Starting phenix.real_space_refine on Sun Jul 5 13:44:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ree_19084/07_2026/8ree_19084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ree_19084/07_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_19084/07_2026/8ree_19084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ree_19084/07_2026/8ree_19084.map" model { file = "/net/cci-nas-00/data/ceres_data/8ree_19084/07_2026/8ree_19084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ree_19084/07_2026/8ree_19084.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ree_19084/07_2026/8ree_19084.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ree_19084/07_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-dev-6108/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: {'RNA': 9} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna3p': 8} Chain: "T" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1011 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14675 SG CYS D 70 107.768 114.567 86.352 1.00 46.88 S ATOM 14804 SG CYS D 88 106.510 115.411 90.421 1.00 47.95 S ATOM 20917 SG CYS D 898 100.880 47.137 83.808 1.00 25.68 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 166 " occ=0.89 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.89 Time building chain proxies: 4.73, per 1000 atoms: 0.17 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: 2.28 Conformation dependent library (CDL) restraints added in 931.6 milliseconds 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: 2.78 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: 6.68 Time building geometry restraints manager: 3.08 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: 39851 2.89 - 5.79: 255 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: 16514 34.83 - 69.65: 974 69.65 - 104.48: 55 104.48 - 139.31: 1 139.31 - 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 - 0.036: 3211 0.036 - 0.072: 1066 0.072 - 0.109: 420 0.109 - 0.145: 85 0.145 - 0.181: 6 Chirality restraints: 4788 Sorted by residual: chirality pdb=" CB VAL M 278 " pdb=" CA VAL M 278 " pdb=" CG1 VAL M 278 " pdb=" CG2 VAL M 278 " both_signs ideal model delta sigma weight residual False -2.63 -2.81 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CB ILE M 170 " pdb=" CA ILE M 170 " pdb=" CG1 ILE M 170 " pdb=" CG2 ILE M 170 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" P DT N 4 " pdb=" OP1 DT N 4 " pdb=" OP2 DT N 4 " pdb=" O5' DT N 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.49 -0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 4785 not shown) Planarity restraints: 4906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 566 " 0.080 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO C 567 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO C 567 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO C 567 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D1184 " -0.081 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PRO D1185 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO D1185 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO D1185 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 204 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO C 205 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO C 205 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 205 " -0.059 5.00e-02 4.00e+02 ... (remaining 4903 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 172 2.53 - 3.12: 21462 3.12 - 3.71: 44955 3.71 - 4.31: 57724 4.31 - 4.90: 97826 Nonbonded interactions: 222139 Sorted by model distance: nonbonded pdb=" O3' C R 7 " pdb="MG MG D1501 " model vdw 1.936 2.170 nonbonded pdb=" O LEU D 71 " pdb="ZN ZN D1502 " model vdw 2.127 2.230 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.147 2.170 nonbonded pdb=" OD1 ASP C 354 " pdb=" OG1 THR C 356 " model vdw 2.153 3.040 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1501 " model vdw 2.157 2.170 ... (remaining 222134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.490 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.520 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.730 ------------------------------------------------------------------------------- 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 : 0.669 14.474 40154 Z= 0.400 Chirality : 0.043 0.181 4788 Planarity : 0.005 0.124 4906 Dihedral : 19.564 174.137 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 0.66869 / 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 : 0.769 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: 0.1939 time to fit residues: 228.2540 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 : 0.944 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.092326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.065872 restraints weight = 119748.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.067955 restraints weight = 57912.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.069314 restraints weight = 35575.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.070181 restraints weight = 25865.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.070712 restraints weight = 21215.791| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 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 = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 29227 Z= 0.218 Angle : 0.797 11.038 40154 Z= 0.416 Chirality : 0.047 0.319 4788 Planarity : 0.006 0.082 4906 Dihedral : 16.473 173.390 5046 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 5.57 % Allowed : 30.36 % Favored : 64.07 % 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: -0.77 (0.14), residues: 3587 helix: 0.73 (0.14), residues: 1275 sheet: -0.14 (0.27), residues: 362 loop : -1.48 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1156 TYR 0.042 0.003 TYR C 62 PHE 0.022 0.003 PHE C 57 TRP 0.018 0.002 TRP C 807 HIS 0.010 0.002 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.22 (29224) covalent geometry : angle 0.79719 / 0.42 (40154) hydrogen bonds : bond 0.04711 / 3.24 ( 1188) hydrogen bonds : angle 5.04460 / 3.50 ( 3306) metal coordination : bond 0.00176 / 0.09 ( 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 633 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 487 time to evaluate : 0.959 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: 0.8392 (OUTLIER) cc_final: 0.8134 (t80) REVERT: A 47 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8781 (mm) REVERT: A 77 ASP cc_start: 0.6015 (OUTLIER) cc_final: 0.5010 (t0) REVERT: B 92 VAL cc_start: 0.6601 (m) cc_final: 0.6154 (t) REVERT: B 95 LYS cc_start: 0.6948 (mtmm) cc_final: 0.6733 (mtmm) REVERT: B 118 ASP cc_start: 0.7483 (t0) cc_final: 0.7096 (t0) REVERT: B 197 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7997 (p0) REVERT: C 31 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8107 (tp-100) REVERT: C 239 MET cc_start: 0.5954 (tpt) cc_final: 0.5465 (tpp) REVERT: C 456 VAL cc_start: 0.7044 (OUTLIER) cc_final: 0.6604 (p) REVERT: C 492 MET cc_start: 0.7716 (tpp) cc_final: 0.7385 (tpp) REVERT: C 681 MET cc_start: 0.6045 (mtt) cc_final: 0.5678 (mtm) REVERT: C 876 GLU cc_start: 0.4468 (pm20) cc_final: 0.4184 (pt0) REVERT: C 1066 MET cc_start: 0.7552 (mmm) cc_final: 0.7115 (mmm) REVERT: C 1098 LEU cc_start: 0.5081 (OUTLIER) cc_final: 0.4806 (mp) REVERT: