 (ttt) cc_final: 0.8581 (ppp) REVERT: C 1321 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8776 (tp30) REVERT: C 1337 ILE cc_start: 0.9175 (mp) cc_final: 0.8916 (tp) REVERT: D 29 MET cc_start: 0.8618 (ttp) cc_final: 0.8351 (tmm) REVERT: D 130 MET cc_start: 0.6275 (mpp) cc_final: 0.5490 (mpp) REVERT: D 201 LEU cc_start: 0.8382 (mt) cc_final: 0.7674 (tp) REVERT: D 390 LEU cc_start: 0.9356 (tp) cc_final: 0.9105 (mm) REVERT: D 497 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8481 (mp0) REVERT: D 581 MET cc_start: 0.9310 (tpp) cc_final: 0.8993 (mmt) REVERT: D 604 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8895 (ptm) REVERT: D 644 MET cc_start: 0.8942 (mpp) cc_final: 0.8596 (mpp) REVERT: D 698 MET cc_start: 0.9604 (mmm) cc_final: 0.9227 (mmm) REVERT: D 822 MET cc_start: 0.8788 (mmm) cc_final: 0.8283 (mmm) REVERT: D 993 GLU cc_start: 0.3073 (mt-10) cc_final: 0.2701 (mt-10) REVERT: D 995 TYR cc_start: 0.5989 (m-10) cc_final: 0.4456 (m-10) REVERT: E 7 GLN cc_start: 0.8746 (tp40) cc_final: 0.7958 (tm-30) REVERT: E 8 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8218 (m-30) REVERT: E 40 PRO cc_start: 0.8855 (Cg_exo) cc_final: 0.8586 (Cg_endo) outliers start: 79 outliers final: 53 residues processed: 354 average time/residue: 0.1727 time to fit residues: 103.4885 Evaluate side-chains 330 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 272 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 56 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 605 TYR Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 871 LEU 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 1361 THR Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 357 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 271 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 298 optimal weight: 7.9990 chunk 212 optimal weight: 50.0000 chunk 337 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 243 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS C 554 HIS C 604 HIS ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 364 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.083329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.055736 restraints weight = 127573.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.057417 restraints weight = 65851.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.058502 restraints weight = 43456.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.059180 restraints weight = 33636.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.059554 restraints weight = 28931.540| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 1.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 29227 Z= 0.243 Angle : 0.827 25.262 40154 Z= 0.419 Chirality : 0.046 0.428 4788 Planarity : 0.006 0.092 4906 Dihedral : 16.595 178.010 5048 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.83 % Favored : 93.11 % Rotamer: Outliers : 2.52 % Allowed : 35.62 % Favored : 61.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.14), residues: 3587 helix: 0.58 (0.14), residues: 1296 sheet: -0.61 (0.27), residues: 362 loop : -1.59 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 98 TYR 0.034 0.002 TYR D 269 PHE 0.032 0.002 PHE C 934 TRP 0.017 0.002 TRP D 409 HIS 0.023 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00546 (29224) covalent geometry : angle 0.82697 (40154) hydrogen bonds : bond 0.04372 ( 1188) hydrogen bonds : angle 4.72203 ( 3306) metal coordination : bond 0.00533 ( 3) ********************** 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 327 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 261 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8323 (tp40) REVERT: A 80 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8373 (tm-30) REVERT: A 141 SER cc_start: 0.7548 (OUTLIER) cc_final: 0.7301 (p) REVERT: A 199 ASP cc_start: 0.8588 (t0) cc_final: 0.8301 (t0) REVERT: B 51 MET cc_start: 0.8508 (mmm) cc_final: 0.8095 (tmm) REVERT: C 40 GLU cc_start: 0.8725 (tp30) cc_final: 0.8391 (tp30) REVERT: C 403 MET cc_start: 0.8064 (tmm) cc_final: 0.7526 (tmm) REVERT: C 459 MET cc_start: 0.9202 (mmm) cc_final: 0.8975 (mmm) REVERT: C 800 MET cc_start: 0.8792 (mmm) cc_final: 0.8563 (mmm) REVERT: C 834 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8454 (tm-30) REVERT: C 1321 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8428 (tp30) REVERT: D 130 MET cc_start: 0.7499 (mpp) cc_final: 0.6710 (mpp) REVERT: D 248 ASP cc_start: 0.8712 (t0) cc_final: 0.8120 (t70) REVERT: D 330 MET cc_start: 0.9099 (ptt) cc_final: 0.8814 (ptm) REVERT: D 390 LEU cc_start: 0.9348 (tp) cc_final: 0.9136 (mm) REVERT: D 428 THR cc_start: 0.9242 (p) cc_final: 0.8231 (p) REVERT: D 497 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8646 (mp0) REVERT: D 581 MET cc_start: 0.9326 (tpp) cc_final: 0.9089 (mmt) REVERT: D 644 MET cc_start: 0.8897 (mpp) cc_final: 0.8459 (mpp) REVERT: D 822 MET cc_start: 0.8731 (mmm) cc_final: 0.8390 (mmm) REVERT: D 995 TYR cc_start: 0.6110 (m-10) cc_final: 0.4434 (m-10) REVERT: E 8 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8291 (m-30) REVERT: E 30 MET cc_start: 0.8804 (tpt) cc_final: 0.8569 (tpt) outliers start: 66 outliers final: 47 residues processed: 314 average time/residue: 0.1702 time to fit residues: 91.4825 Evaluate side-chains 286 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 237 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 56 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 605 TYR Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain C residue 1299 ASN Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 871 LEU 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 1347 LEU Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain M residue 160 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 346 optimal weight: 50.0000 chunk 221 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 298 optimal weight: 20.0000 chunk 303 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS C 568 ASN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.082135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.054499 restraints weight = 130135.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.056142 restraints weight = 67698.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.057195 restraints weight = 45017.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.057842 restraints weight = 35108.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.058187 restraints weight = 30337.112| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 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 = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 1.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 29227 Z= 0.252 Angle : 0.814 16.730 40154 Z= 0.414 Chirality : 0.047 0.249 4788 Planarity : 0.005 0.074 4906 Dihedral : 16.638 178.422 5048 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.22 % Favored : 92.72 % Rotamer: Outliers : 2.44 % Allowed : 35.78 % Favored : 61.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.14), residues: 3587 helix: 0.47 (0.14), residues: 1288 sheet: -0.70 (0.27), residues: 361 loop : -1.61 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 322 TYR 0.030 0.002 TYR C1281 PHE 0.025 0.002 PHE C 157 TRP 0.021 0.002 TRP M 126 HIS 0.071 0.002 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00573 (29224) covalent geometry : angle 0.81379 (40154) hydrogen bonds : bond 0.04408 ( 1188) hydrogen bonds : angle 4.86682 ( 3306) metal coordination : bond 0.00482 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6761.95 seconds wall clock time: 116 minutes 44.98 seconds (7004.98 seconds total)