Starting phenix.real_space_refine on Tue Sep 15 21:38:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6kj6_0700/09_2026/6kj6_0700.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kj6_0700/09_2026/6kj6_0700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6kj6_0700/09_2026/6kj6_0700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kj6_0700/09_2026/6kj6_0700.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6kj6_0700/09_2026/6kj6_0700.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6kj6_0700/09_2026/6kj6_0700.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kj6_0700/09_2026/6kj6_0700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kj6_0700/09_2026/6kj6_0700.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 23524 atoms to isotropic. 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 96 5.49 5 Mg 1 5.21 5 S 90 5.16 5 C 16482 2.51 5 N 4854 2.21 5 O 4971 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26496 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1554 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 8, 'GLU:plan': 15, 'ASN:plan1': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 115 Chain: "B" Number of atoms: 1446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1446 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 217} Unresolved non-hydrogen bonds: 316 Unresolved non-hydrogen angles: 401 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 25, 'GLN:plan1': 5, 'ASP:plan': 12, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 208 Chain: "C" Number of atoms: 9527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 9527 Classifications: {'peptide': 1327} Incomplete info: {'truncation_to_alanine': 264} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1271} Chain breaks: 2 Unresolved non-hydrogen bonds: 958 Unresolved non-hydrogen angles: 1205 Unresolved non-hydrogen dihedrals: 744 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'ASP:plan': 58, 'GLU:plan': 69, 'GLN:plan1': 14, 'ASN:plan1': 11, 'HIS:plan': 4, 'ARG:plan': 15, 'PHE:plan': 3, 'TYR:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 689 Chain: "D" Number of atoms: 8668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1265, 8668 Classifications: {'peptide': 1265} Incomplete info: {'truncation_to_alanine': 337} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 52, 'TRANS': 1209} Chain breaks: 11 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1220 Unresolved non-hydrogen angles: 1502 Unresolved non-hydrogen dihedrals: 972 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLU:plan': 71, 'ASP:plan': 47, 'ARG:plan': 30, 'HIS:plan': 5, 'GLN:plan1': 15, 'ASN:plan1': 10, 'PHE:plan': 6, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 747 Chain: "E" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 518 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 3, 'ASP:plan': 2, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "F" Number of atoms: 2050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2050 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 7, 'TRANS': 269} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 7, 'GLU:plan': 18, 'ASN:plan1': 2, 'ARG:plan': 7, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 150 Chain: "G" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 950 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "H" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 949 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "I" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 102 Classifications: {'RNAv2': 5} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna3p': 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 729 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 4, 'ASP:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 90 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12927 SG CYS D 70 77.253 47.414 32.397 1.00 67.56 S ATOM 12941 SG CYS D 72 73.183 47.966 31.781 1.00 70.93 S ATOM 13020 SG CYS D 85 75.686 48.144 28.660 1.00 79.04 S ATOM 13044 SG CYS D 88 74.709 51.023 30.741 1.00 68.65 S ATOM 17628 SG CYS D 814 117.829 102.319 35.662 1.00 57.28 S ATOM 18078 SG CYS D 888 115.599 102.113 39.893 1.00 55.18 S ATOM 18136 SG CYS D 898 119.239 102.212 39.789 1.00 47.46 S Time building chain proxies: 5.36, per 1000 atoms: 0.20 Number of scatterers: 26496 At special positions: 0 Unit cell: (183.534, 173.394, 138.918, 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 90 16.00 P 96 15.00 Mg 1 11.99 O 4971 8.00 N 4854 7.00 C 16482 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: 2.37 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 70 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 72 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 88 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 85 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 898 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 888 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 814 " Number of angles added : 6 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6476 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 41 sheets defined 26.5% alpha, 8.3% beta 10 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 35 through 41 removed outlier: 3.651A pdb=" N LEU A 39 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 212 through 217 removed outlier: 4.051A pdb=" N ILE A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'B' and resid 36 through 45 removed outlier: 4.973A pdb=" N ALA B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 Processing helix chain 'B' and resid 77 through 85 removed outlier: 3.582A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 226 removed outlier: 3.854A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG B 219 " --> pdb=" O GLU B 215 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 40 Processing helix chain 'C' and resid 48 through 53 removed outlier: 3.957A pdb=" N PHE C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 198 through 201 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 216 through 221 removed outlier: 3.715A pdb=" N LEU C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 292 removed outlier: 3.690A pdb=" N TYR C 291 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 324 Processing helix chain 'C' and resid 349 through 354 removed outlier: 3.892A pdb=" N VAL C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP C 354 " --> pdb=" O THR C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 349 through 354' Processing helix chain 'C' and resid 362 through 371 removed outlier: 3.652A pdb=" N ILE C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 390 removed outlier: 3.927A pdb=" N GLU C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 410 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.533A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS C 430 " --> pdb=" O ILE C 426 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C 433 " --> pdb=" O MET C 429 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 473 removed outlier: 4.899A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN C 462 " --> pdb=" O GLU C 458 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL C 466 " --> pdb=" O ASN C 462 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 481 removed outlier: 3.976A pdb=" N ARG C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU C 479 " --> pdb=" O VAL C 475 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 474 through 481' Processing helix chain 'C' and resid 488 through 492 removed outlier: 3.944A pdb=" N MET C 492 " --> pdb=" O PRO C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 501 removed outlier: 3.548A pdb=" N ALA C 501 " --> pdb=" O ILE C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 528 removed outlier: 4.112A pdb=" N ILE C 524 " --> pdb=" O PRO C 520 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N HIS C 526 " --> pdb=" O SER C 522 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.585A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 825 removed outlier: 3.805A pdb=" N VAL C 823 " --> pdb=" O SER C 819 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN C 824 " --> pdb=" O GLU C 820 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU C 825 " --> pdb=" O ARG C 821 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 819 through 825' Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.781A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 907 removed outlier: 3.798A pdb=" N ALA C 904 " --> pdb=" O LYS C 900 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 962 removed outlier: 3.600A