C 1131 MET cc_start: 0.8383 (ptp) cc_final: 0.8098 (ptp) REVERT: C 1229 TYR cc_start: 0.8087 (OUTLIER) cc_final: 0.6269 (t80) REVERT: C 1235 LEU cc_start: 0.7179 (mp) cc_final: 0.6712 (mp) REVERT: C 1274 GLU cc_start: 0.5368 (OUTLIER) cc_final: 0.4784 (mm-30) REVERT: C 1289 GLU cc_start: 0.6153 (tm-30) cc_final: 0.5826 (tm-30) REVERT: C 1337 ILE cc_start: 0.8530 (mt) cc_final: 0.8223 (mt) REVERT: D 92 VAL cc_start: 0.1697 (OUTLIER) cc_final: 0.1320 (p) REVERT: D 232 ASN cc_start: 0.3368 (OUTLIER) cc_final: 0.2720 (t0) REVERT: D 237 MET cc_start: 0.1713 (OUTLIER) cc_final: 0.1284 (tmm) REVERT: D 375 GLU cc_start: 0.7222 (tp30) cc_final: 0.6762 (tp30) REVERT: D 452 LEU cc_start: 0.7440 (mt) cc_final: 0.7111 (mm) REVERT: D 724 MET cc_start: 0.7098 (mtp) cc_final: 0.6791 (mpp) REVERT: D 747 MET cc_start: 0.6222 (mtm) cc_final: 0.5990 (mpp) REVERT: D 864 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6844 (mt) REVERT: D 982 LEU cc_start: 0.8590 (mt) cc_final: 0.8347 (pp) REVERT: D 993 GLU cc_start: 0.0499 (mt-10) cc_final: -0.2166 (mt-10) REVERT: D 1260 MET cc_start: 0.7054 (tpp) cc_final: 0.6709 (tpp) REVERT: E 7 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7906 (tp40) REVERT: E 59 ILE cc_start: 0.5183 (OUTLIER) cc_final: 0.4948 (pt) REVERT: E 63 ILE cc_start: 0.7095 (OUTLIER) cc_final: 0.6795 (pt) REVERT: M 376 MET cc_start: -0.0897 (tpt) cc_final: -0.1817 (tpt) outliers start: 146 outliers final: 45 residues processed: 590 average time/residue: 0.1587 time to fit residues: 152.5889 Evaluate side-chains 478 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 418 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 57 THR Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 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 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 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 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 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 864 LEU 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 E residue 46 THR 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: 0.9990 chunk 123 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 218 optimal weight: 0.4980 chunk 224 optimal weight: 0.2980 chunk 320 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 chunk 28 optimal weight: 10.0000 chunk 25 optimal weight: 50.0000 chunk 186 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.093100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.067026 restraints weight = 118261.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.069140 restraints weight = 57333.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.070514 restraints weight = 35182.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.071388 restraints weight = 25425.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.071965 restraints weight = 20771.692| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 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 = 0.3299 r_free = 0.3299 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: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5774 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29227 Z= 0.144 Angle : 0.713 15.009 40154 Z= 0.363 Chirality : 0.044 0.236 4788 Planarity : 0.005 0.134 4906 Dihedral : 16.432 172.996 5044 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.55 % Favored : 94.37 % Rotamer: Outliers : 4.31 % Allowed : 30.58 % Favored : 65.10 % 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: -0.73 (0.14), residues: 3587 helix: 0.81 (0.15), residues: 1292 sheet: -0.17 (0.26), residues: 375 loop : -1.52 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 339 TYR 0.033 0.002 TYR C 756 PHE 0.013 0.002 PHE D 141 TRP 0.011 0.001 TRP D 115 HIS 0.007 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (29224) covalent geometry : angle 0.71344 / 0.36 (40154) hydrogen bonds : bond 0.04183 / 2.86 ( 1188) hydrogen bonds : angle 4.80671 / 3.35 ( 3306) metal coordination : bond 0.00133 / 0.07 ( 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: 113 poor density : 428 time to evaluate : 0.998 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: 0.8306 (OUTLIER) cc_final: 0.8046 (t80) REVERT: A 77 ASP cc_start: 0.6573 (OUTLIER) cc_final: 0.6089 (t0) REVERT: A 159 ILE cc_start: 0.4715 (mm) cc_final: 0.4367 (mm) REVERT: A 316 MET cc_start: 0.2767 (mmm) cc_final: 0.2036 (mmm) REVERT: C 35 PHE cc_start: 0.7035 (t80) cc_final: 0.6099 (t80) REVERT: C 239 MET cc_start: 0.6252 (tpt) cc_final: 0.4757 (tpp) REVERT: C 488 MET cc_start: 0.5444 (mtt) cc_final: 0.4636 (mtt) REVERT: C 611 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6093 (mt-10) REVERT: C 685 MET cc_start: 0.6856 (mmt) cc_final: 0.6319 (mmm) REVERT: C 741 MET cc_start: 0.8382 (mmm) cc_final: 0.7873 (mmt) REVERT: C 749 ASP cc_start: 0.4277 (OUTLIER) cc_final: 0.4005 (t0) REVERT: C 756 TYR cc_start: 0.2721 (m-80) cc_final: 0.2281 (m-80) REVERT: C 793 GLU cc_start: 0.6344 (tt0) cc_final: 0.6039 (tt0) REVERT: C 800 MET cc_start: 0.7342 (mmm) cc_final: 0.6615 (mmm) REVERT: C 825 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7538 (mt-10) REVERT: C 1066 MET cc_start: 0.7627 (mmm) cc_final: 0.7272 (mmm) REVERT: C 1098 LEU cc_start: 0.5214 (OUTLIER) cc_final: 0.4933 (mp) REVERT: C 1229 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.6380 (t80) REVERT: C 1235 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6724 (mp) REVERT: C 1274 GLU cc_start: 0.5172 (OUTLIER) cc_final: 0.4459 (mm-30) REVERT: D 57 PHE cc_start: 0.4194 (m-10) cc_final: 0.3878 (m-10) REVERT: D 114 ILE cc_start: 0.5032 (OUTLIER) cc_final: 0.4803 (tt) REVERT: D 298 MET cc_start: 0.7759 (mtp) cc_final: 0.7181 (mmm) REVERT: D 356 THR cc_start: 0.7088 (p) cc_final: 0.6597 (t) REVERT: D 375 GLU cc_start: 0.7313 (tp30) cc_final: 0.6904 (tp30) REVERT: D 452 LEU cc_start: 0.7301 (mt) cc_final: 0.6955 (mm) REVERT: D 699 ASP cc_start: 0.8361 (m-30) cc_final: 0.7895 (t0) REVERT: D 747 MET cc_start: 0.6383 (mtm) cc_final: 0.6124 (mpp) REVERT: D 995 TYR cc_start: 0.4608 (m-80) cc_final: 0.4338 (m-10) REVERT: D 1260 MET cc_start: 0.7101 (tpp) cc_final: 0.6735 (tpp) REVERT: E 17 PHE cc_start: 0.6098 (m-80) cc_final: 0.5856 (m-80) REVERT: E 48 VAL cc_start: 0.6748 (OUTLIER) cc_final: 0.6386 (p) REVERT: E 58 LEU cc_start: 0.7766 (tp) cc_final: 0.7522 (tt) REVERT: E 59 ILE cc_start: 0.5114 (OUTLIER) cc_final: 0.4434 (tt) REVERT: E 63 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6728 (pt) outliers start: 113 outliers final: 58 residues processed: 501 average time/residue: 0.1562 time to fit residues: 130.1801 Evaluate side-chains 455 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 385 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 57 THR Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 173 VAL 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 841 ARG Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1229 TYR Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1291 LEU Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1304 MET Chi-restraints excluded: chain D residue 114 ILE 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 839 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1255 VAL 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 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 278 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 357 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 282 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 chunk 252 optimal weight: 10.0000 chunk 232 optimal weight: 7.9990 chunk 278 optimal weight: 7.9990 chunk 291 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 286 optimal weight: 0.0010 chunk 33 optimal weight: 1.9990 chunk 166 optimal weight: 0.3980 overall best weight: 1.