Starting phenix.real_space_refine on Thu Oct 29 20:40:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ltj_0974/10_2026/6ltj_0974.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ltj_0974/10_2026/6ltj_0974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ltj_0974/10_2026/6ltj_0974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ltj_0974/10_2026/6ltj_0974.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ltj_0974/10_2026/6ltj_0974.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ltj_0974/10_2026/6ltj_0974.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ltj_0974/10_2026/6ltj_0974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ltj_0974/10_2026/6ltj_0974.map" } resolution = 3.7 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= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 238 5.49 5 S 150 5.16 5 C 20942 2.51 5 N 6119 2.21 5 O 6833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34283 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 739 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 726 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "D" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 682 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "E" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 739 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "G" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 727 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "H" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 700 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 4606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4606 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 14, 'TRANS': 536} Chain breaks: 11 Chain: "J" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2612 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 15, 'TRANS': 318} Chain breaks: 4 Chain: "K" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2482 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain breaks: 3 Chain: "L" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3670 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 25, 'TRANS': 440} Chain breaks: 4 Chain: "M" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2277 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 13, 'TRANS': 269} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "N" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2120 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 6, 'TRANS': 254} Chain breaks: 3 Chain: "O" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2632 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 19, 'TRANS': 305} Chain breaks: 3 Chain: "P" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 2015 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 14, 'TRANS': 224} Chain breaks: 2 Chain: "Q" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 860 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "R" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 580 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "X" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2424 Classifications: {'DNA': 119} Link IDs: {'rna3p': 118} Chain: "Y" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2455 Classifications: {'DNA': 119} Link IDs: {'rna3p': 118} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17569 SG CYS L2094 67.231 67.353 64.589 1.00 48.48 S Time building chain proxies: 6.91, per 1000 atoms: 0.20 Number of scatterers: 34283 At special positions: 0 Unit cell: (223.6, 175.76, 183.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 150 16.00 P 238 15.00 O 6833 8.00 N 6119 7.00 C 20942 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: 3.13 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L2301 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2019 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2021 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2090 " pdb="ZN ZN L2301 " - pdb=" SG CYS L2094 " Number of angles added : 3 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6972 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 27 sheets defined 63.5% alpha, 5.3% beta 100 base pairs and 205 stacking pairs defined. Time for finding SS restraints: 4.95 Creating SS restraints... Processing helix chain 'A' and resid 42 through 54 Processing helix chain 'A' and resid 60 through 76 Processing helix chain 'A' and resid 82 through 111 Processing helix chain 'A' and resid 117 through 128 removed outlier: 3.876A pdb=" N ILE A 121 " --> pdb=" O MET A 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.808A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.985A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.640A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.690A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.885A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.569A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.875A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 