Starting phenix.real_space_refine on Sat Aug 8 13:04:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ree_19084/08_2026/8ree_19084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ree_19084/08_2026/8ree_19084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ree_19084/08_2026/8ree_19084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ree_19084/08_2026/8ree_19084.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ree_19084/08_2026/8ree_19084.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ree_19084/08_2026/8ree_19084.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ree_19084/08_2026/8ree_19084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ree_19084/08_2026/8ree_19084.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: {'RNAv2': 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: 6.49, per 1000 atoms: 0.23 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: 2.85 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6706 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 44 sheets defined 39.3% alpha, 13.7% beta 42 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 3.89 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: 8.29 Time building geometry restraints manager: 3.72 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=" C1' DT N 9 " pdb=" N1 DT N 9 " ideal model delta sigma weight residual 1.468 1.529 -0.061 1.40e-02 5.10e+03 1.90e+01 bond pdb=" C3' DA T 16 " pdb=" C2' DA T 16 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DC N 11 " pdb=" C2' DC N 11 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DT N 4 " pdb=" C2' DT N 4 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DA N 7 " pdb=" C2' DA N 7 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.76e+00 ... (remaining 29219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 39848 2.89 - 5.79: 258 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=" O4' DC T -4 " pdb=" C4' DC T -4 " pdb=" C3' DC T -4 " ideal model delta sigma weight residual 106.00 103.32 2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT N -17 " pdb=" C4 DT N -17 " pdb=" O4 DT N -17 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 ... (remaining 40149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 16512 34.83 - 69.65: 978 69.65 - 104.48: 54 104.48 - 139.31: 0 139.31 - 174.14: 3 Dihedral angle restraints: 17547 sinusoidal: 7156 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 17544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3648 0.046 - 0.092: 869 0.092 - 0.138: 255 0.138 - 0.184: 7 0.184 - 0.230: 9 Chirality restraints: 4788 Sorted by residual: chirality pdb=" P G R 4 " pdb=" OP1 G R 4 " pdb=" OP2 G R 4 " pdb=" O5' G R 4 " both_signs ideal model delta sigma weight residual True 2.17 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" P C R 7 " pdb=" OP1 C R 7 " pdb=" OP2 C R 7 " pdb=" O5' C R 7 " both_signs ideal model delta sigma weight residual True 2.17 -2.39 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" P G R 2 " pdb=" OP1 G R 2 " pdb=" OP2 G R 2 " pdb=" O5' G R 2 " both_signs ideal model delta sigma weight residual True 2.17 -2.39 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 37.250 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 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: 0.020 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3498 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 : 0.004 0.105 29227 Z= 0.240 Angle : 0.672 14.474 40154 Z= 0.401 Chirality : 0.044 0.230 4788 Planarity : 0.005 0.124 4906 Dihedral : 19.543 174.137 10841 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 are 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/Z covalent geometry : bond 0.00389 / 0.24 (29224) covalent geometry : angle 0.67185 / 0.40 (40154) hydrogen bonds : bond 0.18775 / 12.67 ( 1188) hydrogen bonds : angle 6.43340 / 4.53 ( 3306) metal coordination : bond 0.00202 / 0.10 ( 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 : 0.821 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: 0.5820 (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: 0.2010 time to fit residues: 238.5389 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 : 1.011 ------------------------------------------------------------------------------- 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... A 23 HIS A 84 ASN A 268 ASN B 227 GLN C 517 GLN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN C 965 GLN C1237 HIS ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 300 GLN D 335 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN D 921 GLN D1350 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.092310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.065844 restraints weight = 119759.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.067929 restraints weight = 57930.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.069286 restraints weight = 35596.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.070165 restraints weight = 25884.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.070641 restraints weight = 21235.111| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 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 = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5779 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 29227 Z= 0.207 Angle : 0.819 10.850 40154 Z= 0.420 Chirality : 0.048 0.277 4788 Planarity : 0.006 0.080 4906 Dihedral : 16.360 173.618 5046 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.97 % Favored : 93.95 % Rotamer: Outliers : 5.73 % Allowed : 30.09 % Favored : 64.18 % 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 are not related in a simple way. whole: -0.81 (0.14), residues: 3587 helix: 0.67 (0.14), residues: 1275 sheet: -0.16 (0.27), residues: 362 loop : -1.49 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1156 TYR 0.044 0.003 TYR C 62 PHE 0.023 0.003 PHE C 828 TRP 0.026 0.002 TRP C 807 HIS 0.010 0.002 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (29224) covalent geometry : angle 0.81898 / 0.42 (40154) hydrogen bonds : bond 0.04672 / 3.22 ( 1188) hydrogen bonds : angle 5.04219 / 3.50 ( 3306) metal coordination : bond 0.00226 / 0.12 ( 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 645 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 495 time to evaluate : 0.835 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: A 35 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.8127 (t80) REVERT: A 77 ASP cc_start: 0.6051 (OUTLIER) cc_final: 0.5047 (t0) REVERT: A 159 ILE cc_start: 0.5006 (mm) cc_final: 0.4736 (mm) REVERT: A 316 MET cc_start: 0.2470 (mmm) cc_final: 0.1584 (mmm) REVERT: B 92 VAL cc_start: 0.6634 (m) cc_final: 0.6171 (t) REVERT: B 95 LYS cc_start: 0.6980 (mtmm) cc_final: 0.6762 (mtmm) REVERT: B 118 ASP cc_start: 0.7419 (t0) cc_final: 0.6964 (t0) REVERT: B 121 VAL cc_start: 0.8219 (t) cc_final: 0.7900 (m) REVERT: B 197 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7950 (p0) REVERT: B 201 LEU cc_start: 0.7551 (tt) cc_final: 0.7303 (tt) REVERT: C 31 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8130 (tp-100) REVERT: C 239 MET cc_start: 0.6020 (tpt) cc_final: 0.5491 (tpp) REVERT: C 385 PHE cc_start: 0.7814 (m-80) cc_final: 0.7601 (m-80) REVERT: C 456 VAL cc_start: 0.7104 (OUTLIER) cc_final: 0.6667 (p) REVERT: C 492 MET cc_start: 0.7725 (tpp) cc_final: 0.7368 (tpp) REVERT: C 681 MET cc_start: 0.6101 (mtt) cc_final: 0.5803 (mtm) REVERT: C 876 GLU cc_start: 0.4416 (pm20) cc_final: 0.4112 (pt0) REVERT: C 1066 MET cc_start: 0.7696 (mmm) cc_final: 0.7324 (mmm) REVERT: C 1098 LEU cc_start: 0.5134 (OUTLIER) cc_final: 0.4850 (mp) REVERT: C 1131 MET cc_start: 0.8384 (ptp) cc_final: 0.8027 (ptp) REVERT: C 1143 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8601 (pp20) REVERT: C 1229 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.6287 (t80) REVERT: C 1235 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6800 (mp) REVERT: C 1274 GLU cc_start: 0.5344 (OUTLIER) cc_final: 0.4744 (mm-30) REVERT: C 1290 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.6570 (tpt) REVERT: D 92 VAL cc_start: 0.1708 (OUTLIER) cc_final: 0.1327 (p) REVERT: D 232 ASN cc_start: 0.3389 (OUTLIER) cc_final: 0.2615 (t0) REVERT: D 237 MET cc_start: 0.1733 (OUTLIER) cc_final: 0.1250 (tmm) REVERT: D 375 GLU cc_start: 0.7265 (tp30) cc_final: 0.6835 (tp30) REVERT: D 452 LEU cc_start: 0.7454 (mt) cc_final: 0.7091 (mm) REVERT: D 555 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.6992 (t80) REVERT: D 724 MET cc_start: 0.7164 (mtp) cc_final: 0.6863 (mpp) REVERT: D 747 MET cc_start: 0.6189 (mtm) cc_final: 0.5958 (mpp) REVERT: D 864 LEU cc_start: 0.7162 (tp) cc_final: 0.6849 (mt) REVERT: D 982 LEU cc_start: 0.8535 (mt) cc_final: 0.8321 (pp) REVERT: D 993 GLU cc_start: 0.0535 (mt-10) cc_final: -0.2129 (mt-10) REVERT: D 1260 MET cc_start: 0.7016 (tpp) cc_final: 0.6686 (tpp) REVERT: E 7 GLN cc_start: 0.8349 (mm-40) cc_final: 0.7939 (tp40) REVERT: E 48 VAL cc_start: 0.6638 (OUTLIER) cc_final: 0.6317 (p) REVERT: E 59 ILE cc_start: 0.5189 (OUTLIER) cc_final: 0.4973 (pt) REVERT: E 63 ILE cc_start: 0.7105 (OUTLIER) cc_final: 0.6807 (pt) REVERT: M 376 MET cc_start: -0.0864 (tpt) cc_final: -0.1780 (tpt) outliers start: 150 outliers final: 51 residues processed: 603 average time/residue: 0.1676 time to fit residues: 164.5500 Evaluate side-chains 488 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 420 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 57 THR Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 1094 VAL 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 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 1290 MET Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 353 SER 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 555 TYR Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1352 ILE Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 63 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: 0.5980 chunk 50 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 87 optimal weight: 0.2980 chunk 218 optimal weight: 0.0370 chunk 224 optimal weight: 0.9990 chunk 320 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 chunk 28 optimal weight: 6.9990 chunk 25 optimal weight: 50.0000 chunk 186 optimal weight: 0.6980 overall best weight: 0.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS A 186 ASN B 227 GLN C 568 ASN D 229 GLN D 276 ASN D 450 HIS ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.093022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.066944 restraints weight = 118321.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.069055 restraints weight = 57326.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.070424 restraints weight = 35141.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.071336 restraints weight = 25393.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.071855 restraints weight = 20661.168| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5808 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29227 Z= 0.144 Angle : 0.721 15.099 40154 Z= 0.364 Chirality : 0.045 0.245 4788 Planarity : 0.006 0.141 4906 Dihedral : 16.316 173.204 5044 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.63 % Favored : 94.31 % Rotamer: Outliers : 4.43 % Allowed : 31.00 % Favored : 64.57 % 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 are not related in a simple way. whole: -0.74 (0.14), residues: 3587 helix: 0.80 (0.15), residues: 1288 sheet: -0.18 (0.26), residues: 375 loop : -1.51 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 218 TYR 0.033 0.002 TYR C 756 PHE 0.020 0.002 PHE M 403 TRP 0.011 0.001 TRP D 115 HIS 0.005 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (29224) covalent geometry : angle 0.72109 / 0.36 (40154) hydrogen bonds : bond 0.04169 / 2.84 ( 1188) hydrogen bonds : angle 4.78520 / 3.34 ( 3306) metal coordination : bond 0.00104 / 0.05 ( 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 541 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 425 time to evaluate : 0.728 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: A 35 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.8082 (t80) REVERT: A 51 MET cc_start: 0.7405 (mmp) cc_final: 0.7184 (mmm) REVERT: A 77 ASP cc_start: 0.6504 (OUTLIER) cc_final: 0.6041 (t0) REVERT: A 316 MET cc_start: 0.2736 (mmm) cc_final: 0.1954 (mmm) REVERT: B 92 VAL cc_start: 0.6675 (m) cc_final: 0.6196 (t) REVERT: B 118 ASP cc_start: 0.7431 (t0) cc_final: 0.6961 (t0) REVERT: B 121 VAL cc_start: 0.8224 (t) cc_final: 0.7864 (m) REVERT: C 35 PHE cc_start: 0.7093 (t80) cc_final: 0.6183 (t80) REVERT: C 239 MET cc_start: 0.6255 (tpt) cc_final: 0.4772 (tpp) REVERT: C 488 MET cc_start: 0.5494 (mtt) cc_final: 0.4940 (mtt) REVERT: C 611 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.5824 (mt-10) REVERT: C 685 MET cc_start: 0.6886 (mmt) cc_final: 0.6315 (mmm) REVERT: C 741 MET cc_start: 0.8397 (mmm) cc_final: 0.7887 (mmt) REVERT: C 749 ASP cc_start: 0.4284 (OUTLIER) cc_final: 0.4034 (t0) REVERT: C 756 TYR cc_start: 0.2723 (m-80) cc_final: 0.2307 (m-80) REVERT: C 793 GLU cc_start: 0.6390 (tt0) cc_final: 0.6094 (tt0) REVERT: C 800 MET cc_start: 0.7327 (mmm) cc_final: 0.6622 (mmm) REVERT: C 831 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7873 (mm) REVERT: C 1066 MET cc_start: 0.7530 (mmm) cc_final: 0.7132 (mmm) REVERT: C 1098 LEU cc_start: 0.5298 (OUTLIER) cc_final: 0.5027 (mp) REVERT: C 1143 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8588 (pp20) REVERT: C 1229 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.6385 (t80) REVERT: C 1235 LEU cc_start: 0.7246 (mp) cc_final: 0.6790 (mp) REVERT: C 1274 GLU cc_start: 0.5278 (OUTLIER) cc_final: 0.4581 (mm-30) REVERT: C 1289 GLU cc_start: 0.6773 (tm-30) cc_final: 0.6053 (tm-30) REVERT: D 57 PHE cc_start: 0.4308 (m-10) cc_final: 0.4035 (m-10) REVERT: D 114 ILE cc_start: 0.5061 (OUTLIER) cc_final: 0.4826 (tt) REVERT: D 229 GLN cc_start: 0.6836 (mm110) cc_final: 0.6601 (mm110) REVERT: D 298 MET cc_start: 0.7778 (mtp) cc_final: 0.7181 (mmm) REVERT: D 356 THR cc_start: 0.7180 (p) cc_final: 0.6593 (t) REVERT: D 375 GLU cc_start: 0.7433 (tp30) cc_final: 0.6998 (tp30) REVERT: D 452 LEU cc_start: 0.7380 (mt) cc_final: 0.7014 (mm) REVERT: D 699 ASP cc_start: 0.8400 (m-30) cc_final: 0.7989 (t0) REVERT: D 747 MET cc_start: 0.6403 (mtm) cc_final: 0.6156 (mpp) REVERT: D 993 GLU cc_start: -0.0306 (mt-10) cc_final: -0.0853 (mt-10) REVERT: D 995 TYR cc_start: 0.4747 (m-80) cc_final: 0.4440 (m-10) REVERT: D 1260 MET cc_start: 0.7061 (tpp) cc_final: 0.6623 (tpp) REVERT: D 1340 LYS cc_start: 0.4766 (ptmm) cc_final: 0.3468 (ptmm) REVERT: E 58 LEU cc_start: 0.7768 (tp) cc_final: 0.7515 (tt) REVERT: E 59 ILE cc_start: 0.5161 (OUTLIER) cc_final: 0.4472 (tt) REVERT: E 63 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6786 (pt) outliers start: 116 outliers final: 55 residues processed: 501 average time/residue: 0.1590 time to fit residues: 133.5025 Evaluate side-chains 451 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 385 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU 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 68 TYR Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 569 ILE 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 680 LEU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1124 ILE 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 1274 GLU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 429 LEU 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 612 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 682 VAL 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 1249 ASN Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1356 LEU Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 59 ILE 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 292 ASP 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: 0.7980 chunk 68 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 chunk 232 optimal weight: 4.9990 chunk 278 optimal weight: 6.9990 chunk 291 optimal weight: 0.0870 chunk 194 optimal weight: 1.9990 chunk 286 optimal weight: 0.0670 chunk 33 optimal weight: 9.9990 chunk 166 optimal weight: 0.0970 overall best weight: 0.