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS B 227 GLN D 229 GLN ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 GLN E 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.092199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.066306 restraints weight = 119556.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.068381 restraints weight = 58310.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.069749 restraints weight = 35860.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.070624 restraints weight = 25869.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.071094 restraints weight = 21035.659| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 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 = 0.3282 r_free = 0.3282 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 (14 function evaluations) r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 29227 Z= 0.146 Angle : 0.684 11.460 40154 Z= 0.351 Chirality : 0.044 0.234 4788 Planarity : 0.005 0.087 4906 Dihedral : 16.449 173.023 5044 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.16 % Favored : 93.76 % Rotamer: Outliers : 4.39 % Allowed : 30.85 % Favored : 64.76 % 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: -0.74 (0.14), residues: 3587 helix: 0.84 (0.14), residues: 1291 sheet: -0.27 (0.26), residues: 389 loop : -1.53 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 218 TYR 0.022 0.002 TYR C 62 PHE 0.029 0.002 PHE C 35 TRP 0.012 0.001 TRP D 33 HIS 0.006 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (29224) covalent geometry : angle 0.68391 / 0.35 (40154) hydrogen bonds : bond 0.03943 / 2.68 ( 1188) hydrogen bonds : angle 4.66002 / 3.26 ( 3306) metal coordination : bond 0.00113 / 0.06 ( 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 551 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 436 time to evaluate : 0.767 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: A 35 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.8219 (t80) REVERT: A 77 ASP cc_start: 0.6780 (OUTLIER) cc_final: 0.6367 (t0) REVERT: A 142 MET cc_start: 0.6428 (ttp) cc_final: 0.6034 (ttp) REVERT: A 316 MET cc_start: 0.2900 (mmm) cc_final: 0.2140 (mmm) REVERT: B 205 MET cc_start: 0.7912 (pmm) cc_final: 0.7556 (pmm) REVERT: C 124 MET cc_start: 0.5662 (mpp) cc_final: 0.5400 (mmp) REVERT: C 239 MET cc_start: 0.6251 (tpt) cc_final: 0.4809 (tpp) REVERT: C 488 MET cc_start: 0.5405 (mtt) cc_final: 0.4622 (mtt) REVERT: C 611 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6142 (mt-10) REVERT: C 685 MET cc_start: 0.7057 (mmt) cc_final: 0.6606 (mmm) REVERT: C 749 ASP cc_start: 0.4402 (OUTLIER) cc_final: 0.4155 (t0) REVERT: C 791 LEU cc_start: 0.7583 (mt) cc_final: 0.7259 (mt) REVERT: C 800 MET cc_start: 0.7620 (mmm) cc_final: 0.6740 (mmm) REVERT: C 866 ASP cc_start: 0.3411 (OUTLIER) cc_final: 0.3005 (p0) REVERT: C 921 PRO cc_start: 0.8565 (Cg_exo) cc_final: 0.8307 (Cg_endo) REVERT: C 1066 MET cc_start: 0.7584 (mmm) cc_final: 0.7173 (mmm) REVERT: C 1098 LEU cc_start: 0.5651 (OUTLIER) cc_final: 0.5397 (mp) REVERT: C 1134 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8703 (mp10) REVERT: C 1170 MET cc_start: 0.7990 (tmm) cc_final: 0.6934 (mmt) REVERT: C 1229 TYR cc_start: 0.8175 (OUTLIER) cc_final: 0.6508 (t80) REVERT: C 1235 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7206 (mp) REVERT: C 1290 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6978 (tpt) REVERT: D 229 GLN cc_start: 0.7094 (mm110) cc_final: 0.6889 (mm-40) REVERT: D 298 MET cc_start: 0.7925 (mtp) cc_final: 0.7473 (mmm) REVERT: D 375 GLU cc_start: 0.7838 (tp30) cc_final: 0.7463 (tp30) REVERT: D 581 MET cc_start: 0.7490 (tpp) cc_final: 0.6974 (mmt) REVERT: D 648 GLU cc_start: 0.8551 (mm-30) cc_final: 0.7795 (tm-30) REVERT: D 747 MET cc_start: 0.6551 (mtm) cc_final: 0.6191 (mpp) REVERT: D 960 LEU cc_start: 0.8734 (tt) cc_final: 0.8455 (mt) REVERT: D 993 GLU cc_start: 0.0462 (mt-10) cc_final: 0.0250 (mt-10) REVERT: D 995 TYR cc_start: 0.5030 (m-80) cc_final: 0.4781 (m-10) REVERT: D 1340 LYS cc_start: 0.4937 (ptmm) cc_final: 0.3921 (ptmm) REVERT: D 1344 LEU cc_start: 0.7466 (mp) cc_final: 0.6237 (tt) REVERT: E 48 VAL cc_start: 0.6923 (OUTLIER) cc_final: 0.6569 (p) REVERT: E 59 ILE cc_start: 0.5227 (OUTLIER) cc_final: 0.4132 (mm) outliers start: 115 outliers final: 62 residues processed: 517 average time/residue: 0.1505 time to fit residues: 130.8042 Evaluate side-chains 472 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 399 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 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 144 ILE 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 6 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 158 ASP 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 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 1161 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 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 C residue 1304 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 353 SER 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 641 ILE Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 682 VAL 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 48 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: 8.9990 chunk 362 optimal weight: 40.0000 chunk 231 optimal weight: 0.8980 chunk 295 optimal weight: 40.0000 chunk 51 optimal weight: 5.9990 chunk 86 optimal weight: 50.0000 chunk 34 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS A 41 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 227 GLN C 517 GLN C 604 HIS C 620 ASN C 658 GLN C 761 GLN ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1256 GLN ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1350 ASN M 262 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.089815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.063410 restraints weight = 126735.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.065406 restraints weight = 63364.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.066719 restraints weight = 40010.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.067546 restraints weight = 29651.