4.368A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.648A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.370A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.521A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 35 through 43 removed outlier: 3.865A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.520A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.633A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 387 removed outlier: 3.565A pdb=" N ASN I 387 " --> pdb=" O GLN I 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 409 Processing helix chain 'I' and resid 409 through 428 removed outlier: 3.552A pdb=" N GLN I 415 " --> pdb=" O ASN I 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 430 through 434 Processing helix chain 'I' and resid 446 through 517 removed outlier: 3.882A pdb=" N ALA I 450 " --> pdb=" O SER I 446 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN I 477 " --> pdb=" O GLN I 473 " (cutoff:3.500A) Processing helix chain 'I' and resid 757 through 768 Processing helix chain 'I' and resid 784 through 795 removed outlier: 4.023A pdb=" N TYR I 795 " --> pdb=" O ALA I 791 " (cutoff:3.500A) Processing helix chain 'I' and resid 812 through 826 removed outlier: 3.501A pdb=" N ASN I 817 " --> pdb=" O SER I 813 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TRP I 818 " --> pdb=" O THR I 814 " (cutoff:3.500A) Processing helix chain 'I' and resid 839 through 844 Processing helix chain 'I' and resid 845 through 849 removed outlier: 3.794A pdb=" N LEU I 848 " --> pdb=" O VAL I 845 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG I 849 " --> pdb=" O PRO I 846 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 845 through 849' Processing helix chain 'I' and resid 893 through 898 removed outlier: 4.253A pdb=" N ASN I 898 " --> pdb=" O THR I 894 " (cutoff:3.500A) Processing helix chain 'I' and resid 899 through 901 No H-bonds generated for 'chain 'I' and resid 899 through 901' Processing helix chain 'I' and resid 917 through 925 Processing helix chain 'I' and resid 931 through 939 removed outlier: 3.712A pdb=" N SER I 935 " --> pdb=" O THR I 931 " (cutoff:3.500A) Processing helix chain 'I' and resid 972 through 976 removed outlier: 3.924A pdb=" N PHE I 975 " --> pdb=" O LEU I 972 " (cutoff:3.500A) Processing helix chain 'I' and resid 1001 through 1013 Processing helix chain 'I' and resid 1039 through 1048 Processing helix chain 'I' and resid 1055 through 1059 Processing helix chain 'I' and resid 1079 through 1089 Processing helix chain 'I' and resid 1107 through 1120 Processing helix chain 'I' and resid 1179 through 1182 removed outlier: 4.069A pdb=" N GLN I1182 " --> pdb=" O ASN I1179 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1179 through 1182' Processing helix chain 'I' and resid 1183 through 1192 removed outlier: 4.986A pdb=" N ALA I1190 " --> pdb=" O ALA I1186 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG I1192 " --> pdb=" O ASP I1188 " (cutoff:3.500A) Processing helix chain 'I' and resid 1300 through 1306 Processing helix chain 'I' and resid 1311 through 1323 removed outlier: 4.561A pdb=" N ARG I1323 " --> pdb=" O MET I1319 " (cutoff:3.500A) Processing helix chain 'I' and resid 1352 through 1362 Processing helix chain 'J' and resid 70 through 77 Processing helix chain 'J' and resid 95 through 110 Processing helix chain 'J' and resid 129 through 143 removed outlier: 3.709A pdb=" N HIS J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 162 Processing helix chain 'J' and resid 198 through 213 removed outlier: 3.555A pdb=" N MET J 213 " --> pdb=" O LEU J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 248 through 266 Processing helix chain 'J' and resid 304 through 310 removed outlier: 3.549A pdb=" N GLY J 307 " --> pdb=" O ILE J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 335 Processing helix chain 'J' and resid 340 through 347 Processing helix chain 'J' and resid 359 through 371 removed outlier: 4.058A pdb=" N ARG J 363 " --> pdb=" O SER J 359 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 399 Processing helix chain 'J' and resid 404 through 409 Processing helix chain 'K' and resid 80 through 91 Processing helix chain 'K' and resid 112 through 125 Processing helix chain 'K' and resid 137 through 146 Processing helix chain 'K' and resid 181 through 196 removed outlier: 4.067A pdb=" N ARG K 196 " --> pdb=" O ILE K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 216 removed outlier: 4.961A pdb=" N ARG K 210 " --> pdb=" O ARG K 206 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASP K 211 " --> pdb=" O GLU