pdb=" N LEU C 953 " --> pdb=" O GLU C 949 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN C 955 " --> pdb=" O MET C 951 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 956 " --> pdb=" O GLN C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 972 removed outlier: 3.562A pdb=" N PHE C 972 " --> pdb=" O GLU C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 981 removed outlier: 3.554A pdb=" N VAL C 980 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 990 Processing helix chain 'C' and resid 994 through 998 removed outlier: 4.052A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 994 through 998' Processing helix chain 'C' and resid 1007 through 1030 removed outlier: 4.129A pdb=" N GLN C1013 " --> pdb=" O ASN C1009 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS C1023 " --> pdb=" O ASP C1019 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C1030 " --> pdb=" O GLU C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1107 removed outlier: 3.694A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1113 through 1122 removed outlier: 3.596A pdb=" N ALA C1120 " --> pdb=" O HIS C1116 " (cutoff:3.500A) Processing helix chain 'C' and resid 1123 through 1134 removed outlier: 3.703A pdb=" N ILE C1128 " --> pdb=" O ILE C1124 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN C1129 " --> pdb=" O GLY C1125 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1146 removed outlier: 3.530A pdb=" N GLN C1146 " --> pdb=" O ARG C1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 1192 through 1200 removed outlier: 4.257A pdb=" N LEU C1198 " --> pdb=" O GLU C1194 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1242 removed outlier: 3.913A pdb=" N ASP C1241 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1279 removed outlier: 4.085A pdb=" N TRP C1276 " --> pdb=" O GLU C1272 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA C1277 " --> pdb=" O MET C1273 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU C1278 " --> pdb=" O GLU C1274 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 4.052A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET C1304 " --> pdb=" O GLY C1300 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C1306 " --> pdb=" O THR C1302 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1327 through 1332 Processing helix chain 'D' and resid 29 through 33 Processing helix chain 'D' and resid 131 through 135 Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.507A pdb=" N LEU D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 184 removed outlier: 4.081A pdb=" N GLU D 183 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 223 removed outlier: 3.729A pdb=" N LYS D 222 " --> pdb=" O LYS D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 269 through 278 removed outlier: 3.835A pdb=" N ARG D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 293 removed outlier: 3.599A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 304 removed outlier: 3.527A pdb=" N GLN D 300 " --> pdb=" O LYS D 296 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP D 304 " --> pdb=" O GLN D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.520A pdb=" N ILE D 331 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.579A pdb=" N ILE D 381 " --> pdb=" O PHE D 377 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY D 383 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS D 384 " --> pdb=" O PHE D 380 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 387 " --> pdb=" O GLY D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 402 removed outlier: 3.826A pdb=" N GLU D 402 " --> pdb=" O LYS D 398 " (cutoff:3.500A) 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 453 through 458 removed outlier: 3.741A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 481 removed outlier: 3.604A pdb=" N ARG D 481 " --> pdb=" O LEU D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 513 Processing helix chain 'D' and resid 533 through 538 removed outlier: 3.767A pdb=" N ARG D 538 " --> pdb=" O GLU D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 579 Processing helix chain 'D' and resid 580 through 582 No H-bonds generated for 'chain 'D' and resid 580 through 582' Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.614A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 613 Processing helix chain 'D' and resid 615 through 634 removed outlier: 4.212A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 624 " --> pdb=" O PHE D 620 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N MET D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR D 627 " --> pdb=" O GLN D 623 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE D 629 " --> pdb=" O MET D 625 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA D 630 " --> pdb=" O TYR D 626 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TYR D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA D 632 " --> pdb=" O GLY D 628 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 670 removed outlier: 3.762A pdb=" N ALA D 662 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLU D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE D 664 " --> pdb=" O GLU D 660 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN D 667 " --> pdb=" O GLU D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 696 removed outlier: 3.656A pdb=" N ALA D 688 " --> pdb=" O ASP D 684 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA D 689 " --> pdb=" O ILE D 685 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG D 692 " --> pdb=" O ALA D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 725 removed outlier: 3.593A pdb=" N MET D 724 " --> pdb=" O ASN D 720 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET D 725 " --> pdb=" O SER D 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 720 through 725' Processing helix chain 'D' and resid 768 through 774 removed outlier: 3.700A pdb=" N PHE D 773 " --> pdb=" O VAL D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 777 No H-bonds generated for 'chain 'D' and resid 775 through 777' Processing helix chain 'D' and resid 785 through 790 removed outlier: 3.921A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 794 Processing helix chain 'D' and resid 796 through 805 removed outlier: 3.801A pdb=" N ASP D 802 " --> pdb=" O ARG D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 3.502A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 875 removed outlier: 3.817A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 removed outlier: 3.658A pdb=" N CYS D 888 " --> pdb=" O VAL D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.519A pdb=" N ALA D 919 " --> pdb=" O ILE D 915 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER D 922 " --> pdb=" O ILE D 918 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE D 923 " --> pdb=" O ALA D 919 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY D 924 " --> pdb=" O ALA D 920 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1138 through 1143 removed outlier: 3.693A pdb=" N ASP D1143 " --> pdb=" O PRO D1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1222 removed outlier: 3.618A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU D1221 " --> pdb=" O PRO D1217 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG D1222 " --> pdb=" O HIS D1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1216 through 1222' Processing helix chain 'D' and resid 1229 through 1244 removed outlier: 3.517A pdb=" N ILE D1233 " --> pdb=" O VAL D1229 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN D1238 " --> pdb=" O VAL D1234 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP D1239 " --> pdb=" O ASN D1235 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU D1243 " --> pdb=" O ASP D1239 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1255 through 1261 removed outlier: 3.658A pdb=" N GLN D1259 " --> pdb=" O VAL D1255 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU D1261 " --> pdb=" O VAL D1257 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1332 through 1337 removed outlier: 3.871A pdb=" N VAL D1337 " --> pdb=" O THR D1333 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1371 removed outlier: 3.550A pdb=" N HIS D1366 " --> pdb=" O GLY D1362 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG D1369 " --> pdb=" O TYR D1365 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET D1370 " --> pdb=" O HIS D1366 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG D1371 " --> pdb=" O GLN D1367 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 14 Processing helix chain 'E' and resid 22 through 27 Processing helix chain 'E' and resid 