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.068065 restraints weight = 24657.600| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 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 = 0.3245 r_free = 0.3245 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 (13 function evaluations) r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.7799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.130 29227 Z= 0.307 Angle : 0.965 16.741 40154 Z= 0.514 Chirality : 0.053 0.419 4788 Planarity : 0.007 0.101 4906 Dihedral : 16.776 174.978 5044 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.25 % Favored : 92.64 % Rotamer: Outliers : 6.83 % Allowed : 28.64 % Favored : 64.53 % 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: -1.43 (0.13), residues: 3587 helix: 0.09 (0.14), residues: 1290 sheet: -0.55 (0.26), residues: 353 loop : -1.80 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.060 0.001 ARG D 137 TYR 0.029 0.003 TYR C 215 PHE 0.047 0.004 PHE B 35 TRP 0.027 0.003 TRP D 33 HIS 0.021 0.003 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.31 (29224) covalent geometry : angle 0.96490 / 0.51 (40154) hydrogen bonds : bond 0.05651 / 3.85 ( 1188) hydrogen bonds : angle 5.26767 / 3.69 ( 3306) metal coordination : bond 0.00257 / 0.13 ( 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 672 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 493 time to evaluate : 0.849 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: A 316 MET cc_start: 0.3561 (mmm) cc_final: 0.2872 (mtt) REVERT: A 320 ASN cc_start: 0.7647 (OUTLIER) cc_final: 0.7040 (m-40) REVERT: B 26 VAL cc_start: 0.9286 (t) cc_final: 0.9014 (p) REVERT: B 28 LEU cc_start: 0.8377 (mp) cc_final: 0.8173 (mt) REVERT: B 51 MET cc_start: 0.7160 (tpp) cc_final: 0.6883 (mmm) REVERT: C 68 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.5734 (tt) REVERT: C 96 LEU cc_start: 0.8904 (tt) cc_final: 0.8693 (tp) REVERT: C 100 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6843 (pt) REVERT: C 177 ILE cc_start: 0.7016 (mt) cc_final: 0.6749 (mm) REVERT: C 432 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7900 (pp) REVERT: C 476 LYS cc_start: 0.8628 (mttt) cc_final: 0.7986 (mmmt) REVERT: C 488 MET cc_start: 0.6360 (mtt) cc_final: 0.5598 (mtt) REVERT: C 525 THR cc_start: 0.8860 (t) cc_final: 0.8605 (t) REVERT: C 577 VAL cc_start: 0.9574 (t) cc_final: 0.9303 (m) REVERT: C 672 GLU cc_start: 0.8619 (pm20) cc_final: 0.8261 (pm20) REVERT: C 681 MET cc_start: 0.7937 (mtm) cc_final: 0.7686 (mtm) REVERT: C 715 THR cc_start: 0.8293 (p) cc_final: 0.8062 (t) REVERT: C 732 ILE cc_start: 0.9379 (mt) cc_final: 0.9101 (mp) REVERT: C 773 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6596 (mt) REVERT: C 800 MET cc_start: 0.8783 (mmm) cc_final: 0.8227 (mmm) REVERT: C 815 SER cc_start: 0.9172 (m) cc_final: 0.8663 (p) REVERT: C 836 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7818 (tt) REVERT: C 876 GLU cc_start: 0.7696 (pt0) cc_final: 0.7290 (pt0) REVERT: C 921 PRO cc_start: 0.9022 (Cg_exo) cc_final: 0.8756 (Cg_endo) REVERT: C 1066 MET cc_start: 0.8852 (mmm) cc_final: 0.8368 (mmm) REVERT: C 1080 ASN cc_start: 0.9444 (m-40) cc_final: 0.9159 (m-40) REVERT: C 1137 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7944 (mp0) REVERT: C 1273 MET cc_start: 0.5512 (ptm) cc_final: 0.3303 (mpp) REVERT: C 1329 GLU cc_start: 0.7926 (tt0) cc_final: 0.7417 (tt0) REVERT: C 1335 ILE cc_start: 0.8748 (mt) cc_final: 0.8246 (tp) REVERT: D 78 LEU cc_start: 0.8361 (tp) cc_final: 0.7836 (tp) REVERT: D 229 GLN cc_start: 0.7520 (mm110) cc_final: 0.7301 (mm-40) REVERT: D 233 LYS cc_start: 0.3115 (OUTLIER) cc_final: 0.2681 (mtmt) REVERT: D 298 MET cc_start: 0.8328 (mtp) cc_final: 0.7896 (mmp) REVERT: D 390 LEU cc_start: 0.8705 (tp) cc_final: 0.8257 (mm) REVERT: D 400 MET cc_start: 0.8372 (mpp) cc_final: 0.7973 (ptp) REVERT: D 428 THR cc_start: 0.7027 (m) cc_final: 0.6171 (p) REVERT: D 466 MET cc_start: 0.8501 (ttp) cc_final: 0.7438 (ttm) REVERT: D 472 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6453 (pp) REVERT: D 495 ASN cc_start: 0.8342 (p0) cc_final: 0.7835 (p0) REVERT: D 497 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8538 (mm-30) REVERT: D 543 SER cc_start: 0.8437 (t) cc_final: 0.7945 (p) REVERT: D 627 THR cc_start: 0.8572 (m) cc_final: 0.8292 (p) REVERT: D 643 ASP cc_start: 0.8580 (m-30) cc_final: 0.8053 (t70) REVERT: D 648 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8036 (tm-30) REVERT: D 652 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8190 (pm20) REVERT: D 764 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8152 (tmm-80) REVERT: D 960 LEU cc_start: 0.8869 (tt) cc_final: 0.8562 (mt) REVERT: D 1220 ILE cc_start: 0.8952 (mt) cc_final: 0.8506 (mt) REVERT: D 1320 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7849 (mm) REVERT: E 8 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7771 (m-30) REVERT: E 59 ILE cc_start: 0.6418 (OUTLIER) cc_final: 0.6063 (mm) REVERT: M 278 VAL cc_start: 0.2665 (OUTLIER) cc_final: 0.2246 (t) outliers start: 179 outliers final: 82 residues processed: 625 average time/residue: 0.1602 time to fit residues: 165.1588 Evaluate side-chains 506 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 410 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 320 ASN 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 B residue 193 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 576 SER 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 773 LEU Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 825 GLU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 1052 VAL 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 1206 THR Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1229 TYR Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 233 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 574 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 764 ARG Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1320 ILE 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 39 VAL 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 M residue 122 ASP Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 406 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 264 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 281 optimal weight: 30.0000 chunk 44 optimal weight: 5.9990 chunk 271 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 chunk 261 optimal weight: 7.9990 chunk 107 optimal weight: 0.2980 chunk 229 optimal weight: 5.9990 chunk 213 optimal weight: 6.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS A 37 HIS ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1324 ASN D 469 HIS D 477 GLN D 488 ASN D 489 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.088987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.062431 restraints weight = 124333.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.064416 restraints weight = 62308.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.065715 restraints weight = 39370.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.066490 restraints weight = 29149.