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.092919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.067036 restraints weight = 118621.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.069135 restraints weight = 57637.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.070507 restraints weight = 35285.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.071374 restraints weight = 25386.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.071951 restraints weight = 20676.718| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5859 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29227 Z= 0.131 Angle : 0.680 10.861 40154 Z= 0.344 Chirality : 0.044 0.253 4788 Planarity : 0.005 0.084 4906 Dihedral : 16.318 173.074 5044 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.66 % Favored : 94.26 % Rotamer: Outliers : 3.89 % Allowed : 31.84 % Favored : 64.26 % 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 are not related in a simple way. whole: -0.71 (0.14), residues: 3587 helix: 0.85 (0.15), residues: 1292 sheet: -0.12 (0.26), residues: 383 loop : -1.54 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 133 TYR 0.022 0.001 TYR C 62 PHE 0.021 0.002 PHE C 35 TRP 0.007 0.001 TRP C1276 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (29224) covalent geometry : angle 0.67970 / 0.34 (40154) hydrogen bonds : bond 0.03789 / 2.58 ( 1188) hydrogen bonds : angle 4.63163 / 3.24 ( 3306) metal coordination : bond 0.00084 / 0.04 ( 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 519 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 417 time to evaluate : 1.028 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: A 35 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.8093 (t80) REVERT: A 51 MET cc_start: 0.7409 (mmp) cc_final: 0.7080 (mmm) REVERT: A 77 ASP cc_start: 0.6503 (OUTLIER) cc_final: 0.6170 (t0) REVERT: A 316 MET cc_start: 0.2647 (mmm) cc_final: 0.1971 (mmm) REVERT: B 118 ASP cc_start: 0.7430 (t0) cc_final: 0.6987 (t0) REVERT: B 121 VAL cc_start: 0.8229 (t) cc_final: 0.7906 (m) REVERT: B 205 MET cc_start: 0.7733 (pmm) cc_final: 0.7307 (pmm) REVERT: C 239 MET cc_start: 0.6417 (tpt) cc_final: 0.4974 (tpp) REVERT: C 488 MET cc_start: 0.5729 (mtt) cc_final: 0.5129 (mtt) REVERT: C 492 MET cc_start: 0.7916 (tpp) cc_final: 0.7678 (tpp) REVERT: C 611 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.5876 (mt-10) REVERT: C 685 MET cc_start: 0.6935 (mmt) cc_final: 0.6457 (mmm) REVERT: C 741 MET cc_start: 0.8375 (mmm) cc_final: 0.7844 (mmt) REVERT: C 749 ASP cc_start: 0.4314 (OUTLIER) cc_final: 0.4088 (t0) REVERT: C 800 MET cc_start: 0.7485 (mmm) cc_final: 0.6685 (mmm) REVERT: C 866 ASP cc_start: 0.3326 (OUTLIER) cc_final: 0.3018 (p0) REVERT: C 1066 MET cc_start: 0.7461 (mmm) cc_final: 0.7091 (mmm) REVERT: C 1098 LEU cc_start: 0.5425 (OUTLIER) cc_final: 0.5154 (mp) REVERT: C 1134 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8677 (mp10) REVERT: C 1143 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8594 (pp20) REVERT: C 1170 MET cc_start: 0.7927 (tmm) cc_final: 0.6607 (mmt) REVERT: C 1229 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.6402 (t80) REVERT: C 1235 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7083 (mp) REVERT: C 1274 GLU cc_start: 0.5199 (OUTLIER) cc_final: 0.4504 (mm-30) REVERT: C 1289 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6290 (tm-30) REVERT: D 229 GLN cc_start: 0.6971 (mm110) cc_final: 0.6755 (mm-40) REVERT: D 298 MET cc_start: 0.7799 (mtp) cc_final: 0.7332 (mmm) REVERT: D 375 GLU cc_start: 0.7620 (tp30) cc_final: 0.7246 (tp30) REVERT: D 452 LEU cc_start: 0.7485 (mt) cc_final: 0.7124 (mm) REVERT: D 581 MET cc_start: 0.7368 (tpp) cc_final: 0.6905 (mmt) REVERT: D 643 ASP cc_start: 0.7662 (m-30) cc_final: 0.6881 (t0) REVERT: D 648 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7723 (tm-30) REVERT: D 699 ASP cc_start: 0.8420 (m-30) cc_final: 0.8021 (t0) REVERT: D 722 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8278 (tp) REVERT: D 960 LEU cc_start: 0.8697 (tt) cc_final: 0.8413 (mt) REVERT: D 1260 MET cc_start: 0.7486 (tpp) cc_final: 0.7023 (tpt) REVERT: D 1344 LEU cc_start: 0.7058 (mp) cc_final: 0.5998 (tt) REVERT: E 59 ILE cc_start: 0.4974 (OUTLIER) cc_final: 0.4644 (mm) outliers start: 102 outliers final: 58 residues processed: 485 average time/residue: 0.1486 time to fit residues: 121.8713 Evaluate side-chains 455 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 386 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU 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 110 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 733 VAL 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 822 VAL Chi-restraints excluded: chain C residue 841 ARG Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1124 ILE 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 1278 LEU Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 722 ILE 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 1334 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 277 LEU Chi-restraints excluded: chain M residue 287 VAL 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: 9.9990 chunk 222 optimal weight: 0.9990 chunk 362 optimal weight: 50.0000 chunk 231 optimal weight: 10.0000 chunk 295 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 242 optimal weight: 0.3980 chunk 103 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 GLN ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS D 489 ASN D1350 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.091998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.065810 restraints weight = 120479.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.067878 restraints weight = 58650.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.069204 restraints weight = 36102.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.070105 restraints weight = 26286.