45 through 50 removed outlier: 3.709A pdb=" N ALA E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 57 removed outlier: 3.880A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 removed outlier: 3.585A pdb=" N ASP E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 removed outlier: 3.655A pdb=" N GLN E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 85 removed outlier: 3.781A pdb=" N GLU F 76 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL F 77 " --> pdb=" O ALA F 73 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TYR F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG F 81 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG F 82 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU F 84 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG F 85 " --> pdb=" O ARG F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 98 removed outlier: 3.510A pdb=" N ARG F 91 " --> pdb=" O ASP F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 106 removed outlier: 3.643A pdb=" N LYS F 104 " --> pdb=" O ARG F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 132 removed outlier: 4.146A pdb=" N ASN F 124 " --> pdb=" O ILE F 120 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY F 126 " --> pdb=" O GLU F 122 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE F 128 " --> pdb=" O ASN F 124 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG F 129 " --> pdb=" O LEU F 125 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU F 132 " --> pdb=" O ILE F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 160 removed outlier: 3.524A pdb=" N ILE F 150 " --> pdb=" O ALA F 146 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLN F 152 " --> pdb=" O TRP F 148 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 176 removed outlier: 4.201A pdb=" N GLU F 174 " --> pdb=" O HIS F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 190 removed outlier: 4.360A pdb=" N ALA F 182 " --> pdb=" O TYR F 178 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU F 184 " --> pdb=" O ARG F 180 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N HIS F 187 " --> pdb=" O ARG F 183 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LYS F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 203 removed outlier: 4.028A pdb=" N ALA F 199 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN F 201 " --> pdb=" O GLU F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 210 removed outlier: 3.619A pdb=" N VAL F 209 " --> pdb=" O PRO F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 237 removed outlier: 3.795A pdb=" N ASP F 236 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 251 removed outlier: 3.564A pdb=" N THR F 250 " --> pdb=" O PRO F 246 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN F 251 " --> pdb=" O GLU F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 263 removed outlier: 4.001A pdb=" N VAL F 260 " --> pdb=" O LYS F 256 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS F 261 " --> pdb=" O GLN F 257 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP F 262 " --> pdb=" O SER F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 277 removed outlier: 3.802A pdb=" N GLU F 272 " --> pdb=" O ALA F 268 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG F 276 " --> pdb=" O GLU F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 296 removed outlier: 3.695A pdb=" N GLU F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 310 removed outlier: 3.578A pdb=" N VAL F 307 " --> pdb=" O ARG F 303 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU F 308 " --> pdb=" O GLN F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 321 removed outlier: 3.578A pdb=" N GLU F 315 " --> pdb=" O ARG F 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 19 removed outlier: 3.521A pdb=" N LYS J 14 " --> pdb=" O SER J 10 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA J 18 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU J 19 " --> pdb=" O LYS J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 110 removed outlier: 3.534A pdb=" N ARG J 101 " --> pdb=" O GLU J 97 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU J 102 " --> pdb=" O HIS J 98 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU J 110 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.653A pdb=" N GLU A 29 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 14 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.772A pdb=" N GLY A 53 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A 149 " --> pdb=" O GLY A 53 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 55 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.572A pdb=" N GLU A 122 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 104 removed outlier: 3.649A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 31 removed outlier: 5.398A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 102 removed outlier: 4.002A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.731A pdb=" N GLU B 122 " --> pdb=" O ARG B 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 66 through 69 removed outlier: 3.537A pdb=" N GLN C 69 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 73 through 74 Processing sheet with id=AB1, first strand: chain 'C' and resid 93 through 95 Processing sheet with id=AB2, first strand: chain 'C' and resid 143 through 145 Processing sheet with id=AB3, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.552A pdb=" N SER C 531 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 158 through 159 removed outlier: 3.652A pdb=" N ASP C 185 " --> pdb=" O ARG C 197 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 228 through 229 Processing sheet with id=AB6, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AB7, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.752A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.555A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 722 through 727 removed outlier: 7.158A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.740A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC3, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC4, first strand: chain 'C' and resid 798 through 803 removed outlier: 3.674A pdb=" N MET C1230 " --> pdb=" O MET C 800 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 835 through 840 removed outlier: 3.516A pdb=" N VAL C1050 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AC7, first strand: chain 'C' and resid 1065 through 1066 Processing sheet with id=AC8, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.565A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN D 424 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.565A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1335 through 1337 Processing sheet with id=AD2, first strand: chain 'D' and resid 34 through 37 removed outlier: 4.278A pdb=" N SER D 34 " --> pdb=" O MET D 102 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N HIS D 104 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLY D 36 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLU D 106 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.641A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AD4, first strand: chain 'D' and resid 261 through 262 removed outlier: 3.634A pdb=" N THR D 262 " --> pdb=" O THR F 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.962A pdb=" N ARG D 551 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL D 548 " --> pdb=" O THR D 572 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 820 through 821 Processing sheet with id=AD7, first strand: chain 'D' and resid 825 through 826 removed outlier: 7.367A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 847 through 848 removed outlier: 3.519A pdb=" N ASP D 847 " --> pdb=" O VAL D 858 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL D 858 " --> pdb=" O ASP D 847 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 949 through 951 removed outlier: 3.503A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA D1001 " --> pdb=" O ILE D 975 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE D 975 " --> pdb=" O ALA D1001 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 991 through 996 removed outlier: 4.171A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 982 " --> pdb=" O TYR D 995 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1034 through 1038 removed outlier: 3.872A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA D1077 " --> pdb=" O THR D1038 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1046 through 1049 removed outlier: 4.170A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER D1058 " --> pdb=" O