K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 231 Processing helix chain 'K' and resid 252 through 257 Processing helix chain 'K' and resid 258 through 261 Processing helix chain 'K' and resid 263 through 268 Processing helix chain 'K' and resid 273 through 284 Processing helix chain 'K' and resid 289 through 296 Processing helix chain 'K' and resid 301 through 305 Processing helix chain 'K' and resid 308 through 321 Processing helix chain 'K' and resid 337 through 345 removed outlier: 3.581A pdb=" N ILE K 345 " --> pdb=" O ILE K 341 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 353 removed outlier: 5.799A pdb=" N SER K 350 " --> pdb=" O ALA K 347 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR K 351 " --> pdb=" O SER K 348 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN K 353 " --> pdb=" O SER K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 366 Processing helix chain 'K' and resid 367 through 372 removed outlier: 3.577A pdb=" N ARG K 372 " --> pdb=" O ILE K 369 " (cutoff:3.500A) Processing helix chain 'L' and resid 1645 through 1649 Processing helix chain 'L' and resid 1668 through 1679 removed outlier: 4.055A pdb=" N GLY L1679 " --> pdb=" O SER L1675 " (cutoff:3.500A) Processing helix chain 'L' and resid 1680 through 1697 Processing helix chain 'L' and resid 1698 through 1701 removed outlier: 3.727A pdb=" N ILE L1701 " --> pdb=" O ASP L1698 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1698 through 1701' Processing helix chain 'L' and resid 1705 through 1709 Processing helix chain 'L' and resid 1711 through 1729 Processing helix chain 'L' and resid 1740 through 1745 Processing helix chain 'L' and resid 1840 through 1846 removed outlier: 3.578A pdb=" N TRP L1844 " --> pdb=" O GLY L1840 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE L1846 " --> pdb=" O LEU L1842 " (cutoff:3.500A) Processing helix chain 'L' and resid 1971 through 1992 Processing helix chain 'L' and resid 1996 through 2002 removed outlier: 4.201A pdb=" N GLU L2000 " --> pdb=" O GLY L1996 " (cutoff:3.500A) Processing helix chain 'L' and resid 2004 through 2016 removed outlier: 4.406A pdb=" N LEU L2016 " --> pdb=" O GLY L2012 " (cutoff:3.500A) Processing helix chain 'L' and resid 2049 through 2068 removed outlier: 3.644A pdb=" N MET L2055 " --> pdb=" O ASP L2051 " (cutoff:3.500A) Processing helix chain 'L' and resid 2069 through 2071 No H-bonds generated for 'chain 'L' and resid 2069 through 2071' Processing helix chain 'L' and resid 2077 through 2094 Proline residue: L2083 - end of helix Processing helix chain 'L' and resid 2113 through 2127 Processing helix chain 'L' and resid 2128 through 2137 Processing helix chain 'L' and resid 2140 through 2158 removed outlier: 3.723A pdb=" N LEU L2144 " --> pdb=" O PRO L2140 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG L2158 " --> pdb=" O PHE L2154 " (cutoff:3.500A) Processing helix chain 'L' and resid 2160 through 2178 Processing helix chain 'L' and resid 2178 through 2187 removed outlier: 3.654A pdb=" N ALA L2182 " --> pdb=" O ASP L2178 " (cutoff:3.500A) Processing helix chain 'L' and resid 2190 through 2209 removed outlier: 3.703A pdb=" N GLN L2209 " --> pdb=" O ALA L2205 " (cutoff:3.500A) Processing helix chain 'L' and resid 2228 through 2243 Processing helix chain 'L' and resid 2247 through 2252 removed outlier: 3.552A pdb=" N PHE L2251 " --> pdb=" O ASN L2247 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR L2252 " --> pdb=" O HIS L2248 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2247 through 2252' Processing helix chain 'L' and resid 2254 through 2264 Processing helix chain 'L' and resid 2268 through 2284 Processing helix chain 'M' and resid 29 through 36 Processing helix chain 'M' and resid 41 through 47 Processing helix chain 'M' and resid 56 through 66 Processing helix chain 'M' and resid 80 through 84 Processing helix chain 'M' and resid 93 through 98 Processing helix chain 'M' and resid 173 through 181 Processing helix chain 'M' and resid 214 through 226 Processing helix chain 'M' and resid 229 through 248 Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 289 through 302 Processing helix chain 'M' and resid 305 through 324 removed outlier: 4.135A pdb=" N THR M 309 " --> pdb=" O GLY M 305 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA M 312 " --> pdb=" O VAL M 308 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS M 324 " --> pdb=" O SER M 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 342 through 348 Processing helix chain 'M' and resid 357 through 381 removed outlier: 3.741A pdb=" N THR M 381 " --> pdb=" O ARG M 377 " (cutoff:3.500A) Processing helix chain 'N' and resid 427 through 431 Processing helix chain 'N' and resid 440 through 446 Processing helix chain 'N' and resid 447 through 452 removed outlier: 4.692A