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.070641 restraints weight = 21448.683| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 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 = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 29227 Z= 0.154 Angle : 0.691 12.813 40154 Z= 0.351 Chirality : 0.044 0.254 4788 Planarity : 0.005 0.086 4906 Dihedral : 16.356 173.531 5044 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.91 % Favored : 94.03 % Rotamer: Outliers : 4.39 % Allowed : 31.00 % 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 are not related in a simple way. whole: -0.66 (0.14), residues: 3587 helix: 0.93 (0.15), residues: 1289 sheet: -0.14 (0.26), residues: 389 loop : -1.52 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 799 TYR 0.032 0.002 TYR D1365 PHE 0.022 0.002 PHE C 390 TRP 0.011 0.001 TRP D 33 HIS 0.006 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (29224) covalent geometry : angle 0.69053 / 0.35 (40154) hydrogen bonds : bond 0.03806 / 2.61 ( 1188) hydrogen bonds : angle 4.54650 / 3.18 ( 3306) metal coordination : bond 0.00101 / 0.05 ( 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 567 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 452 time to evaluate : 1.156 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: A 35 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.8309 (t80) REVERT: A 51 MET cc_start: 0.7683 (mmp) cc_final: 0.7204 (mmm) REVERT: A 77 ASP cc_start: 0.6975 (OUTLIER) cc_final: 0.6549 (t0) REVERT: A 316 MET cc_start: 0.2838 (mmm) cc_final: 0.2526 (mmm) REVERT: B 118 ASP cc_start: 0.7766 (t0) cc_final: 0.7309 (t0) REVERT: B 121 VAL cc_start: 0.8324 (t) cc_final: 0.7926 (m) REVERT: B 197 ASP cc_start: 0.8482 (m-30) cc_final: 0.8258 (p0) REVERT: B 205 MET cc_start: 0.8013 (pmm) cc_final: 0.7676 (pmm) REVERT: C 239 MET cc_start: 0.6346 (tpt) cc_final: 0.4979 (tpp) REVERT: C 488 MET cc_start: 0.5945 (mtp) cc_final: 0.5290 (mtt) REVERT: C 492 MET cc_start: 0.8158 (tpp) cc_final: 0.7842 (tpp) REVERT: C 589 THR cc_start: 0.7581 (m) cc_final: 0.7075 (p) REVERT: C 681 MET cc_start: 0.6375 (mtp) cc_final: 0.6143 (ptp) REVERT: C 685 MET cc_start: 0.7375 (mmt) cc_final: 0.7134 (mmm) REVERT: C 741 MET cc_start: 0.8308 (mmm) cc_final: 0.7875 (mmt) REVERT: C 791 LEU cc_start: 0.7939 (mt) cc_final: 0.7581 (mt) REVERT: C 800 MET cc_start: 0.7919 (mmm) cc_final: 0.7010 (mmm) REVERT: C 866 ASP cc_start: 0.3631 (OUTLIER) cc_final: 0.3371 (p0) REVERT: C 921 PRO cc_start: 0.8538 (Cg_exo) cc_final: 0.8270 (Cg_endo) REVERT: C 1066 MET cc_start: 0.7782 (mmm) cc_final: 0.7315 (mmm) REVERT: C 1115 THR cc_start: 0.7279 (p) cc_final: 0.7062 (p) REVERT: C 1131 MET cc_start: 0.8827 (ptp) cc_final: 0.8146 (ppp) REVERT: C 1134 GLN cc_start: 0.9281 (mm-40) cc_final: 0.8829 (mp10) REVERT: C 1143 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8732 (pp20) REVERT: C 1170 MET cc_start: 0.7919 (tmm) cc_final: 0.6878 (mmt) REVERT: C 1229 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.6712 (t80) REVERT: C 1273 MET cc_start: 0.2943 (ptm) cc_final: 0.0657 (mpp) REVERT: C 1289 GLU cc_start: 0.7497 (tm-30) cc_final: 0.6596 (tm-30) REVERT: C 1290 MET cc_start: 0.7422 (tpt) cc_final: 0.6716 (tpt) REVERT: D 229 GLN cc_start: 0.7200 (mm110) cc_final: 0.6920 (mm-40) REVERT: D 298 MET cc_start: 0.7991 (mtp) cc_final: 0.7487 (mmp) REVERT: D 452 LEU cc_start: 0.8024 (mt) cc_final: 0.7695 (mm) REVERT: D 466 MET cc_start: 0.7052 (ttp) cc_final: 0.6462 (ttm) REVERT: D 474 LEU cc_start: 0.6100 (OUTLIER) cc_final: 0.5211 (pp) REVERT: D 525 MET cc_start: 0.7222 (ppp) cc_final: 0.6744 (ppp) REVERT: D 574 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8953 (p) REVERT: D 581 MET cc_start: 0.7682 (tpp) cc_final: 0.7287 (mmt) REVERT: D 644 MET cc_start: 0.7743 (mpp) cc_final: 0.7535 (mpp) REVERT: D 648 GLU cc_start: 0.8594 (mm-30) cc_final: 0.7793 (tm-30) REVERT: D 847 ASP cc_start: 0.6845 (OUTLIER) cc_final: 0.6101 (p0) REVERT: D 960 LEU cc_start: 0.8826 (tt) cc_final: 0.8544 (mt) REVERT: D 993 GLU cc_start: 0.1747 (mt-10) cc_final: 0.0499 (mt-10) REVERT: D 1220 ILE cc_start: 0.8247 (mt) cc_final: 0.7918 (mt) REVERT: D 1260 MET cc_start: 0.7919 (tpp) cc_final: 0.7445 (tpt) REVERT: D 1340 LYS cc_start: 0.4916 (ptmm) cc_final: 0.3960 (ptmm) outliers start: 115 outliers final: 63 residues processed: 532 average time/residue: 0.1458 time to fit residues: 130.9749 Evaluate side-chains 471 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 401 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU 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 B residue 12 ARG Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 GLU 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 530 ILE Chi-restraints excluded: chain C residue 533 LEU 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 841 ARG Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 1076 ILE 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 1201 LEU Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1229 TYR Chi-restraints excluded: chain C residue 1278 LEU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 574 VAL 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 847 ASP Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 277 LEU Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 357 GLN 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: 10.0000 chunk 181 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 281 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 271 optimal weight: 20.0000 chunk 186 optimal weight: 9.9990 chunk 261 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS A 186 ASN C 658 GLN C 832 HIS ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1256 GLN ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 419 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** M 121 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.089805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.063450 restraints weight = 124672.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.065442 restraints weight = 62367.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.066711 restraints weight = 39283.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.067588 restraints weight = 29117.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.068103 restraints weight = 24083.042| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 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 = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (17 function evaluations) r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.7324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.206 29227 Z= 0.256 Angle : 0.835 16.401 40154 Z= 0.439 Chirality : 0.050 0.416 4788 Planarity : 0.007 0.134 4906 Dihedral : 16.499 174.310 5044 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.80 % Favored : 93.09 % Rotamer: Outliers : 6.07 % Allowed : 29.82 % Favored : 64.11 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.14), residues: 3587 helix: 0.49 (0.14), residues: 1286 sheet: -0.38 (0.27), residues: 358 loop : -1.67 (0.13), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG D 836 TYR 0.023 0.002 TYR C1281 PHE 0.060 0.004 PHE C 157 TRP 0.023 0.002 TRP D 868 HIS 0.011 0.002 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.26 (29224) covalent geometry : angle 0.83537 / 0.44 (40154) hydrogen bonds : bond 0.04535 / 3.12 ( 1188) hydrogen bonds : angle 4.85195 / 3.41 ( 3306) metal coordination : bond 0.00437 / 0.22 ( 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 630 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 471 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8676 (t80) REVERT: A 51 MET cc_start: 0.8331 (mmp) cc_final: 0.8020 (mmm) REVERT: A 68 TYR cc_start: 0.8103 (m-80) cc_final: 0.7808 (m-80) REVERT: A 283 GLN cc_start: 0.5298 (OUTLIER) cc_final: 0.4581 (mm110) REVERT: A 307 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8790 (mt) REVERT: A 316 MET cc_start: 0.2922 (mmm) cc_final: 0.1613 (mmm) REVERT: C 40 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8004 (mm-30) REVERT: C 96 LEU cc_start: 0.8919 (tt) cc_final: 0.8669 (tp) REVERT: C 488 MET cc_start: 0.6237 (mtt) cc_final: 