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.067047 restraints weight = 24348.716| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.8787 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= 0.200 Angle : 0.747 14.373 40154 Z= 0.388 Chirality : 0.047 0.499 4788 Planarity : 0.005 0.085 4906 Dihedral : 16.635 173.933 5044 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.24 % Favored : 93.64 % Rotamer: Outliers : 4.73 % Allowed : 31.65 % Favored : 63.61 % 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: -1.18 (0.14), residues: 3587 helix: 0.40 (0.14), residues: 1299 sheet: -0.52 (0.27), residues: 365 loop : -1.72 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 235 TYR 0.030 0.002 TYR D 68 PHE 0.044 0.002 PHE B 35 TRP 0.009 0.001 TRP D 33 HIS 0.012 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (29224) covalent geometry : angle 0.74699 / 0.39 (40154) hydrogen bonds : bond 0.04102 / 2.85 ( 1188) hydrogen bonds : angle 4.76960 / 3.32 ( 3306) metal coordination : bond 0.01060 / 0.53 ( 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 535 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 411 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9254 (mm) REVERT: A 122 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7205 (pm20) REVERT: A 316 MET cc_start: 0.4135 (mmm) cc_final: 0.3272 (mtt) REVERT: C 40 GLU cc_start: 0.8123 (tp30) cc_final: 0.7911 (tp30) REVERT: C 195 PHE cc_start: 0.6602 (OUTLIER) cc_final: 0.5805 (m-10) REVERT: C 476 LYS cc_start: 0.8669 (mttt) cc_final: 0.7950 (mmmt) REVERT: C 577 VAL cc_start: 0.9556 (t) cc_final: 0.9332 (m) REVERT: C 605 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.6892 (t80) REVERT: C 672 GLU cc_start: 0.8737 (pm20) cc_final: 0.8343 (pm20) REVERT: C 685 MET cc_start: 0.8786 (mmm) cc_final: 0.8485 (mmm) REVERT: C 715 THR cc_start: 0.8468 (p) cc_final: 0.8201 (t) REVERT: C 773 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6934 (tt) REVERT: C 800 MET cc_start: 0.8833 (mmm) cc_final: 0.8376 (mmm) REVERT: C 815 SER cc_start: 0.9127 (m) cc_final: 0.8783 (p) REVERT: C 921 PRO cc_start: 0.9003 (Cg_exo) cc_final: 0.8736 (Cg_endo) REVERT: C 951 MET cc_start: 0.8867 (ptp) cc_final: 0.8640 (mpp) REVERT: C 1066 MET cc_start: 0.8385 (mmm) cc_final: 0.7404 (mmm) REVERT: C 1119 MET cc_start: 0.8542 (mmm) cc_final: 0.8205 (mmm) REVERT: C 1137 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8010 (mp0) REVERT: C 1273 MET cc_start: 0.5750 (ptm) cc_final: 0.4180 (mpp) REVERT: C 1274 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6616 (mp0) REVERT: C 1281 TYR cc_start: 0.7712 (m-80) cc_final: 0.7482 (m-80) REVERT: C 1304 MET cc_start: 0.8525 (mmm) cc_final: 0.8283 (mmm) REVERT: C 1329 GLU cc_start: 0.8138 (tt0) cc_final: 0.7574 (tt0) REVERT: C 1335 ILE cc_start: 0.8779 (mt) cc_final: 0.8348 (tp) REVERT: D 229 GLN cc_start: 0.7736 (mm110) cc_final: 0.7448 (mm-40) REVERT: D 298 MET cc_start: 0.8483 (mtp) cc_final: 0.8151 (mmp) REVERT: D 322 ARG cc_start: 0.6921 (mtt180) cc_final: 0.5620 (mtt180) REVERT: D 384 LYS cc_start: 0.7458 (mttt) cc_final: 0.7208 (ttpt) REVERT: D 390 LEU cc_start: 0.8896 (tp) cc_final: 0.8529 (mm) REVERT: D 400 MET cc_start: 0.8336 (mpp) cc_final: 0.7763 (ptp) REVERT: D 428 THR cc_start: 0.7159 (m) cc_final: 0.6948 (p) REVERT: D 648 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8167 (tm-30) REVERT: D 743 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8784 (ppp) REVERT: D 764 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8259 (tmm-80) REVERT: D 960 LEU cc_start: 0.8942 (tt) cc_final: 0.8599 (mt) REVERT: D 993 GLU cc_start: 0.2760 (mt-10) cc_final: -0.0078 (mt-10) REVERT: D 1307 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.6871 (mp) REVERT: D 1370 MET cc_start: 0.8698 (tpp) cc_final: 0.7970 (ptp) REVERT: E 8 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7892 (m-30) REVERT: E 17 PHE cc_start: 0.7496 (m-80) cc_final: 0.7179 (m-80) REVERT: E 42 GLU cc_start: 0.8384 (mp0) cc_final: 0.8152 (mp0) outliers start: 124 outliers final: 70 residues processed: 501 average time/residue: 0.1462 time to fit residues: 122.9906 Evaluate side-chains 456 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 376 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 GLU 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 B residue 192 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 605 TYR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 1082 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 1184 THR Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 489 ASN Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 764 ARG Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 775 SER Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1253 ILE Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain M residue 277 LEU Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 406 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 65 optimal weight: 20.0000 chunk 134 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 157 optimal weight: 0.7980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 GLN C1080 ASN C1324 ASN D 435 GLN D 489 ASN ** M 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.088824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.061971 restraints weight = 126710.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.063928 restraints weight = 64211.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.065210 restraints weight = 41048.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.066034 restraints weight = 30726.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.066493 restraints weight = 25710.576| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (22 function evaluations) r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.9499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29227 Z= 0.173 Angle : 0.742 14.085 40154 Z= 0.377 Chirality : 0.045 0.264 4788 Planarity : 0.005 0.078 4906 Dihedral : 16.592 173.328 5044 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.27 % Favored : 93.64 % Rotamer: Outliers : 4.66 % Allowed : 32.07 % Favored : 63.27 % 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: -0.96 (0.14), residues: 3587 helix: 0.70 (0.14), residues: 1281 sheet: -0.34 (0.28), residues: 347 loop : -1.66 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D1304 TYR 0.022 0.002 TYR D1363 PHE 0.035 0.002 PHE E 17 TRP 0.008 0.001 TRP C1276 HIS 0.008 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (29224) covalent geometry : angle 0.74159 / 0.38 (40154) hydrogen bonds : bond 0.03886 / 2.69 ( 1188) hydrogen bonds : angle 4.59085 / 3.19 ( 3306) metal coordination : bond 0.00204 / 0.10 ( 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 510 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 388 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9213 (mm) REVERT: A 122 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7193 (pm20) REVERT: A 199 ASP cc_start: 0.8675 (t0) cc_final: 0.8427 (t0) REVERT: A 269 CYS cc_start: 0.3847 (OUTLIER) cc_final: 0.3612 (m) REVERT: A 316 MET cc_start: 0.4248 (mmm) cc_final: 0.3476 (mtt) REVERT: B 51 MET cc_start: 0.7957 (mmm) cc_final: 0.7460 (mmm) REVERT: B 78 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7740 (pt) REVERT: C 142 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7492 (mm-30) REVERT: C 195 PHE cc_start: 0.6346 (OUTLIER) cc_final: 0.5979 (m-10) REVERT: C 403 MET cc_start: 0.7183 (tmm) cc_final: 0.6785 (tmm) REVERT: C 494 ASN cc_start: 0.5478 (t0) cc_final: 0.5196 (t0) REVERT: C 577 VAL cc_start: 0.9635 (t) cc_final: 0.9393 (m) REVERT: C 605 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7048 (t80) REVERT: C 672 GLU cc_start: 0.8873 (pm20) cc_final: 0.8492 (pm20) REVERT: C 749 ASP cc_start: 0.6220 (OUTLIER) cc_final: 0.5378 (t0) REVERT: C 800 MET cc_start: 0.8800 (mmm) cc_final: 0.8388 (mmm) REVERT: C 815 SER cc_start: 0.9172 (m) cc_final: 0.8816 (p) REVERT: C 921 PRO cc_start: 0.8974 (Cg_exo) cc_final: 0.8705 (Cg_endo) REVERT: C 951 MET cc_start: 0.8949 (ptp) cc_final: 0.8708 (mpp) REVERT: C 1066 MET cc_start: 0.8563 (mmm) cc_final: 0.7690 (mmm) REVERT: C 1107 MET cc_start: 0.8719 (mpp) cc_final: 0.8430 (mpp) REVERT: C 1119 MET cc_start: 0.8732 (mmm) cc_final: 0.8494 (mmm) REVERT: C 1137 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8090 (mp0) REVERT: C 1170 MET cc_start: 0.8454 (tmm) cc_final: 0.8212 (tmm) REVERT: C 1268 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8059 (mt0) REVERT: C 1273 MET cc_start: 0.6048 (ptm) cc_final: 0.4708 (mpp) REVERT: C 1281 TYR cc_start: 0.7555 (m-80) cc_final: 0.7345 (m-80) REVERT: C 1304 MET cc_start: 0.8821 (mmm) cc_final: 0.8398 (mmm) REVERT: C 1328 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7356 (mmmt) REVERT: C 1335 ILE cc_start: 0.8901 (mt) cc_final: 0.8472 (tp) REVERT: D 229 GLN cc_start: 0.7799 (mm110) cc_final: 0.7453 (mm-40) REVERT: D 264 ASP cc_start: 0.8612 (m-30) cc_final: 0.8275 (t70) REVERT: D 298 MET cc_start: 0.8487 (mtp) cc_final: 0.8185 (mmp) REVERT: D 384 LYS cc_start: 0.7735 (mttt) cc_final: 0.7407 (tppt) REVERT: D 390 LEU cc_start: 0.8895 (tp) cc_final: 0.8560 (mm) REVERT: D 400 MET cc_start: 0.8595 (mpp) cc_final: 0.8191 (mtm) REVERT: D 428 THR cc_start: 0.7790 (m) cc_final: 0.7352 (p) REVERT: D 472 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7183 (pt) REVERT: D 484 MET cc_start: 0.9139 (mmm) cc_final: 0.8358 (mmm) REVERT: D 581 MET cc_start: 0.9143 (tpp) cc_final: 0.8757 (mmt) REVERT: D 603 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8830 (mmmm) REVERT: D 620 PHE cc_start: 0.8337 (t80) cc_final: 0.8030 (t80) REVERT: D 648 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8408 (tm-30) REVERT: D 698 MET cc_start: 0.9507 (mmm) cc_final: 0.9073 (mpp) REVERT: D 743 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8825 (ppp) REVERT: D 764 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8302 (tmm-80) REVERT: D 822 MET cc_start: 0.8564 (mmm) cc_final: 0.8104 (mmm) REVERT: D 960 LEU cc_start: 0.8954 (tt) cc_final: 0.8542 (mt) REVERT: D 1370 MET cc_start: 0.8710 (tpp) cc_final: 0.8447 (tpp) REVERT: E 7 GLN cc_start: 0.8538 (tp40) cc_final: 0.7992 (tp40) REVERT: E 8 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8074 (m-30) REVERT: E 19 LEU cc_start: 0.8595 (tp) cc_final: 0.8302 (tt) REVERT: E 26 ARG cc_start: 0.8332 (mmm160) cc_final: 0.8077 (mmm160) REVERT: E 42 GLU cc_start: 0.8382 (mp0) cc_final: 0.8137 (mp0) outliers start: 122 outliers final: 68 residues processed: 482 average time/residue: 0.1391 time to fit residues: 113.8723 Evaluate side-chains 446 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 365 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 GLU 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 6 THR 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 195 PHE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 605 TYR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 1098 LEU Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1328 LYS Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 764 ARG Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1275 LEU 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 1347 LEU Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 287 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 7 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 296 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 272 optimal weight: 8.9990 chunk 213 optimal weight: 0.8980 chunk 216 optimal weight: 20.0000 chunk 150 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 261 optimal weight: 20.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS C 517 GLN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1111 GLN C1299 ASN D 80 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.086969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.059829 restraints weight = 130501.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.061698 restraints weight = 67184.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.062917 restraints weight = 43595.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.063675 restraints weight = 33130.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.064161 restraints weight = 28073.646| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 1.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 29227 Z= 0.241 Angle : 0.802 16.634 40154 Z= 0.418 Chirality : 0.047 0.278 4788 Planarity : 0.006 0.063 4906 Dihedral : 16.663 175.433 5044 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.22 % Favored : 92.70 % Rotamer: Outliers : 4.54 % Allowed : 32.72 % Favored : 62.73 % 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: -1.12 (0.14), residues: 3587 helix: 0.49 (0.14), residues: 1289 sheet: -0.50 (0.27), residues: 373 loop : -1.71 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 403 TYR 0.035 0.002 TYR C 179 PHE 0.044 0.002 PHE E 17 TRP 0.033 0.003 TRP D 236 HIS 0.008 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.24 (29224) covalent geometry : angle 0.80190 / 0.42 (40154) hydrogen bonds : bond 0.04371 / 3.02 ( 1188) hydrogen bonds : angle 4.70246 / 3.26 ( 3306) metal coordination : bond 0.00221 / 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 491 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 372 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8220 (tp-100) REVERT: A 80 GLU cc_start: 0.8514 (mp0) cc_final: 0.8256 (tm-30) REVERT: A 224 LEU cc_start: 0.9360 (tp) cc_final: 0.9150 (tp) REVERT: A 269 CYS cc_start: 0.3906 (OUTLIER) cc_final: 0.3694 (m) REVERT: A 316 MET cc_start: 0.4901 (mmm) cc_final: 0.3850 (mtt) REVERT: B 49 SER cc_start: 0.9020 (m) cc_final: 0.8783 (p) REVERT: B 51 MET cc_start: 0.8376 (mmm) cc_final: 0.7787 (mmm) REVERT: B 78 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8022 (pt) REVERT: C 142 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7887 (mm-30) REVERT: C 177 ILE cc_start: 0.8253 (mt) cc_final: 0.8010 (mm) REVERT: C 403 MET cc_start: 0.7409 (tmm) cc_final: 0.6987 (tmm) REVERT: C 468 LEU cc_start: 0.8492 (mt) cc_final: 0.8207 (mt) REVERT: C 494 ASN cc_start: 0.6175 (t0) cc_final: 0.5895 (t0) REVERT: C 800 MET cc_start: 0.8957 (mmm) cc_final: 0.8560 (mmm) REVERT: C 1107 MET cc_start: 0.8930 (mpp) cc_final: 0.8600 (mpp) REVERT: C 1137 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8242 (mp0) REVERT: C 1170 MET cc_start: 0.8389 (tmm) cc_final: 0.8084 (tmm) REVERT: C 1273 MET cc_start: 0.6615 (ptm) cc_final: 0.6142 (mpp) REVERT: C 1335 ILE cc_start: 0.9206 (mt) cc_final: 0.8792 (tp) REVERT: D 211 GLU cc_start: 0.8573 (tp30) cc_final: 0.8282 (mt-10) REVERT: D 229 GLN cc_start: 0.8175 (mm110) cc_final: 0.7826 (mm-40) REVERT: D 264 ASP cc_start: 0.8789 (m-30) cc_final: 0.8341 (t70) REVERT: D 314 ARG cc_start: 0.5941 (pmt-80) cc_final: 0.5093 (ptm160) REVERT: D 387 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8294 (tp) REVERT: D 390 LEU cc_start: 0.9219 (tp) cc_final: 0.8917 (mm) REVERT: D 404 GLU cc_start: 0.8226 (mp0) cc_final: 0.7996 (mp0) REVERT: D 484 MET cc_start: 0.9285 (mmm) cc_final: 0.9032 (mmm) REVERT: D 644 MET cc_start: 0.8555 (mpp) cc_final: 0.8302 (mpp) REVERT: D 648 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8557 (tm-30) REVERT: D 652 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7907 (pm20) REVERT: D 743 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8737 (ppp) REVERT: D 764 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8587 (tmm-80) REVERT: D 993 GLU cc_start: 