GLN D1049 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1156 through 1157 Processing sheet with id=AE5, first strand: chain 'J' and resid 32 through 34 removed outlier: 3.820A pdb=" N GLU J 61 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR J 68 " --> pdb=" O GLU J 61 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 5.68 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6373 1.33 - 1.45: 5364 1.45 - 1.57: 15031 1.57 - 1.69: 190 1.69 - 1.81: 154 Bond restraints: 27112 Sorted by residual: bond pdb=" C3' DA G 29 " pdb=" O3' DA G 29 " ideal model delta sigma weight residual 1.435 1.544 -0.109 1.30e-02 5.92e+03 6.97e+01 bond pdb=" C3' DA G 31 " pdb=" O3' DA G 31 " ideal model delta sigma weight residual 1.435 1.543 -0.108 1.30e-02 5.92e+03 6.91e+01 bond pdb=" C3' DG G 42 " pdb=" O3' DG G 42 " ideal model delta sigma weight residual 1.435 1.524 -0.089 1.30e-02 5.92e+03 4.67e+01 bond pdb=" C1' DT G 21 " pdb=" N1 DT G 21 " ideal model delta sigma weight residual 1.468 1.560 -0.092 1.40e-02 5.10e+03 4.35e+01 bond pdb=" C3' DG G 11 " pdb=" O3' DG G 11 " ideal model delta sigma weight residual 1.435 1.511 -0.076 1.30e-02 5.92e+03 3.46e+01 ... (remaining 27107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 36720 3.53 - 7.06: 550 7.06 - 10.59: 64 10.59 - 14.12: 11 14.12 - 17.65: 1 Bond angle restraints: 37346 Sorted by residual: angle pdb=" O4' DA G 29 " pdb=" C1' DA G 29 " pdb=" N9 DA G 29 " ideal model delta sigma weight residual 108.00 114.60 -6.60 7.00e-01 2.04e+00 8.88e+01 angle pdb=" O4' DG G 37 " pdb=" C1' DG G 37 " pdb=" N9 DG G 37 " ideal model delta sigma weight residual 108.00 114.59 -6.59 7.00e-01 2.04e+00 8.85e+01 angle pdb=" O4' DT G 14 " pdb=" C1' DT G 14 " pdb=" N1 DT G 14 " ideal model delta sigma weight residual 108.00 114.18 -6.18 7.00e-01 2.04e+00 7.80e+01 angle pdb=" O4' DT G 34 " pdb=" C1' DT G 34 " pdb=" N1 DT G 34 " ideal model delta sigma weight residual 108.00 114.05 -6.05 7.00e-01 2.04e+00 7.47e+01 angle pdb=" O4' DG G 38 " pdb=" C1' DG G 38 " pdb=" N9 DG G 38 " ideal model delta sigma weight residual 108.00 113.90 -5.90 7.00e-01 2.04e+00 7.11e+01 ... (remaining 37341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 15418 35.73 - 71.46: 596 71.46 - 107.19: 13 107.19 - 142.92: 1 142.92 - 178.65: 6 Dihedral angle restraints: 16034 sinusoidal: 5998 harmonic: 10036 Sorted by residual: dihedral pdb=" CA VAL B 74 " pdb=" C VAL B 74 " pdb=" N GLN B 75 " pdb=" CA GLN B 75 " ideal model delta harmonic sigma weight residual -180.00 -100.59 -79.41 0 5.00e+00 4.00e-02 2.52e+02 dihedral pdb=" CA GLU B 76 " pdb=" C GLU B 76 " pdb=" N ASP B 77 " pdb=" CA ASP B 77 " ideal model delta harmonic sigma weight residual -180.00 -132.77 -47.23 0 5.00e+00 4.00e-02 8.92e+01 dihedral pdb=" CA GLY B 73 " pdb=" C GLY B 73 " pdb=" N VAL B 74 " pdb=" CA VAL B 74 " ideal model delta harmonic sigma weight residual -180.00 -134.59 -45.41 0 5.00e+00 4.00e-02 8.25e+01 ... (remaining 16031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3636 0.073 - 0.145: 737 0.145 - 0.218: 112 0.218 - 0.291: 18 0.291 - 0.363: 4 Chirality restraints: 4507 Sorted by residual: chirality pdb=" P U I 14 " pdb=" OP1 U I 14 " pdb=" OP2 U I 14 " pdb=" O5' U I 14 " both_signs ideal model delta sigma weight residual True 2.17 -2.54 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" P DC G 28 " pdb=" OP1 DC G 28 " pdb=" OP2 DC G 28 " pdb=" O5' DC G 28 " both_signs ideal model delta sigma weight residual True 2.34 -2.66 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" P DT G 44 " pdb=" OP1 DT G 44 " pdb=" OP2 DT G 44 " pdb=" O5' DT G 44 " both_signs ideal model delta sigma weight residual True 2.34 -2.65 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 4504 not shown) Planarity restraints: 4499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 250 " 0.080 5.00e-02 4.00e+02 1.24e-01 2.45e+01 pdb=" N PRO D 251 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO D 251 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO D 251 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC H 17 " -0.019 2.00e-02 2.50e+03 2.46e-02 1.36e+01 pdb=" N1 DC H 17 " 0.064 2.00e-02 2.50e+03 pdb=" C2 DC H 17 " -0.024 2.00e-02 2.50e+03 pdb=" O2 DC H 17 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DC H 17 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC H 17 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC H 17 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC H 17 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DC H 17 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 496 " -0.060 5.00e-02 4.00e+02 9.04e-02 1.31e+01 pdb=" N PRO C 497 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO C 497 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 497 " -0.050 5.00e-02 4.00e+02 ... (remaining 4496 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 434 2.65 - 3.21: 22178 3.21 - 3.77: 37816 3.77 - 4.34: 49305 4.34 - 4.90: 81656 Nonbonded interactions: 191389 Sorted by model distance: nonbonded pdb=" O3' A I 17 " pdb="MG MG I 101 " model vdw 2.084 2.170 nonbonded pdb=" O2' A I 17 " pdb="MG MG I 101 " model vdw 2.101 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG I 101 " model vdw 2.114 2.170 nonbonded pdb=" O GLN C1111 " pdb=" OG1 THR C1115 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR C 563 " pdb=" O ILE C 569 " model vdw 2.254 3.040 ... (remaining 191384 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 15 or (resid 16 through 18 and (nam \ e N or name CA or name C or name O or name CB )) or resid 19 through 28 or (resi \ d 29 and (name N or name CA or name C or name O or name CB )) or resid 30 throug \ h 37 or (resid 38 and (name N or name CA or name C or name O or name CB )) or re \ sid 39 through 48 or (resid 49 and (name N or name CA or name C or name O or nam \ e CB )) or resid 50 through 55 or (resid 56 and (name N or name CA or name C or \ name O or name CB )) or resid 57 through 58 or (resid 59 through 62 and (name N \ or name CA or name C or name O or name CB )) or resid 63 or (resid 64 through 72 \ and (name N or name CA or name C or name O or name CB )) or resid 73 or (resid \ 74 through 78 and (name N or name CA or name C or name O or name CB )) or resid \ 79 or (resid 80 and (name N or name CA or name C or name O or name CB )) or resi \ d 81 or (resid 82 and (name N or name CA or name C or name O or name CB )) or re \ sid 83 through 85 or (resid 86 and (name N or name CA or name C or name O or nam \ e CB )) or resid 87 through 91 or (resid 92 through 93 and (name N or name CA or \ name C or name O or name CB )) or resid 94 or (resid 95 through 97 and (name N \ or name CA or name C or name O or name CB )) or resid 98 or (resid 99 and (name \ N or name CA or name C or name O or name CB )) or resid 100 through 101 or (resi \ d 102 through 105 and (name N or name CA or name C or name O or name CB )) or re \ sid 106 or (resid 107 and (name N or name CA or name C or name O or name CB )) o \ r resid 108 through 113 or (resid 114 through 116 and (name N or name CA or name \ C or name O or name CB )) or resid 117 through 120 or (resid 121 through 123 an \ d (name N or name CA or name C or name O or name CB )) or resid 124 through 132 \ or (resid 133 through 139 and (name N or name CA or name C or name O or name CB \ )) or resid 140 through 141 or (resid 142 through 143 and (name N or name CA or \ name C or name O or name CB )) or resid 144 or (resid 145 and (name N or name CA \ or name C or name O or name CB )) or resid 146 or (resid 147 and (name N or nam \ e CA or name C or name O or name CB )) or resid 148 through 155 or (resid 166 an \ d (name N or name CA or name C or name O or name CB )) or resid 167 or (resid 16 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 169 or (resi \ d 170 through 172 and (name N or name CA or name C or name O or name CB )) or re \ sid 173 or (resid 174 through 176 and (name N or name CA or name C or name O or \ name CB )) or resid 177 through 185 or (resid 186 and (name N or name CA or name \ C or name O or name CB )) or resid 187 through 194 or (resid 195 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE )) or ( \ resid 196 through 199 and (name N or name CA or name C or name O or name CB )) o \ r resid 200 through 204 or (resid 205 through 206 and (name N or name CA or name \ C or name O or name CB )) or resid 207 or (resid 208 and (name N or name CA or \ name C or name O or name CB )) or resid 209 through 232)) selection = (chain 'B' and (resid 8 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or (resid 11 through 12 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )) or