pdb=" N GLY N 452 " --> pdb=" O GLU N 448 " (cutoff:3.500A) Processing helix chain 'N' and resid 458 through 475 removed outlier: 3.532A pdb=" N LEU N 475 " --> pdb=" O ASP N 471 " (cutoff:3.500A) Processing helix chain 'N' and resid 482 through 490 removed outlier: 3.677A pdb=" N ASN N 489 " --> pdb=" O ALA N 485 " (cutoff:3.500A) Processing helix chain 'N' and resid 493 through 507 Processing helix chain 'N' and resid 603 through 616 Processing helix chain 'N' and resid 620 through 628 removed outlier: 3.553A pdb=" N SER N 624 " --> pdb=" O TRP N 620 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY N 628 " --> pdb=" O SER N 624 " (cutoff:3.500A) Processing helix chain 'N' and resid 631 through 641 Processing helix chain 'N' and resid 672 through 682 Processing helix chain 'N' and resid 685 through 702 Processing helix chain 'N' and resid 859 through 949 Processing helix chain 'O' and resid 439 through 446 removed outlier: 3.599A pdb=" N ARG O 443 " --> pdb=" O HIS O 439 " (cutoff:3.500A) Processing helix chain 'O' and resid 447 through 450 Processing helix chain 'O' and resid 458 through 475 Processing helix chain 'O' and resid 482 through 490 removed outlier: 3.824A pdb=" N CYS O 486 " --> pdb=" O THR O 482 " (cutoff:3.500A) Processing helix chain 'O' and resid 493 through 507 Processing helix chain 'O' and resid 602 through 616 Processing helix chain 'O' and resid 619 through 628 Processing helix chain 'O' and resid 631 through 641 Processing helix chain 'O' and resid 645 through 650 Processing helix chain 'O' and resid 657 through 661 removed outlier: 4.133A pdb=" N TYR O 661 " --> pdb=" O PRO O 658 " (cutoff:3.500A) Processing helix chain 'O' and resid 671 through 684 removed outlier: 3.740A pdb=" N THR O 676 " --> pdb=" O PRO O 672 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE O 679 " --> pdb=" O SER O 675 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL O 684 " --> pdb=" O LEU O 680 " (cutoff:3.500A) Processing helix chain 'O' and resid 685 through 705 removed outlier: 3.535A pdb=" N GLU O 705 " --> pdb=" O SER O 701 " (cutoff:3.500A) Processing helix chain 'O' and resid 711 through 716 Processing helix chain 'O' and resid 868 through 952 removed outlier: 4.276A pdb=" N LYS O 872 " --> pdb=" O ALA O 868 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 132 removed outlier: 3.688A pdb=" N LYS P 131 " --> pdb=" O MET P 128 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE P 132 " --> pdb=" O ALA P 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 128 through 132' Processing helix chain 'P' and resid 134 through 141 Processing helix chain 'P' and resid 143 through 173 removed outlier: 3.606A pdb=" N TYR P 147 " --> pdb=" O GLU P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 306 Processing helix chain 'P' and resid 312 through 327 Processing helix chain 'P' and resid 353 through 355 No H-bonds generated for 'chain 'P' and resid 353 through 355' Processing helix chain 'P' and resid 356 through 361 Processing helix chain 'P' and resid 400 through 411 Processing helix chain 'P' and resid 414 through 447 removed outlier: 3.830A pdb=" N ASP P 447 " --> pdb=" O SER P 443 " (cutoff:3.500A) Processing helix chain 'P' and resid 447 through 468 Processing helix chain 'P' and resid 478 through 484 removed outlier: 3.701A pdb=" N PHE P 483 " --> pdb=" O GLU P 480 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN P 484 " --> pdb=" O PHE P 481 " (cutoff:3.500A) Processing helix chain 'P' and resid 486 through 505 Processing helix chain 'Q' and resid 186 through 207 Processing helix chain 'Q' and resid 220 through 276 Processing helix chain 'R' and resid 14 through 38 Processing helix chain 'R' and resid 58 through 62 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.224A pdb=" N ARG A 80 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.589A pdb=" N ILE A 116 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.194A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.768A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.133A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.470A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'I' and resid 991 through 992 Processing sheet with id=AB3, first strand: chain 'I' and resid 991 through 992 removed outlier: 5.702A pdb=" N LEU I1100 " --> pdb=" O ILE I1172 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 35 through 38 removed outlier: 6.529A pdb=" N LEU J 14 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N SER J 123 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N PHE J 16 " --> pdb=" O SER J 123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 41 through 43 Processing sheet with id=AB6, first strand: chain 'J' and resid 88 through 89 Processing sheet with id=AB7, first strand: chain 'J' and