0.2801 (mt-10) cc_final: 0.2460 (tt0) REVERT: D 1220 ILE cc_start: 0.9314 (mt) cc_final: 0.9002 (mt) REVERT: D 1334 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: E 7 GLN cc_start: 0.8565 (tp40) cc_final: 0.7995 (tp40) REVERT: E 8 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8247 (m-30) REVERT: E 19 LEU cc_start: 0.8884 (tp) cc_final: 0.8665 (tt) REVERT: E 42 GLU cc_start: 0.8554 (mp0) cc_final: 0.8298 (mp0) outliers start: 119 outliers final: 72 residues processed: 457 average time/residue: 0.1500 time to fit residues: 117.3142 Evaluate side-chains 410 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 330 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 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 B residue 181 GLU Chi-restraints excluded: chain B residue 203 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 138 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 359 ARG 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 550 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 642 ASP Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 764 ARG Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1289 ASN 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 E residue 43 ASN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 60 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 37 optimal weight: 3.9990 chunk 106 optimal weight: 0.0170 chunk 360 optimal weight: 50.0000 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 330 optimal weight: 40.0000 chunk 155 optimal weight: 30.0000 chunk 78 optimal weight: 30.0000 chunk 150 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 462 ASN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.087355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.060259 restraints weight = 130760.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.062129 restraints weight = 67083.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.063338 restraints weight = 43514.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.064106 restraints weight = 33163.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.064523 restraints weight = 28175.726| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 1.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 29227 Z= 0.168 Angle : 0.744 12.249 40154 Z= 0.379 Chirality : 0.045 0.245 4788 Planarity : 0.005 0.073 4906 Dihedral : 16.638 174.891 5044 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.24 % Favored : 93.67 % Rotamer: Outliers : 3.09 % Allowed : 34.75 % Favored : 62.16 % 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: -0.98 (0.14), residues: 3587 helix: 0.65 (0.15), residues: 1280 sheet: -0.51 (0.27), residues: 376 loop : -1.64 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 279 TYR 0.023 0.001 TYR D1365 PHE 0.030 0.002 PHE E 17 TRP 0.018 0.002 TRP M 285 HIS 0.005 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (29224) covalent geometry : angle 0.74420 / 0.38 (40154) hydrogen bonds : bond 0.03917 / 2.65 ( 1188) hydrogen bonds : angle 4.62681 / 3.22 ( 3306) metal coordination : bond 0.00218 / 0.11 ( 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 420 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 339 time to evaluate : 1.138 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: 0.7872 (mt-10) cc_final: 0.7186 (tp30) REVERT: A 75 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8114 (tp-100) REVERT: A 269 CYS cc_start: 0.3907 (OUTLIER) cc_final: 0.3701 (m) REVERT: A 316 MET cc_start: 0.5013 (mmm) cc_final: 0.4211 (mtt) REVERT: B 49 SER cc_start: 0.8974 (m) cc_final: 0.8764 (p) REVERT: B 51 MET cc_start: 0.8418 (mmm) cc_final: 0.7847 (mmm) REVERT: B 78 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8057 (pt) REVERT: C 142 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7479 (mm-30) REVERT: C 177 ILE cc_start: 0.8511 (mt) cc_final: 0.8222 (mm) REVERT: C 403 MET cc_start: 0.7506 (tmm) cc_final: 0.6980 (tmm) REVERT: C 468 LEU cc_start: 0.8487 (mt) cc_final: 0.8182 (mt) REVERT: C 488 MET cc_start: 0.6870 (mtt) cc_final: 0.6240 (mtt) REVERT: C 732 ILE cc_start: 0.9507 (mt) cc_final: 0.9287 (mm) REVERT: C 800 MET cc_start: 0.8925 (mmm) cc_final: 0.8523 (mmm) REVERT: C 1066 MET cc_start: 0.8719 (mmm) cc_final: 0.8280 (mmm) REVERT: C 1107 MET cc_start: 0.8998 (mpp) cc_final: 0.8721 (mpp) REVERT: C 1119 MET cc_start: 0.8929 (mmm) cc_final: 0.8440 (tpp) REVERT: C 1170 MET cc_start: 0.8345 (tmm) cc_final: 0.8070 (tmm) REVERT: C 1180 MET cc_start: 0.9303 (tpp) cc_final: 0.8941 (tpt) REVERT: C 1230 MET cc_start: 0.8955 (tmm) cc_final: 0.8388 (ttt) REVERT: C 1273 MET cc_start: 0.6583 (ptm) cc_final: 0.6301 (mpp) REVERT: D 201 LEU cc_start: 0.8213 (mt) cc_final: 0.7436 (tp) REVERT: D 229 GLN cc_start: 0.8166 (mm110) cc_final: 0.7779 (mm-40) REVERT: D 237 MET cc_start: 0.5918 (tmm) cc_final: 0.5631 (mtp) REVERT: D 264 ASP cc_start: 0.8795 (m-30) cc_final: 0.8484 (t70) REVERT: D 275 ARG cc_start: 0.8360 (mmt-90) cc_final: 0.8103 (tpt170) REVERT: D 314 ARG cc_start: 0.5812 (pmt-80) cc_final: 0.5322 (ptm160) REVERT: D 390 LEU cc_start: 0.9181 (tp) cc_final: 0.8909 (mm) REVERT: D 484 MET cc_start: 0.9461 (mmm) cc_final: 0.9061 (mmm) REVERT: D 497 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8409 (mp0) REVERT: D 581 MET cc_start: 0.9326 (tpp) cc_final: 0.9011 (mmt) REVERT: D 603 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.9068 (mmmm) REVERT: D 644 MET cc_start: 0.8545 (mpp) cc_final: 0.8303 (mtm) REVERT: D 648 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8608 (tm-30) REVERT: D 652 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7883 (pm20) REVERT: D 743 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8766 (ppp) REVERT: D 747 MET cc_start: 0.6236 (OUTLIER) cc_final: 0.5981 (mpp) REVERT: D 764 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8537 (tmm-80) REVERT: D 837 ASP cc_start: 0.8864 (t0) cc_final: 0.8651 (t70) REVERT: D 869 CYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7306 (t) REVERT: D 1261 LEU cc_start: 0.9265 (mp) cc_final: 0.9055 (mp) REVERT: D 1334 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: E 7 GLN cc_start: 0.8711 (tp40) cc_final: 0.8145 (tp40) REVERT: E 8 ASP cc_start: 0.8642 (p0) cc_final: 0.8208 (m-30) REVERT: E 19 LEU cc_start: 0.8871 (tp) cc_final: 0.8610 (tp) REVERT: E 40 PRO cc_start: 0.8526 (Cg_exo) cc_final: 0.8174 (Cg_endo) REVERT: M 170 ILE cc_start: 0.3935 (pt) cc_final: 0.2473 (pt) outliers start: 81 outliers final: 53 residues processed: 401 average time/residue: 0.1640 time to fit residues: 111.6550 Evaluate side-chains 382 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 320 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL 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 78 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 764 ARG Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 210 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 271 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 298 optimal weight: 7.9990 chunk 212 optimal weight: 20.0000 chunk 337 optimal weight: 40.0000 chunk 85 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 243 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS C 462 ASN ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.085498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.058421 restraints weight = 128985.