resid 13 through 14 or (resid \ 15 through 18 and (name N or name CA or name C or name O or name CB )) or resid \ 19 through 20 or (resid 21 and (name N or name CA or name C or name O or name CB \ )) or resid 22 through 32 or (resid 33 and (name N or name CA or name C or name \ O or name CB )) or resid 34 through 40 or (resid 41 through 42 and (name N or n \ ame CA or name C or name O or name CB )) or resid 43 through 124 or (resid 125 a \ nd (name N or name CA or name C or name O or name CB )) or resid 126 through 138 \ or (resid 139 and (name N or name CA or name C or name O or name CB )) or resid \ 140 through 155 or resid 166 through 195 or (resid 196 through 199 and (name N \ or name CA or name C or name O or name CB )) or resid 200 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.860 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 : 0.010 0.494 27119 Z= 0.497 Angle : 1.137 32.462 37352 Z= 0.673 Chirality : 0.062 0.363 4507 Planarity : 0.008 0.124 4499 Dihedral : 18.152 178.651 9558 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.94 % Favored : 86.00 % Rotamer: Outliers : 1.08 % Allowed : 14.06 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.21 % 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: -5.39 (0.11), residues: 3450 helix: -4.32 (0.10), residues: 1060 sheet: -3.54 (0.25), residues: 314 loop : -3.31 (0.11), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG F 85 TYR 0.043 0.003 TYR D 165 PHE 0.022 0.002 PHE J 73 TRP 0.025 0.002 TRP C 807 HIS 0.013 0.002 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00860 / 0.47 (27112) covalent geometry : angle 1.11619 / 0.67 (37346) hydrogen bonds : bond 0.30576 / 21.24 ( 491) hydrogen bonds : angle 10.68308 / 7.30 ( 1270) metal coordination : bond 0.27865 / 17.39 ( 7) metal coordination : angle 17.02038 / 11.71 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 370 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.9005 (mtpp) cc_final: 0.8754 (tttt) REVERT: C 403 MET cc_start: 0.8821 (tmm) cc_final: 0.8586 (tmm) REVERT: C 459 MET cc_start: 0.9005 (mtm) cc_final: 0.8602 (mtp) REVERT: C 461 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8171 (tm-30) REVERT: C 517 GLN cc_start: 0.7986 (tt0) cc_final: 0.7728 (tt0) REVERT: C 644 LEU cc_start: 0.8887 (mt) cc_final: 0.8499 (mt) REVERT: C 798 GLN cc_start: 0.8466 (mp10) cc_final: 0.8175 (mp10) REVERT: C 919 ARG cc_start: 0.8850 (ptp-110) cc_final: 0.8636 (ptp90) REVERT: C 1022 LYS cc_start: 0.5731 (pttp) cc_final: 0.5501 (tmtt) REVERT: C 1273 MET cc_start: 0.8991 (ttm) cc_final: 0.8788 (ttm) REVERT: C 1304 MET cc_start: 0.8654 (tpt) cc_final: 0.8430 (tpp) REVERT: D 192 MET cc_start: 0.3991 (ptm) cc_final: 0.3367 (mmt) REVERT: D 298 MET cc_start: 0.8618 (ttm) cc_final: 0.8173 (ttm) REVERT: D 340 GLN cc_start: 0.8223 (tt0) cc_final: 0.7942 (tt0) REVERT: D 462 ASP cc_start: 0.8251 (m-30) cc_final: 0.7972 (m-30) REVERT: D 604 MET cc_start: 0.8646 (ttp) cc_final: 0.8344 (ttm) REVERT: D 806 ASP cc_start: 0.8008 (m-30) cc_final: 0.7416 (t0) REVERT: D 925 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8392 (tm-30) REVERT: E 29 GLN cc_start: 0.8463 (mt0) cc_final: 0.8247 (mt0) REVERT: F 121 GLU cc_start: 0.8699 (tp30) cc_final: 0.8462 (tp30) outliers start: 23 outliers final: 16 residues processed: 389 average time/residue: 0.2010 time to fit residues: 119.8912 Evaluate side-chains 311 residues out of total 2992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 295 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1285 TYR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain J residue 50 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.0870 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.0070 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 HIS A 147 GLN A 208 ASN C 649 GLN C 688 GLN C 832 HIS C1257 GLN D 104 HIS D 266 ASN D 419 HIS D 736 GLN D 771 GLN D 979 ASN D1019 ASN D1086 ASN D1098 GLN D1350 ASN F 59 GLN F 160 ASN F 187 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.138071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.104234 restraints weight = 42946.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.103116 restraints weight = 38580.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.103819 restraints weight = 39182.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.104051 restraints weight = 30059.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.104880 restraints weight = 24362.826| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27119 Z= 0.124 Angle : 0.662 17.943 37352 Z= 0.350 Chirality : 0.045 0.295 4507 Planarity : 0.005 0.066 4499 Dihedral : 17.406 179.664 4836 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.12 % Favored : 91.86 % Rotamer: Outliers : 2.34 % Allowed : 16.92 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.80 (0.11), residues: 3450 helix: -3.98 (0.10), residues: 1080 sheet: -2.79 (0.25), residues: 329 loop : -2.88 (0.12), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 85 TYR 0.020 0.001 TYR B 177 PHE 0.017 0.001 PHE C 156 TRP 0.012 0.001 TRP D 33 HIS 0.004 0.001 HIS F 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (27112) covalent geometry : angle 0.65161 / 0.35 (37346) hydrogen bonds : bond 0.05807 / 3.98 ( 491) hydrogen bonds : angle 6.71917 / 4.59 ( 1270) metal coordination : bond 0.01554 / 0.87 ( 7) metal coordination : angle 9.06907 / 8.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 329 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8985 (mtpp) cc_final: 0.8731 (tttt) REVERT: B 41 ASN cc_start: 0.8927 (t0) cc_final: 0.8718 (t0) REVERT: B 223 ILE cc_start: 0.9199 (mm) cc_final: 0.8999 (tp) REVERT: C 403 MET cc_start: 0.8741 (tmm) cc_final: 0.8526 (tmm) REVERT: C 836 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8751 (pp) REVERT: C 919 ARG cc_start: 0.8929 (ptp-110) cc_final: 0.8695 (ptp90) REVERT: C 1022 LYS cc_start: 0.5262 (pttp) cc_final: 0.4908 (tmtt) REVERT: C 1194 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7022 (mt-10) REVERT: C 1243 MET cc_start: 0.8765 (tmm) cc_final: 0.8400 (tmm) REVERT: D 192 MET cc_start: 0.4424 (ptm) cc_final: 0.3592 (mmt) REVERT: D 298 MET cc_start: 0.8291 (ttm) cc_final: 0.8030 (ttm) REVERT: D 806 ASP cc_start: 0.8037 (m-30) cc_final: 0.7494 (t0) REVERT: E 44 ASP cc_start: 0.8392 (m-30) cc_final: 0.7906 (m-30) REVERT: F 97 SER cc_start: 0.8703 (p) cc_final: 0.8400 (m) outliers start: 50 outliers final: 27 residues processed: 365 average time/residue: 0.1720 time to fit residues: 101.6711 Evaluate side-chains 319 residues out of total 2992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 291 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1285 TYR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain J residue 34 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 309 optimal weight: 0.0020 chunk 60 optimal weight: 0.0020 chunk 281 optimal weight: 30.0000 chunk 92 optimal weight: 7.9990 chunk 68 optimal weight: 50.0000 chunk 75 optimal weight: 8.9990 chunk 259 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN D 340 GLN F 201 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.138972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.104629 restraints weight = 43036.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.103856 restraints weight = 38831.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.104492 restraints weight = 38016.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.104636 restraints weight = 30228.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.105331 restraints weight = 24664.072| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 27119 Z= 0.111 Angle : 0.590 17.224 37352 Z= 0.311 Chirality : 0.043 0.191 4507 Planarity : 0.004 0.060 4499 Dihedral : 17.032 177.903 4825 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.76 % Allowed : 19.12 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.32 (0.12), residues: 3450 helix: -3.52 (0.12), residues: 1091 sheet: -2.56 (0.26), residues: 326 loop : -2.60 (0.12), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 3 TYR 0.020 0.001 TYR B 177 PHE 0.018 0.001 PHE C 156 TRP 0.007 0.001 TRP D 33 HIS 0.004 0.001 HIS F 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (27112) covalent geometry : angle 0.57932 / 0.31 (37346) hydrogen bonds : bond 0.04355 / 3.01 ( 491) hydrogen bonds : angle 5.79496 / 4.00 ( 1270) metal coordination : bond 0.02440 / 1.24 ( 7) metal coordination : angle 8.79631 / 7.