0.5810 (mtt) REVERT: C 492 MET cc_start: 0.8565 (tpp) cc_final: 0.8309 (tpp) REVERT: C 672 GLU cc_start: 0.8528 (pm20) cc_final: 0.8171 (pm20) REVERT: C 763 THR cc_start: 0.9284 (p) cc_final: 0.9026 (t) REVERT: C 773 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.5934 (mt) REVERT: C 782 VAL cc_start: 0.8986 (t) cc_final: 0.8758 (p) REVERT: C 800 MET cc_start: 0.8563 (mmm) cc_final: 0.7635 (mmm) REVERT: C 833 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7944 (tp) REVERT: C 921 PRO cc_start: 0.8870 (Cg_exo) cc_final: 0.8600 (Cg_endo) REVERT: C 1066 MET cc_start: 0.8346 (mmm) cc_final: 0.8028 (mmm) REVERT: C 1070 HIS cc_start: 0.8052 (m90) cc_final: 0.7697 (m170) REVERT: C 1119 MET cc_start: 0.8447 (mmm) cc_final: 0.8215 (mmm) REVERT: C 1131 MET cc_start: 0.9165 (ptp) cc_final: 0.8587 (ptp) REVERT: C 1134 GLN cc_start: 0.9353 (mm-40) cc_final: 0.8971 (mp10) REVERT: C 1176 LEU cc_start: 0.8990 (mp) cc_final: 0.8753 (pp) REVERT: C 1184 THR cc_start: 0.8325 (p) cc_final: 0.8047 (p) REVERT: C 1229 TYR cc_start: 0.9175 (OUTLIER) cc_final: 0.6971 (t80) REVERT: C 1268 GLN cc_start: 0.8554 (mp10) cc_final: 0.6483 (mp10) REVERT: C 1289 GLU cc_start: 0.8411 (tm-30) cc_final: 0.7994 (tm-30) REVERT: C 1294 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7989 (mtmt) REVERT: C 1329 GLU cc_start: 0.7928 (tt0) cc_final: 0.7717 (tt0) REVERT: C 1330 ILE cc_start: 0.8608 (mt) cc_final: 0.8396 (mt) REVERT: D 130 MET cc_start: 0.2343 (mpp) cc_final: 0.1838 (mpp) REVERT: D 229 GLN cc_start: 0.7484 (mm110) cc_final: 0.7208 (mm-40) REVERT: D 233 LYS cc_start: 0.2049 (OUTLIER) cc_final: 0.1738 (mtmt) REVERT: D 298 MET cc_start: 0.8310 (mtp) cc_final: 0.7812 (mmp) REVERT: D 390 LEU cc_start: 0.8604 (tp) cc_final: 0.8267 (mm) REVERT: D 452 LEU cc_start: 0.9050 (mt) cc_final: 0.8813 (mm) REVERT: D 466 MET cc_start: 0.7679 (ttp) cc_final: 0.7430 (ttm) REVERT: D 620 PHE cc_start: 0.7877 (t80) cc_final: 0.7372 (t80) REVERT: D 644 MET cc_start: 0.8255 (mpp) cc_final: 0.7660 (mpp) REVERT: D 648 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8105 (tm-30) REVERT: D 652 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8060 (pm20) REVERT: D 836 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8845 (tpt-90) REVERT: D 960 LEU cc_start: 0.8857 (tt) cc_final: 0.8461 (mt) REVERT: D 993 GLU cc_start: 0.2016 (mt-10) cc_final: 0.0601 (mt-10) REVERT: D 1220 ILE cc_start: 0.8765 (mt) cc_final: 0.8385 (mt) REVERT: E 8 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7737 (m-30) REVERT: E 17 PHE cc_start: 0.7580 (m-80) cc_final: 0.7137 (m-80) REVERT: E 48 VAL cc_start: 0.7856 (OUTLIER) cc_final: 0.7402 (p) outliers start: 159 outliers final: 85 residues processed: 581 average time/residue: 0.1690 time to fit residues: 166.2191 Evaluate side-chains 504 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 407 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 158 ASP 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 594 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 635 THR 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 748 ILE Chi-restraints excluded: chain C residue 750 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 822 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 833 ILE Chi-restraints excluded: chain C residue 836 LEU 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 1172 LEU 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 1278 LEU Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1294 LYS Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 233 LYS Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 836 ARG 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 1261 LEU Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1310 THR 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 48 VAL Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 277 LEU Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 357 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 65 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 189 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 78 optimal weight: 30.0000 chunk 87 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS A 186 ASN B 128 HIS C 573 ASN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 GLN C1080 ASN C1220 GLN C1324 ASN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** M 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.089926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.063446 restraints weight = 125580.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.065479 restraints weight = 62457.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.066800 restraints weight = 39247.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.067648 restraints weight = 29013.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.068126 restraints weight = 24091.419| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 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 = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.7861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 29227 Z= 0.159 Angle : 0.715 13.515 40154 Z= 0.361 Chirality : 0.045 0.261 4788 Planarity : 0.005 0.091 4906 Dihedral : 16.424 174.060 5044 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.74 % Favored : 94.20 % Rotamer: Outliers : 4.31 % Allowed : 32.57 % Favored : 63.12 % 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 are not related in a simple way. whole: -0.92 (0.14), residues: 3587 helix: 0.71 (0.14), residues: 1298 sheet: -0.41 (0.26), residues: 371 loop : -1.64 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 33 TYR 0.029 0.002 TYR D 995 PHE 0.015 0.002 PHE C 390 TRP 0.007 0.001 TRP D 33 HIS 0.004 0.001 HIS D 419 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (29224) covalent geometry : angle 0.71469 / 0.36 (40154) hydrogen bonds : bond 0.03737 / 2.56 ( 1188) hydrogen bonds : angle 4.55862 / 3.18 ( 3306) metal coordination : bond 0.00109 / 0.05 ( 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 523 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 410 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: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8578 (t80) REVERT: A 47 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9197 (mm) REVERT: A 51 MET cc_start: 0.8362 (mmp) cc_final: 0.8056 (mmm) REVERT: B 51 MET cc_start: 0.7014 (tpp) cc_final: 0.6639 (tpp) REVERT: B 152 TYR cc_start: 0.7280 (t80) cc_final: 0.7045 (t80) REVERT: C 40 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7839 (mm-30) REVERT: C 385 PHE cc_start: 0.8374 (m-80) cc_final: 0.8119 (m-80) REVERT: C 424 ASP cc_start: 0.7416 (t0) cc_final: 0.7202 (m-30) REVERT: C 488 MET cc_start: 0.6272 (OUTLIER) cc_final: 0.5732 (mtt) REVERT: C 492 MET cc_start: 0.8564 (tpp) cc_final: 0.8342 (tpp) REVERT: C 672 GLU cc_start: 0.8631 (pm20) cc_final: 0.8204 (pm20) REVERT: C 763 THR cc_start: 0.9377 (p) cc_final: 0.9126 (t) REVERT: C 773 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.6140 (mt) REVERT: C 800 MET cc_start: 0.8624 (mmm) cc_final: 0.8193 (mmm) REVERT: C 921 PRO cc_start: 0.8929 (Cg_exo) cc_final: 0.8664 (Cg_endo) REVERT: C 1066 MET cc_start: 0.8235 (mmm) cc_final: 0.7979 (mmm) REVERT: C 1070 HIS cc_start: 0.7925 (m90) cc_final: 0.7561 (m170) REVERT: C 1119 MET cc_start: 0.8352 (mmm) cc_final: 0.8104 (mmm) REVERT: C 1184 THR cc_start: 0.8242 (p) cc_final: 0.7917 (p) REVERT: C 1273 MET cc_start: 0.4650 (ptm) cc_final: 0.2709 (mpp) REVERT: C 1289 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7833 (tm-30) REVERT: C 1290 