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.060137 restraints weight = 66883.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.061252 restraints weight = 43968.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.061965 restraints weight = 33967.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.062379 restraints weight = 29119.429| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 1.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 29227 Z= 0.247 Angle : 0.825 18.513 40154 Z= 0.422 Chirality : 0.048 0.566 4788 Planarity : 0.006 0.086 4906 Dihedral : 16.696 175.860 5044 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.36 % Favored : 92.56 % Rotamer: Outliers : 3.09 % Allowed : 35.05 % Favored : 61.86 % 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: -1.17 (0.14), residues: 3587 helix: 0.46 (0.14), residues: 1299 sheet: -0.61 (0.28), residues: 354 loop : -1.74 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 278 TYR 0.023 0.002 TYR D1365 PHE 0.019 0.002 PHE D 377 TRP 0.019 0.002 TRP D 33 HIS 0.006 0.001 HIS D 897 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.25 (29224) covalent geometry : angle 0.82474 / 0.42 (40154) hydrogen bonds : bond 0.04517 / 3.06 ( 1188) hydrogen bonds : angle 4.81334 / 3.33 ( 3306) metal coordination : bond 0.00258 / 0.13 ( 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 398 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 317 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7733 (t0) cc_final: 0.7502 (t0) REVERT: A 29 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7595 (tp30) REVERT: A 35 PHE cc_start: 0.8951 (m-80) cc_final: 0.8679 (m-80) REVERT: A 47 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9358 (mm) REVERT: A 75 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8406 (tp-100) REVERT: A 316 MET cc_start: 0.5341 (mmm) cc_final: 0.4344 (mtt) REVERT: B 51 MET cc_start: 0.8570 (mmm) cc_final: 0.8026 (mmm) REVERT: C 57 PHE cc_start: 0.6518 (m-80) cc_final: 0.5735 (m-80) REVERT: C 142 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8046 (mm-30) REVERT: C 403 MET cc_start: 0.7710 (tmm) cc_final: 0.7355 (tmm) REVERT: C 468 LEU cc_start: 0.8695 (mt) cc_final: 0.8106 (mt) REVERT: C 488 MET cc_start: 0.7125 (mtt) cc_final: 0.6517 (mtt) REVERT: C 800 MET cc_start: 0.8903 (mmm) cc_final: 0.8523 (mmm) REVERT: C 838 CYS cc_start: 0.7027 (t) cc_final: 0.6761 (t) REVERT: C 872 TYR cc_start: 0.8554 (m-10) cc_final: 0.8201 (m-10) REVERT: C 1066 MET cc_start: 0.8774 (mmm) cc_final: 0.8372 (mmm) REVERT: C 1107 MET cc_start: 0.9099 (mpp) cc_final: 0.8818 (mpp) REVERT: C 1119 MET cc_start: 0.9036 (mmm) cc_final: 0.8410 (tpp) REVERT: C 1170 MET cc_start: 0.8342 (tmm) cc_final: 0.8130 (tmm) REVERT: C 1180 MET cc_start: 0.9359 (tpp) cc_final: 0.9034 (tpt) REVERT: C 1230 MET cc_start: 0.8977 (tmm) cc_final: 0.8436 (ttt) REVERT: C 1240 ASP cc_start: 0.8650 (t0) cc_final: 0.8389 (t0) REVERT: C 1289 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8333 (tm-30) REVERT: C 1335 ILE cc_start: 0.9286 (mt) cc_final: 0.8978 (tp) REVERT: D 78 LEU cc_start: 0.8846 (tp) cc_final: 0.8564 (tp) REVERT: D 201 LEU cc_start: 0.8508 (mt) cc_final: 0.7695 (tp) REVERT: D 211 GLU cc_start: 0.8846 (mm-30) cc_final: 0.7868 (pt0) REVERT: D 229 GLN cc_start: 0.8351 (mm110) cc_final: 0.8020 (mm-40) REVERT: D 275 ARG cc_start: 0.8671 (mmt-90) cc_final: 0.8310 (tpt170) REVERT: D 314 ARG cc_start: 0.6331 (pmt-80) cc_final: 0.5997 (ptm160) REVERT: D 390 LEU cc_start: 0.9302 (tp) cc_final: 0.9040 (mm) REVERT: D 484 MET cc_start: 0.9386 (mmm) cc_final: 0.9115 (mmm) REVERT: D 486 SER cc_start: 0.9430 (m) cc_final: 0.9206 (p) REVERT: D 603 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.9155 (ttmm) REVERT: D 652 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7818 (pm20) REVERT: D 698 MET cc_start: 0.9546 (mmp) cc_final: 0.9114 (mmm) REVERT: D 743 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8655 (ppp) REVERT: D 747 MET cc_start: 0.6184 (mpp) cc_final: 0.5888 (mpp) REVERT: D 764 ARG cc_start: 0.9324 (OUTLIER) cc_final: 0.8584 (tmm-80) REVERT: D 869 CYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7610 (t) REVERT: D 1261 LEU cc_start: 0.9309 (mp) cc_final: 0.9049 (mp) REVERT: D 1334 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: E 7 GLN cc_start: 0.8728 (tp40) cc_final: 0.8177 (tp40) REVERT: E 8 ASP cc_start: 0.8641 (p0) cc_final: 0.8233 (m-30) REVERT: E 19 LEU cc_start: 0.8932 (tp) cc_final: 0.8582 (tp) outliers start: 81 outliers final: 58 residues processed: 380 average time/residue: 0.1653 time to fit residues: 105.6141 Evaluate side-chains 359 residues out of total 3093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 294 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 203 ILE 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 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 203 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 138 ILE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 652 GLU Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 764 ARG Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 871 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain D residue 1334 GLU Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 210 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 346 optimal weight: 0.0870 chunk 221 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 298 optimal weight: 30.0000 chunk 303 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 271 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.086502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.059558 restraints weight = 127965.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.061372 restraints weight = 65661.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.062541 restraints weight = 42818.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.063259 restraints weight = 32760.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.063717 restraints weight = 27949.235| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 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 = 0.3153 r_free = 0.3153 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: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 1.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29227 Z= 0.159 Angle : 0.771 18.069 40154 Z= 0.390 Chirality : 0.045 0.339 4788 Planarity : 0.005 0.075 4906 Dihedral : 16.680 175.426 5044 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.22 % Favored : 93.70 % Rotamer: Outliers : 2.75 % Allowed : 35.55 % Favored : 61.70 % 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: -1.01 (0.14), residues: 3587 helix: 0.61 (0.15), residues: 1295 sheet: -0.50 (0.27), residues: 360 loop : -1.66 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 540 TYR 0.030 0.002 TYR B 177 PHE 0.039 0.002 PHE C 464 TRP 0.015 0.001 TRP C1276 HIS 0.007 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (29224) covalent geometry : angle 0.77076 / 0.39 (40154) hydrogen bonds : bond 0.03893 / 2.66 ( 1188) hydrogen bonds : angle 4.62663 / 3.21 ( 3306) metal coordination : bond 0.00276 / 0.14 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5916.32 seconds wall clock time: 102 minutes 12.23 seconds (6132.23 seconds total)