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 318 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8990 (mtpp) cc_final: 0.8626 (tttt) REVERT: A 207 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.9000 (p) REVERT: B 47 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8367 (pp) REVERT: B 156 SER cc_start: 0.9186 (m) cc_final: 0.8985 (p) REVERT: C 22 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9006 (mt) REVERT: C 82 VAL cc_start: 0.8925 (t) cc_final: 0.8643 (p) REVERT: C 836 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8698 (pp) REVERT: C 947 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7514 (tm-30) REVERT: C 1022 LYS cc_start: 0.5315 (pttp) cc_final: 0.4960 (tmtt) REVERT: C 1194 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6860 (mt-10) REVERT: C 1243 MET cc_start: 0.8774 (tmm) cc_final: 0.8185 (tmm) REVERT: D 298 MET cc_start: 0.8255 (ttm) cc_final: 0.7996 (ttm) REVERT: E 44 ASP cc_start: 0.8483 (m-30) cc_final: 0.7960 (m-30) REVERT: F 97 SER cc_start: 0.8743 (p) cc_final: 0.8402 (m) REVERT: F 121 GLU cc_start: 0.8442 (tp30) cc_final: 0.7952 (tp30) REVERT: J 54 TRP cc_start: 0.7782 (m100) cc_final: 0.7483 (m100) outliers start: 59 outliers final: 37 residues processed: 360 average time/residue: 0.1621 time to fit residues: 94.8127 Evaluate side-chains 328 residues out of total 2992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 287 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1285 TYR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain J residue 34 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 305 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 349 optimal weight: 8.9990 chunk 192 optimal weight: 20.0000 chunk 168 optimal weight: 6.9990 chunk 249 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 26 optimal weight: 40.0000 chunk 69 optimal weight: 0.9980 chunk 240 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 HIS A 147 GLN C 517 GLN D1350 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.135328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.105088 restraints weight = 43159.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.104671 restraints weight = 72125.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.105384 restraints weight = 68144.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.105435 restraints weight = 41093.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.106824 restraints weight = 36400.208| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 27119 Z= 0.270 Angle : 0.687 18.387 37352 Z= 0.355 Chirality : 0.046 0.169 4507 Planarity : 0.005 0.074 4499 Dihedral : 17.131 177.817 4824 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 4.26 % Allowed : 20.06 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.12), residues: 3450 helix: -3.29 (0.12), residues: 1093 sheet: -2.51 (0.28), residues: 304 loop : -2.69 (0.12), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 3 TYR 0.017 0.002 TYR D1365 PHE 0.020 0.002 PHE C 156 TRP 0.008 0.001 TRP J 54 HIS 0.006 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.27 (27112) covalent geometry : angle 0.67617 / 0.35 (37346) hydrogen bonds : bond 0.04542 / 3.18 ( 491) hydrogen bonds : angle 5.83246 / 4.01 ( 1270) metal coordination : bond 0.01209 / 0.59 ( 7) metal coordination : angle 9.54984 / 8.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 293 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8938 (mtpp) cc_final: 0.8656 (tttt) REVERT: A 207 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.9082 (p) REVERT: B 47 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8564 (pp) REVERT: B 156 SER cc_start: 0.9222 (m) cc_final: 0.8952 (p) REVERT: C 22 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8914 (mt) REVERT: C 836 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8613 (pp) REVERT: C 896 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.8961 (p) REVERT: C 1022 LYS cc_start: 0.5470 (pttp) cc_final: 0.5117 (tmtt) REVERT: C 1243 MET cc_start: 0.8999 (tmm) cc_final: 0.8306 (tmm) REVERT: D 192 MET cc_start: 0.4116 (ptm) cc_final: 0.3328 (mmp) REVERT: D 298 MET cc_start: 0.8194 (ttm) cc_final: 0.7973 (ttm) REVERT: D 1040 MET cc_start: 0.3176 (ttm) cc_final: 0.0759 (tpp) REVERT: E 44 ASP cc_start: 0.8454 (m-30) cc_final: 0.8008 (m-30) REVERT: E 70 GLN cc_start: 0.7665 (tm-30) cc_final: 0.7355 (tm-30) REVERT: F 121 GLU cc_start: 0.8468 (tp30) cc_final: 0.8082 (tp30) outliers start: 91 outliers final: 60 residues processed: 362 average time/residue: 0.1647 time to fit residues: 98.3688 Evaluate side-chains 347 residues out of total 2992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 282 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1285 TYR Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain J residue 50 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 166 optimal weight: 1.9990 chunk 234 optimal weight: 20.0000 chunk 279 optimal weight: 0.0970 chunk 270 optimal weight: 8.9990 chunk 325 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 351 optimal weight: 20.0000 chunk 162 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 291 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN C 510 GLN C 517 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.137663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107969 restraints weight = 43209.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.107204 restraints weight = 74267.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.108148 restraints weight = 68388.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.108121 restraints weight = 41523.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.108598 restraints weight = 37940.246| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27119 Z= 0.126 Angle : 0.580 15.675 37352 Z= 0.304 Chirality : 0.043 0.167 4507 Planarity : 0.004 0.052 4499 Dihedral : 17.001 178.296 4824 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.98 % Allowed : 20.71 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.95 (0.13), residues: 3450 helix: -3.03 (0.13), residues: 1099 sheet: -2.37 (0.28), residues: 315 loop : -2.49 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 3 TYR 0.014 0.001 TYR B 177 PHE 0.019 0.001 PHE C 156 TRP 0.006 0.001 TRP J 54 HIS 0.005 0.001 HIS F 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (27112) covalent geometry : angle 0.57164 / 0.30 (37346) hydrogen bonds : bond 0.03803 / 2.63 ( 491) hydrogen bonds : angle 5.41261 / 3.75 ( 1270) metal coordination : bond 0.00644 / 0.33 ( 7) metal coordination : angle 7.98712 / 7.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 304 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8908 (mtpp) cc_final: 0.8525 (tttt) REVERT: B 156 SER cc_start: 0.9152 (m) cc_final: 0.8947 (p) REVERT: C 836 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8601 (pp) REVERT: C 919 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8509 (mtp85) REVERT: C 1022 LYS cc_start: 0.5316 (pttp) cc_final: 0.5103 (tmtt) REVERT: C 1243 MET cc_start: 0.8937 (tmm) cc_final: 0.8315 (tmm) REVERT: D 298 MET cc_start: 0.8146 (ttm) cc_final: 0.7844 (ttm) REVERT: D 725 MET cc_start: 0.8108 (mtt) cc_final: 0.7854 (mtt) REVERT: D 1040 MET cc_start: 0.3444 (ttm) cc_final: 0.0858 (tpp) REVERT: E 44 ASP cc_start: 0.8477 (m-30) cc_final: 0.8016 (m-30) REVERT: E 70 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7314 (tm-30) REVERT: F 121 GLU cc_start: 0.8373 (tp30) cc_final: 0.7966 (tp30) outliers start: 85 outliers final: 54 residues processed: 365 average time/residue: 0.1595 time to fit residues: 95.3758 Evaluate side-chains 339 residues out of total 2992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 283 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 1002 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1285 TYR Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain J residue 34 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 241 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 295 optimal weight: 3.9990 chunk 253 optimal weight: 0.0010 chunk 119 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 342 optimal weight: 30.0000 chunk 315 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 37 HIS C 517 GLN ** F 270 GLN ** 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 = 0.3591 r_free = 0.3591 target = 0.135080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.101134 restraints weight = 43915.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.099200 restraints weight = 41871.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.100606 restraints weight = 41724.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.100505 restraints weight = 30028.