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7887 (ttt) REVERT: C 1294 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7950 (mttp) REVERT: C 1329 GLU cc_start: 0.8151 (tt0) cc_final: 0.7748 (tt0) REVERT: C 1330 ILE cc_start: 0.8611 (mt) cc_final: 0.8403 (mt) REVERT: D 229 GLN cc_start: 0.7575 (mm110) cc_final: 0.7271 (mm-40) REVERT: D 233 LYS cc_start: 0.2552 (OUTLIER) cc_final: 0.2157 (mtmt) REVERT: D 246 PRO cc_start: 0.6294 (Cg_exo) cc_final: 0.6000 (Cg_endo) REVERT: D 298 MET cc_start: 0.8292 (mtp) cc_final: 0.7869 (mmp) REVERT: D 330 MET cc_start: 0.6679 (ppp) cc_final: 0.6460 (ppp) REVERT: D 384 LYS cc_start: 0.6931 (tttt) cc_final: 0.6380 (mtpt) REVERT: D 390 LEU cc_start: 0.8604 (tp) cc_final: 0.8271 (mm) REVERT: D 452 LEU cc_start: 0.9055 (mt) cc_final: 0.8844 (mm) REVERT: D 525 MET cc_start: 0.8052 (ptm) cc_final: 0.7590 (ppp) REVERT: D 581 MET cc_start: 0.8601 (tpp) cc_final: 0.8019 (mmt) REVERT: D 620 PHE cc_start: 0.7968 (t80) cc_final: 0.7430 (t80) REVERT: D 648 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8103 (tm-30) REVERT: D 652 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8046 (pm20) REVERT: D 743 MET cc_start: 0.8900 (tmm) cc_final: 0.8666 (ppp) REVERT: D 836 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8903 (tpt-90) REVERT: D 960 LEU cc_start: 0.8811 (tt) cc_final: 0.8472 (mp) REVERT: D 993 GLU cc_start: 0.1839 (mt-10) cc_final: 0.0703 (mt-10) REVERT: D 995 TYR cc_start: 0.5072 (m-10) cc_final: 0.4670 (m-10) REVERT: D 1220 ILE cc_start: 0.8718 (mt) cc_final: 0.8444 (mt) REVERT: E 8 ASP cc_start: 0.8200 (p0) cc_final: 0.7634 (m-30) REVERT: E 17 PHE cc_start: 0.7643 (m-80) cc_final: 0.7112 (m-80) REVERT: E 42 GLU cc_start: 0.8147 (mp0) cc_final: 0.7885 (mp0) outliers start: 113 outliers final: 64 residues processed: 488 average time/residue: 0.1543 time to fit residues: 130.4157 Evaluate side-chains 459 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 386 time to evaluate : 1.642 ------------------------------------------------------------------------------- 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 47 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 84 GLU 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 488 MET 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 642 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1056 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 1278 LEU Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1294 LYS Chi-restraints excluded: chain C residue 1295 SER 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 244 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 836 ARG Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1238 GLN Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1334 GLU 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 M residue 277 LEU Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 357 GLN Chi-restraints excluded: chain M residue 406 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 7 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 296 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 272 optimal weight: 30.0000 chunk 213 optimal weight: 8.9990 chunk 216 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 119 optimal weight: 0.7980 chunk 261 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1314 GLN C1324 ASN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.089544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.063100 restraints weight = 126533.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.065120 restraints weight = 62875.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.066441 restraints weight = 39559.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.067234 restraints weight = 29320.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.067778 restraints weight = 24470.504| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 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 = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.8711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 29227 Z= 0.168 Angle : 0.742 15.897 40154 Z= 0.376 Chirality : 0.045 0.267 4788 Planarity : 0.005 0.090 4906 Dihedral : 16.394 173.726 5044 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.61 % Favored : 93.34 % Rotamer: Outliers : 3.93 % Allowed : 33.41 % Favored : 62.66 % 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 are not related in a simple way. whole: -0.91 (0.14), residues: 3587 helix: 0.76 (0.14), residues: 1287 sheet: -0.45 (0.26), residues: 380 loop : -1.65 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C1301 TYR 0.024 0.002 TYR D 68 PHE 0.016 0.002 PHE C 390 TRP 0.012 0.001 TRP D 33 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (29224) covalent geometry : angle 0.74249 / 0.38 (40154) hydrogen bonds : bond 0.03743 / 2.56 ( 1188) hydrogen bonds : angle 4.49787 / 3.11 ( 3306) metal coordination : bond 0.00218 / 0.11 ( 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 509 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 406 time to evaluate : 1.135 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 47 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9234 (mm) REVERT: A 51 MET cc_start: 0.8439 (mmp) cc_final: 0.8115 (tpp) REVERT: A 269 CYS cc_start: 0.3686 (OUTLIER) cc_final: 0.3450 (m) REVERT: B 51 MET cc_start: 0.7359 (tpp) cc_final: 0.6894 (tpp) REVERT: B 78 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7644 (pt) REVERT: B 177 TYR cc_start: 0.7436 (m-80) cc_final: 0.7178 (m-80) REVERT: C 403 MET cc_start: 0.7090 (tmm) cc_final: 0.6744 (tmm) REVERT: C 488 MET cc_start: 0.6462 (OUTLIER) cc_final: 0.5962 (mtt) REVERT: C 492 MET cc_start: 0.8660 (tpp) cc_final: 0.8321 (tpp) REVERT: C 577 VAL cc_start: 0.9454 (t) cc_final: 0.9241 (m) REVERT: C 672 GLU cc_start: 0.8693 (pm20) cc_final: 0.8397 (pm20) REVERT: C 685 MET cc_start: 0.8648 (mmm) cc_final: 0.8424 (mmm) REVERT: C 715 THR cc_start: 0.8461 (p) cc_final: 0.8218 (t) REVERT: C 773 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6601 (mt) REVERT: C 800 MET cc_start: 0.8825 (mmm) cc_final: 0.8452 (mmm) REVERT: C 815 SER cc_start: 0.8917 (m) cc_final: 0.8602 (p) REVERT: C 921 PRO cc_start: 0.8977 (Cg_exo) cc_final: 0.8716 (Cg_endo) REVERT: C 1070 HIS cc_start: 0.7933 (m90) cc_final: 0.7483 (m-70) REVERT: C 1095 ASP cc_start: 0.9146 (t0) cc_final: 0.8923 (t0) REVERT: C 1119 MET cc_start: 0.8558 (mmm) cc_final: 0.8231 (mmm) REVERT: C 1180 MET cc_start: 0.9087 (tpp) cc_final: 0.8705 (tpt) REVERT: C 1273 MET cc_start: 0.5293 (ptm) cc_final: 0.3330 (mpp) REVERT: C 1289 GLU cc_start: 0.8446 (tm-30) cc_final: 0.7857 (tm-30) REVERT: C 1290 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8027 (ttt) REVERT: C 1294 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7302 (mptt) REVERT: C 1295 SER cc_start: 0.8143 (OUTLIER) cc_final: 0.7908 (p) REVERT: C 1329 GLU cc_start: 0.8183 (tt0) cc_final: 0.7752 (tt0) REVERT: D 229 GLN cc_start: 0.7814 (mm110) cc_final: 0.7467 (mm-40) REVERT: D 246 PRO cc_start: 0.6355 (Cg_exo) cc_final: 0.6065 (Cg_endo) REVERT: D 264 ASP cc_start: 0.8499 (m-30) cc_final: 0.8213 (t70) REVERT: D 298 MET cc_start: 0.8433 (mtp) cc_final: 0.8116 (mmp) REVERT: D 330 MET cc_start: 0.7014 (ppp) cc_final: 0.6777 (ppp) REVERT: D 384 LYS cc_start: 0.7352 (tttt) cc_final: 0.6570 (mmmm) REVERT: D 390 LEU cc_start: 0.8784 (tp) cc_final: 0.8478 (mm) REVERT: D 430 HIS cc_start: 0.8385 (p-80) cc_final: 0.7936 (p90) REVERT: D 466 MET cc_start: 0.8202 (ttm) cc_final: 0.7890 (tpp) REVERT: D 620 PHE cc_start: 0.8301 (t80) cc_final: 0.7674 (t80) REVERT: D 