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.101521 restraints weight = 24335.124| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 27119 Z= 0.218 Angle : 0.631 16.018 37352 Z= 0.327 Chirality : 0.045 0.269 4507 Planarity : 0.004 0.052 4499 Dihedral : 17.059 178.071 4824 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 4.50 % Allowed : 21.79 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.92 (0.13), residues: 3450 helix: -2.92 (0.13), residues: 1095 sheet: -2.33 (0.29), residues: 301 loop : -2.54 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 3 TYR 0.017 0.001 TYR A 185 PHE 0.021 0.001 PHE C 156 TRP 0.006 0.001 TRP C 807 HIS 0.005 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 (27112) covalent geometry : angle 0.62295 / 0.33 (37346) hydrogen bonds : bond 0.04022 / 2.81 ( 491) hydrogen bonds : angle 5.42883 / 3.75 ( 1270) metal coordination : bond 0.00802 / 0.41 ( 7) metal coordination : angle 8.08432 / 7.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 291 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8926 (ttt90) REVERT: A 200 LYS cc_start: 0.8994 (mtpp) cc_final: 0.8706 (tttt) REVERT: B 156 SER cc_start: 0.9281 (m) cc_final: 0.9023 (p) REVERT: B 182 ARG cc_start: 0.8233 (tpt170) cc_final: 0.7996 (tpt170) REVERT: C 826 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7789 (t0) REVERT: C 836 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8545 (pp) REVERT: C 896 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.8893 (p) REVERT: C 919 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8521 (mtp85) REVERT: C 1022 LYS cc_start: 0.5412 (pttp) cc_final: 0.5009 (tmtt) REVERT: C 1243 MET cc_start: 0.8931 (tmm) cc_final: 0.8299 (tmm) REVERT: C 1315 MET cc_start: 0.7608 (tmm) cc_final: 0.7362 (tmm) REVERT: D 192 MET cc_start: 0.4261 (ptm) cc_final: 0.3483 (mmp) REVERT: D 1040 MET cc_start: 0.3250 (ttm) cc_final: 0.0768 (tpp) REVERT: E 44 ASP cc_start: 0.8525 (m-30) cc_final: 0.8003 (m-30) REVERT: E 70 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7385 (tm-30) REVERT: F 75 GLU cc_start: 0.8562 (pm20) cc_final: 0.8342 (pm20) REVERT: F 121 GLU cc_start: 0.8510 (tp30) cc_final: 0.8178 (tp30) outliers start: 96 outliers final: 72 residues processed: 363 average time/residue: 0.1636 time to fit residues: 97.2339 Evaluate side-chains 357 residues out of total 2992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 280 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 1002 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1285 TYR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain J residue 34 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 88 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 197 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 293 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 326 optimal weight: 0.0570 chunk 25 optimal weight: 4.9990 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 517 GLN D 266 ASN ** F 270 GLN ** 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 = 0.3620 r_free = 0.3620 target = 0.137344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.103403 restraints weight = 43477.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.101498 restraints weight = 41631.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.102355 restraints weight = 41128.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.102963 restraints weight = 27557.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.103113 restraints weight = 24401.202| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27119 Z= 0.118 Angle : 0.566 11.159 37352 Z= 0.297 Chirality : 0.043 0.231 4507 Planarity : 0.004 0.054 4499 Dihedral : 16.953 178.153 4824 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.80 % Allowed : 23.10 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.69 (0.13), residues: 3450 helix: -2.75 (0.14), residues: 1115 sheet: -2.16 (0.29), residues: 299 loop : -2.38 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 3 TYR 0.012 0.001 TYR B 177 PHE 0.019 0.001 PHE C 156 TRP 0.005 0.001 TRP D1020 HIS 0.005 0.001 HIS F 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (27112) covalent geometry : angle 0.56182 / 0.30 (37346) hydrogen bonds : bond 0.03560 / 2.47 ( 491) hydrogen bonds : angle 5.16438 / 3.58 ( 1270) metal coordination : bond 0.00482 / 0.25 ( 7) metal coordination : angle 5.32725 / 4.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 296 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8988 (mtpp) cc_final: 0.8770 (tttt) REVERT: C 826 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7729 (t0) REVERT: C 836 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8565 (pp) REVERT: C 896 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.8909 (p) REVERT: C 919 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8527 (mtp85) REVERT: C 1022 LYS cc_start: 0.5324 (pttp) cc_final: 0.4966 (tmtt) REVERT: C 1243 MET cc_start: 0.8853 (tmm) cc_final: 0.8248 (tmm) REVERT: C 1315 MET cc_start: 0.7564 (tmm) cc_final: 0.7170 (tmm) REVERT: D 192 MET cc_start: 0.4848 (ptm) cc_final: 0.3856 (mmp) REVERT: D 1040 MET cc_start: 0.3271 (ttm) cc_final: 0.0737 (tpp) REVERT: E 44 ASP cc_start: 0.8458 (m-30) cc_final: 0.7962 (m-30) REVERT: E 70 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7329 (tm-30) REVERT: F 75 GLU cc_start: 0.8615 (pm20) cc_final: 0.8378 (pm20) REVERT: F 121 GLU cc_start: 0.8442 (tp30) cc_final: 0.8095 (tp30) outliers start: 81 outliers final: 62 residues processed: 356 average time/residue: 0.1639 time to fit residues: 96.7857 Evaluate side-chains 345 residues out of total 2992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 279 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 1002 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1285 TYR Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain J residue 34 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 134 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 350 optimal weight: 9.9990 chunk 221 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 294 optimal weight: 8.9990 chunk 318 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 192 optimal weight: 0.0040 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 517 GLN ** F 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.103659 restraints weight = 43865.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.101996 restraints weight = 41561.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.103339 restraints weight = 41701.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.103399 restraints weight = 26227.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104363 restraints weight = 22901.810| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27119 Z= 0.119 Angle : 0.565 11.191 37352 Z= 0.295 Chirality : 0.043 0.235 4507 Planarity : 0.004 0.050 4499 Dihedral : 16.906 177.772 4824 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.98 % Allowed : 23.10 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.13), residues: 3450 helix: -2.61 (0.14), residues: 1116 sheet: -2.00 (0.30), residues: 297 loop : -2.36 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 3 TYR 0.018 0.001 TYR A 185 PHE 0.023 0.001 PHE C 156 TRP 0.005 0.001 TRP J 57 HIS 0.005 0.001 HIS F 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (27112) covalent geometry : angle 0.56123 / 0.29 (37346) hydrogen bonds : bond 0.03511 / 2.43 ( 491) hydrogen bonds : angle 5.07315 / 3.53 ( 1270) metal coordination : bond 0.00468 / 0.24 ( 7) metal coordination : angle 4.94013 / 3.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 288 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 TYR cc_start: 0.8169 (p90) cc_final: 0.7891 (p90) REVERT: A 200 LYS cc_start: 0.9009 (mtpp) cc_final: 0.8763 (tttt) REVERT: C 826 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7685 (t0) REVERT: C 896 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8900 (p) REVERT: C 919 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8517 (mtp85) REVERT: C 949 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7988 (mp0) REVERT: C 1022 LYS cc_start: 0.5249 (pttp) cc_final: 0.4923 (tmtt) REVERT: C 1243 MET cc_start: 0.8858 (tmm) cc_final: 0.8240 (tmm) REVERT: C 1315 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7136 (tmm) REVERT: D 1040 MET cc_start: 0.3330 (ttm) cc_final: 0.0766 (tpp) REVERT: E 44 ASP cc_start: 0.8473 (m-30) cc_final: 0.7962 (m-30) REVERT: E 70 GLN cc_start: 0.7660 (tm-30) cc_final: 0.7336 (tm-30) REVERT: F 75 GLU cc_start: 0.8640 (pm20) cc_final: 0.8431 (pm20) REVERT: F 121 GLU cc_start: 0.8418 (tp30) cc_final: 0.8079 (tp30) outliers start: 85 outliers final: 64 residues processed: 347 average time/residue: 0.1609 time to fit residues: 92.8419 Evaluate side-chains 353 residues out of total 2992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 285 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1285 TYR Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain J residue 34 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 70 optimal weight: 20.0000 chunk 317 optimal weight: 0.8980 chunk 36 optimal weight: 50.0000 chunk 171 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 26 optimal weight: 40.0000 chunk 249 optimal weight: 0.9980 chunk 323 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 274 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.136016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.103014 restraints weight = 43687.