648 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8269 (tm-30) REVERT: D 743 MET cc_start: 0.8958 (tmm) cc_final: 0.8733 (ppp) REVERT: D 836 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8646 (tpt170) REVERT: D 960 LEU cc_start: 0.8893 (tt) cc_final: 0.8521 (mt) REVERT: D 993 GLU cc_start: 0.1724 (mt-10) cc_final: 0.0363 (mt-10) REVERT: D 995 TYR cc_start: 0.5036 (m-10) cc_final: 0.4683 (m-10) REVERT: D 1156 LEU cc_start: 0.7276 (pt) cc_final: 0.7005 (pp) REVERT: E 7 GLN cc_start: 0.8578 (tp40) cc_final: 0.8376 (tp40) REVERT: E 8 ASP cc_start: 0.8256 (p0) cc_final: 0.7689 (m-30) REVERT: E 17 PHE cc_start: 0.7887 (m-80) cc_final: 0.7436 (m-80) REVERT: E 26 ARG cc_start: 0.7874 (mmm160) cc_final: 0.7423 (mmm160) REVERT: E 42 GLU cc_start: 0.8331 (mp0) cc_final: 0.7982 (mp0) outliers start: 103 outliers final: 67 residues processed: 482 average time/residue: 0.1621 time to fit residues: 133.9563 Evaluate side-chains 449 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 373 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 59 VAL Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 70 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 140 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1056 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 1201 LEU Chi-restraints excluded: chain C residue 1278 LEU Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1294 LYS Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 836 ARG Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 277 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 37 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 360 optimal weight: 50.0000 chunk 17 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 330 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 78 optimal weight: 40.0000 chunk 150 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.087396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.060802 restraints weight = 129383.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.062683 restraints weight = 66172.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.063912 restraints weight = 42664.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.064676 restraints weight = 32219.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.065115 restraints weight = 27211.378| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 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 = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 1.0349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.313 29227 Z= 0.287 Angle : 0.836 13.876 40154 Z= 0.439 Chirality : 0.050 0.807 4788 Planarity : 0.006 0.096 4906 Dihedral : 16.523 175.300 5044 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.61 % Favored : 93.31 % Rotamer: Outliers : 4.47 % Allowed : 33.60 % Favored : 61.93 % Cbeta Deviations : 0.03 % 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 are not related in a simple way. whole: -1.15 (0.14), residues: 3587 helix: 0.51 (0.14), residues: 1301 sheet: -0.53 (0.26), residues: 357 loop : -1.77 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 278 TYR 0.039 0.002 TYR B 152 PHE 0.019 0.002 PHE C 385 TRP 0.016 0.002 TRP C 183 HIS 0.008 0.001 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.29 (29224) covalent geometry : angle 0.83559 / 0.44 (40154) hydrogen bonds : bond 0.04648 / 3.12 ( 1188) hydrogen bonds : angle 4.74302 / 3.31 ( 3306) metal coordination : bond 0.00300 / 0.15 ( 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 488 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 371 time to evaluate : 1.076 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 29 GLU cc_start: 0.7066 (tp30) cc_final: 0.6540 (tp30) REVERT: A 47 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9229 (mm) REVERT: A 51 MET cc_start: 0.8760 (mmp) cc_final: 0.8277 (mpp) REVERT: A 75 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8354 (tp-100) REVERT: A 80 GLU cc_start: 0.8621 (mp0) cc_final: 0.8326 (pm20) REVERT: A 199 ASP cc_start: 0.8461 (t0) cc_final: 0.8234 (t0) REVERT: A 269 CYS cc_start: 0.3894 (OUTLIER) cc_final: 0.3656 (m) REVERT: B 78 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7958 (pt) REVERT: C 403 MET cc_start: 0.7303 (tmm) cc_final: 0.6891 (tmm) REVERT: C 488 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6569 (mtt) REVERT: C 515 MET cc_start: 0.6579 (ptm) cc_final: 0.5916 (ptt) REVERT: C 685 MET cc_start: 0.8880 (mmm) cc_final: 0.8651 (mmm) REVERT: C 741 MET cc_start: 0.8471 (mmm) cc_final: 0.8242 (mmm) REVERT: C 800 MET cc_start: 0.9028 (mmm) cc_final: 0.8531 (mmm) REVERT: C 828 PHE cc_start: 0.8254 (m-80) cc_final: 0.7822 (t80) REVERT: C 929 ILE cc_start: 0.8516 (mt) cc_final: 0.8306 (mp) REVERT: C 1109 ILE cc_start: 0.8649 (mm) cc_final: 0.8103 (mm) REVERT: C 1119 MET cc_start: 0.8912 (mmm) cc_final: 0.8476 (mmm) REVERT: C 1273 MET cc_start: 0.6073 (ptm) cc_final: 0.5034 (mpp) REVERT: C 1290 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8618 (ttm) REVERT: C 1297 ASP cc_start: 0.6747 (t0) cc_final: 0.6402 (m-30) REVERT: C 1328 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8016 (tppt) REVERT: C 1329 GLU cc_start: 0.8623 (tt0) cc_final: 0.8230 (tt0) REVERT: D 113 HIS cc_start: 0.8666 (m-70) cc_final: 0.8440 (t-90) REVERT: D 229 GLN cc_start: 0.8030 (mm110) cc_final: 0.7657 (mm-40) REVERT: D 264 ASP cc_start: 0.8580 (m-30) cc_final: 0.8262 (t70) REVERT: D 298 MET cc_start: 0.8448 (mtp) cc_final: 0.8213 (mmp) REVERT: D 314 ARG cc_start: 0.5506 (pmt-80) cc_final: 0.5152 (ptm160) REVERT: D 384 LYS cc_start: 0.7820 (tttt) cc_final: 0.7475 (mmmm) REVERT: D 390 LEU cc_start: 0.9025 (tp) cc_final: 0.8747 (mm) REVERT: D 466 MET cc_start: 0.8344 (ttm) cc_final: 0.7592 (tpp) REVERT: D 497 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8178 (mp0) REVERT: D 581 MET cc_start: 0.9210 (tpp) cc_final: 0.8914 (mmt) REVERT: D 648 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8481 (tm-30) REVERT: D 652 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: D 743 MET cc_start: 0.9057 (tmm) cc_final: 0.8784 (ppp) REVERT: D 993 GLU cc_start: 0.2302 (mt-10) cc_final: 0.0960 (mt-10) REVERT: D 995 TYR cc_start: 0.5558 (m-10) cc_final: 0.5191 (m-10) REVERT: D 1334 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: E 7 GLN cc_start: 0.8664 (tp40) cc_final: 0.8031 (tp40) REVERT: E 8 ASP cc_start: 0.8533 (p0) cc_final: 0.7906 (m-30) REVERT: E 17 PHE cc_start: 0.8373 (m-80) cc_final: 0.8009 (m-80) outliers start: 117 outliers final: 67 residues processed: 454 average time/residue: 0.1500 time to fit residues: 117.2656 Evaluate side-chains 418 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 343 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 59 VAL 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 140 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 833 ILE Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1056 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 1251 TYR Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1294 LYS Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1328 LYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 886 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 271 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 298 optimal weight: 9.9990 chunk 212 optimal weight: 0.7980 chunk 337 optimal weight: 30.0000 chunk 85 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 28 optimal weight: 30.0000 chunk 243 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 462 ASN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1299 ASN D 276 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.087397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.060749 restraints weight = 128045.