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.102069 restraints weight = 40709.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.103331 restraints weight = 37072.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.103173 restraints weight = 25276.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104053 restraints weight = 23104.116| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27119 Z= 0.171 Angle : 0.596 13.110 37352 Z= 0.309 Chirality : 0.044 0.220 4507 Planarity : 0.004 0.053 4499 Dihedral : 16.910 179.618 4824 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 4.12 % Allowed : 23.10 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.13), residues: 3450 helix: -2.53 (0.14), residues: 1106 sheet: -2.10 (0.30), residues: 288 loop : -2.33 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 158 TYR 0.017 0.001 TYR A 185 PHE 0.026 0.001 PHE C 156 TRP 0.006 0.001 TRP C 807 HIS 0.006 0.001 HIS F 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (27112) covalent geometry : angle 0.59260 / 0.31 (37346) hydrogen bonds : bond 0.03683 / 2.57 ( 491) hydrogen bonds : angle 5.13417 / 3.56 ( 1270) metal coordination : bond 0.00566 / 0.29 ( 7) metal coordination : angle 5.00699 / 4.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 286 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8782 (tttt) REVERT: C 826 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7875 (t0) REVERT: C 896 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8890 (p) REVERT: C 919 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8533 (mtp85) REVERT: C 949 GLU cc_start: 0.8219 (mm-30) cc_final: 0.8019 (mp0) REVERT: C 1022 LYS cc_start: 0.5329 (pttp) cc_final: 0.4838 (tmtt) REVERT: C 1243 MET cc_start: 0.8911 (tmm) cc_final: 0.8264 (tmm) REVERT: C 1315 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7324 (tmm) REVERT: D 192 MET cc_start: 0.4684 (ptm) cc_final: 0.3777 (mmp) REVERT: D 1046 ILE cc_start: 0.0389 (OUTLIER) cc_final: -0.0085 (pt) REVERT: E 44 ASP cc_start: 0.8479 (m-30) cc_final: 0.7980 (m-30) REVERT: E 70 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7381 (tm-30) REVERT: F 116 LEU cc_start: 0.8047 (tt) cc_final: 0.7806 (tt) REVERT: F 121 GLU cc_start: 0.8434 (tp30) cc_final: 0.8129 (tp30) outliers start: 88 outliers final: 73 residues processed: 349 average time/residue: 0.1603 time to fit residues: 93.2523 Evaluate side-chains 360 residues out of total 2992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 282 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1002 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1165 SER Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1285 TYR Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain J residue 34 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 78 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 270 optimal weight: 40.0000 chunk 201 optimal weight: 0.4980 chunk 23 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 184 optimal weight: 0.6980 chunk 70 optimal weight: 20.0000 chunk 282 optimal weight: 40.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107833 restraints weight = 43293.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.106355 restraints weight = 70832.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.107438 restraints weight = 71246.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.107681 restraints weight = 39259.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.108262 restraints weight = 35319.740| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27119 Z= 0.123 Angle : 0.566 11.058 37352 Z= 0.295 Chirality : 0.043 0.278 4507 Planarity : 0.004 0.051 4499 Dihedral : 16.795 177.952 4824 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.56 % Allowed : 23.81 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.40 (0.13), residues: 3450 helix: -2.41 (0.14), residues: 1115 sheet: -2.03 (0.29), residues: 301 loop : -2.25 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 3 TYR 0.013 0.001 TYR B 177 PHE 0.026 0.001 PHE C 156 TRP 0.005 0.001 TRP J 57 HIS 0.005 0.001 HIS F 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (27112) covalent geometry : angle 0.56293 / 0.29 (37346) hydrogen bonds : bond 0.03432 / 2.38 ( 491) hydrogen bonds : angle 4.98090 / 3.47 ( 1270) metal coordination : bond 0.00494 / 0.25 ( 7) metal coordination : angle 4.56450 / 3.68 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 291 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 TYR cc_start: 0.8042 (p90) cc_final: 0.7766 (p90) REVERT: A 200 LYS cc_start: 0.8964 (mtpp) cc_final: 0.8719 (tttt) REVERT: C 826 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7951 (t0) REVERT: C 896 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.8915 (p) REVERT: C 919 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8626 (mtp85) REVERT: C 1022 LYS cc_start: 0.5297 (pttp) cc_final: 0.4874 (tmtt) REVERT: C 1243 MET cc_start: 0.8905 (tmm) cc_final: 0.8247 (tmm) REVERT: C 1315 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7447 (tmm) REVERT: D 192 MET cc_start: 0.4759 (ptm) cc_final: 0.3899 (mmp) REVERT: D 1040 MET cc_start: 0.2947 (ttm) cc_final: 0.0760 (tpp) REVERT: E 44 ASP cc_start: 0.8455 (m-30) cc_final: 0.7995 (m-30) REVERT: E 70 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7344 (tm-30) REVERT: F 116 LEU cc_start: 0.7911 (tt) cc_final: 0.7628 (tt) REVERT: F 121 GLU cc_start: 0.8355 (tp30) cc_final: 0.7989 (tp30) outliers start: 76 outliers final: 66 residues processed: 344 average time/residue: 0.1592 time to fit residues: 91.0146 Evaluate side-chains 352 residues out of total 2992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 282 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1285 TYR Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 462 ASP Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain J residue 34 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 37 optimal weight: 8.9990 chunk 313 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 186 optimal weight: 0.0370 chunk 120 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 32 optimal weight: 40.0000 chunk 71 optimal weight: 50.0000 chunk 334 optimal weight: 3.9990 chunk 282 optimal weight: 50.0000 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 517 GLN C 658 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.136193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.106343 restraints weight = 42889.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.106008 restraints weight = 68474.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.106567 restraints weight = 70005.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.106785 restraints weight = 40521.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.107395 restraints weight = 36347.632| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 27119 Z= 0.206 Angle : 0.618 11.189 37352 Z= 0.320 Chirality : 0.045 0.242 4507 Planarity : 0.004 0.063 4499 Dihedral : 16.811 177.442 4822 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 4.17 % Allowed : 23.38 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.13), residues: 3450 helix: -2.41 (0.14), residues: 1104 sheet: -2.07 (0.29), residues: 300 loop : -2.30 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 158 TYR 0.011 0.001 TYR D1282 PHE 0.030 0.001 PHE C 156 TRP 0.009 0.001 TRP D 686 HIS 0.006 0.001 HIS F 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (27112) covalent geometry : angle 0.61448 / 0.32 (37346) hydrogen bonds : bond 0.03777 / 2.64 ( 491) hydrogen bonds : angle 5.11126 / 3.54 ( 1270) metal coordination : bond 0.00661 / 0.33 ( 7) metal coordination : angle 5.00844 / 4.15 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4219.05 seconds wall clock time: 73 minutes 19.60 seconds (4399.60 seconds total)