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.062638 restraints weight = 64935.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.063858 restraints weight = 41674.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.064609 restraints weight = 31444.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.065094 restraints weight = 26515.792| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 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 = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 1.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 29227 Z= 0.199 Angle : 0.800 14.052 40154 Z= 0.403 Chirality : 0.047 0.247 4788 Planarity : 0.006 0.154 4906 Dihedral : 16.493 174.907 5044 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.83 % Favored : 93.09 % Rotamer: Outliers : 2.67 % Allowed : 35.70 % Favored : 61.63 % 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 are not related in a simple way. whole: -1.14 (0.14), residues: 3587 helix: 0.54 (0.14), residues: 1297 sheet: -0.74 (0.26), residues: 384 loop : -1.73 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 148 TYR 0.052 0.002 TYR B 177 PHE 0.025 0.002 PHE C 464 TRP 0.012 0.002 TRP C1276 HIS 0.006 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (29224) covalent geometry : angle 0.79983 / 0.40 (40154) hydrogen bonds : bond 0.03983 / 2.71 ( 1188) hydrogen bonds : angle 4.60553 / 3.22 ( 3306) metal coordination : bond 0.00280 / 0.14 ( 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 436 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 366 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7322 (tp30) cc_final: 0.6737 (tp30) REVERT: A 35 PHE cc_start: 0.8939 (m-80) cc_final: 0.8575 (m-80) REVERT: A 47 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9277 (mm) REVERT: A 75 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8204 (tp-100) REVERT: A 199 ASP cc_start: 0.8518 (t0) cc_final: 0.8244 (t0) REVERT: A 269 CYS cc_start: 0.3906 (OUTLIER) cc_final: 0.3702 (m) REVERT: B 49 SER cc_start: 0.8970 (m) cc_final: 0.8727 (p) REVERT: B 51 MET cc_start: 0.8332 (mmm) cc_final: 0.7774 (mmm) REVERT: B 78 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8009 (pt) REVERT: C 403 MET cc_start: 0.7416 (tmm) cc_final: 0.6999 (tmm) REVERT: C 468 LEU cc_start: 0.8389 (mt) cc_final: 0.8121 (mt) REVERT: C 488 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6758 (mtt) REVERT: C 494 ASN cc_start: 0.6055 (t0) cc_final: 0.5842 (t0) REVERT: C 515 MET cc_start: 0.6647 (ptm) cc_final: 0.6184 (ptt) REVERT: C 685 MET cc_start: 0.9019 (mmm) cc_final: 0.8816 (mmm) REVERT: C 783 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8525 (mp) REVERT: C 800 MET cc_start: 0.9006 (mmm) cc_final: 0.8676 (mmm) REVERT: C 929 ILE cc_start: 0.8988 (mt) cc_final: 0.8751 (mp) REVERT: C 951 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8644 (mpp) REVERT: C 1066 MET cc_start: 0.8522 (mmm) cc_final: 0.8277 (mmm) REVERT: C 1119 MET cc_start: 0.8939 (mmm) cc_final: 0.8242 (tpp) REVERT: C 1273 MET cc_start: 0.6197 (ptm) cc_final: 0.5725 (mtm) REVERT: C 1274 GLU cc_start: 0.7636 (mp0) cc_final: 0.7038 (mm-30) REVERT: C 1297 ASP cc_start: 0.7162 (t0) cc_final: 0.6920 (t0) REVERT: D 128 LEU cc_start: 0.7452 (mt) cc_final: 0.7065 (mt) REVERT: D 229 GLN cc_start: 0.8248 (mm110) cc_final: 0.7880 (mm-40) REVERT: D 264 ASP cc_start: 0.8801 (m-30) cc_final: 0.8335 (t70) REVERT: D 314 ARG cc_start: 0.6112 (pmt-80) cc_final: 0.5688 (ptm160) REVERT: D 390 LEU cc_start: 0.9152 (tp) cc_final: 0.8906 (mm) REVERT: D 603 LYS cc_start: 0.9410 (tppt) cc_final: 0.9111 (ttmm) REVERT: D 644 MET cc_start: 0.8768 (mpp) cc_final: 0.8529 (mpp) REVERT: D 648 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8629 (tm-30) REVERT: D 652 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7753 (pm20) REVERT: D 837 ASP cc_start: 0.8691 (t0) cc_final: 0.8451 (t70) REVERT: D 993 GLU cc_start: 0.2644 (mt-10) cc_final: 0.1043 (mt-10) REVERT: D 995 TYR cc_start: 0.5619 (m-10) cc_final: 0.5242 (m-10) REVERT: D 1152 GLU cc_start: 0.8634 (tp30) cc_final: 0.8111 (tp30) REVERT: D 1156 LEU cc_start: 0.7800 (pt) cc_final: 0.7240 (pp) REVERT: D 1275 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7891 (mm) REVERT: D 1334 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: E 7 GLN cc_start: 0.8716 (tp40) cc_final: 0.8095 (tp40) REVERT: E 8 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8069 (m-30) REVERT: E 17 PHE cc_start: 0.8738 (m-80) cc_final: 0.8476 (m-80) REVERT: E 30 MET cc_start: 0.8599 (mmt) cc_final: 0.8197 (mmt) outliers start: 70 outliers final: 44 residues processed: 417 average time/residue: 0.1442 time to fit residues: 103.2000 Evaluate side-chains 395 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 341 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 98 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain B residue 12 ARG Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 833 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1056 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 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 320 ASN Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 277 LEU Chi-restraints excluded: chain M residue 287 VAL 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: 10.0000 chunk 58 optimal weight: 10.0000 chunk 298 optimal weight: 9.9990 chunk 303 optimal weight: 0.5980 chunk 229 optimal weight: 0.0040 chunk 216 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 chunk 96 optimal weight: 7.9990 overall best weight: 5.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS A 41 ASN A 132 HIS ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS D 277 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.085887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.058882 restraints weight = 131777.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.060708 restraints weight = 67478.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.061895 restraints weight = 43880.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.062629 restraints weight = 33487.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.063026 restraints weight = 28531.708| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 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 = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 1.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 29227 Z= 0.224 Angle : 0.823 16.235 40154 Z= 0.416 Chirality : 0.047 0.256 4788 Planarity : 0.005 0.095 4906 Dihedral : 16.517 174.665 5044 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.66 % Favored : 93.20 % Rotamer: Outliers : 3.05 % Allowed : 35.59 % Favored : 61.36 % 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 are not related in a simple way. whole: -1.14 (0.14), residues: 3587 helix: 0.51 (0.14), residues: 1301 sheet: -0.55 (0.27), residues: 359 loop : -1.75 (0.13), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C1216 TYR 0.035 0.002 TYR B 177 PHE 0.016 0.002 PHE D1325 TRP 0.019 0.002 TRP M 285 HIS 0.006 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (29224) covalent geometry : angle 0.82320 / 0.42 (40154) hydrogen bonds : bond 0.04343 / 2.95 ( 1188) hydrogen bonds : angle 4.71648 / 3.27 ( 3306) metal coordination : bond 0.00316 / 0.16 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6266.03 seconds wall clock time: 108 minutes 15.40 seconds (6495.40 seconds total)