resid 186 through 187 Processing sheet with id=AB8, first strand: chain 'J' and resid 186 through 187 removed outlier: 6.166A pdb=" N LEU J 168 " --> pdb=" O ILE J 349 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ALA J 351 " --> pdb=" O LEU J 168 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU J 170 " --> pdb=" O ALA J 351 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 18 through 21 removed outlier: 6.498A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 176 through 178 Processing sheet with id=AC2, first strand: chain 'L' and resid 1814 through 1816 removed outlier: 6.197A pdb=" N LYS L1815 " --> pdb=" O ILE O 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'M' and resid 26 through 28 Processing sheet with id=AC4, first strand: chain 'M' and resid 186 through 195 Processing sheet with id=AC5, first strand: chain 'M' and resid 261 through 270 Processing sheet with id=AC6, first strand: chain 'N' and resid 424 through 426 removed outlier: 7.442A pdb=" N ILE N 424 " --> pdb=" O LEU O 534 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'N' and resid 437 through 439 removed outlier: 6.782A pdb=" N VAL N 438 " --> pdb=" O LEU R 71 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 523 through 524 Processing sheet with id=AC9, first strand: chain 'P' and resid 309 through 311 removed outlier: 3.549A pdb=" N MET P 366 " --> pdb=" O LYS P 296 " (cutoff:3.500A) 1703 hydrogen bonds defined for protein. 4950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 256 hydrogen bonds 508 hydrogen bond angles 0 basepair planarities 100 basepair parallelities 205 stacking parallelities Total time for adding SS restraints: 13.07 Time building geometry restraints manager: 4.10 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: 8601 1.33 - 1.46: 9240 1.46 - 1.58: 16840 1.58 - 1.71: 469 1.71 - 1.83: 252 Bond restraints: 35402 Sorted by residual: bond pdb=" C HIS H 46 " pdb=" N PRO H 47 " ideal model delta sigma weight residual 1.334 1.297 0.037 8.40e-03 1.42e+04 1.93e+01 bond pdb=" N VAL I 832 " pdb=" CA VAL I 832 " ideal model delta sigma weight residual 1.456 1.502 -0.046 1.11e-02 8.12e+03 1.74e+01 bond pdb=" C3' DG Y 73 " pdb=" O3' DG Y 73 " ideal model delta sigma weight residual 1.435 1.383 0.052 1.30e-02 5.92e+03 1.59e+01 bond pdb=" C3' DC X 45 " pdb=" O3' DC X 45 " ideal model delta sigma weight residual 1.435 1.384 0.051 1.30e-02 5.92e+03 1.53e+01 bond pdb=" N9 DG Y 32 " pdb=" C4 DG Y 32 " ideal model delta sigma weight residual 1.375 1.344 0.031 8.00e-03 1.56e+04 1.49e+01 ... (remaining 35397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 47186 2.73 - 5.46: 1435 5.46 - 8.19: 156 8.19 - 10.92: 28 10.92 - 13.65: 6 Bond angle restraints: 48811 Sorted by residual: angle pdb=" N GLN I 515 " pdb=" CA GLN I 515 " pdb=" C GLN I 515 " ideal model delta sigma weight residual 111.36 97.71 13.65 1.09e+00 8.42e-01 1.57e+02 angle pdb=" N GLU I 514 " pdb=" CA GLU I 514 " pdb=" C GLU I 514 " ideal model delta sigma weight residual 113.23 102.27 10.96 1.24e+00 6.50e-01 7.81e+01 angle pdb=" N PRO I 913 " pdb=" CA PRO I 913 " pdb=" C PRO I 913 " ideal model delta sigma weight residual 111.41 99.48 11.93 1.50e+00 4.44e-01 6.33e+01 angle pdb=" N ILE J 146 " pdb=" CA ILE J 146 " pdb=" C ILE J 146 " ideal model delta sigma weight residual 109.02 102.66 6.36 9.30e-01 1.16e+00 4.68e+01 angle pdb=" N LYS I 516 " pdb=" CA LYS I 516 " pdb=" C LYS I 516 " ideal model delta sigma weight residual 111.07 104.10 6.97 1.07e+00 8.73e-01 4.24e+01 ... (remaining 48806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.23: 19063 34.23 - 68.46: 1745 68.46 - 102.69: 91 102.69 - 136.92: 4 136.92 - 171.16: 8 Dihedral angle restraints: 20911 sinusoidal: 10213 harmonic: 10698 Sorted by residual: dihedral pdb=" C ASP J 339 " pdb=" N ASP J 339 " pdb=" CA ASP J 339 " pdb=" CB ASP J 339 " ideal model delta harmonic sigma weight residual -122.60 -141.57 18.97 0 2.50e+00 1.60e-01 5.76e+01 dihedral pdb=" C ASP J 71 " pdb=" N ASP J 71 " pdb=" CA ASP J 71 " pdb=" CB ASP J 71 " ideal model delta harmonic sigma weight residual -122.60 -140.47 17.87 0 2.50e+00 1.60e-01 5.11e+01 dihedral pdb=" C ASP K 288 " pdb=" N ASP K 288 " pdb=" CA ASP K 288 " pdb=" CB ASP K 288 " ideal model delta harmonic sigma weight residual -122.60 -140.43 17.83 0 2.50e+00 1.60e-01 5.09e+01 ... (remaining 20908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 5222 0.138 - 0.276: 238 0.276 - 0.414: 25 0.414 - 0.552: 3 0.552 - 0.689: 3 Chirality restraints: 5491 Sorted by residual: chirality pdb=" CA ASP J 339 " pdb=" N ASP J 339 " pdb=" C ASP J 339 " pdb=" CB ASP J 339 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CA ASP J 71 " pdb=" N ASP J 71 " pdb=" C ASP J 71 " pdb=" CB ASP J 71 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CA ASP K 288 " pdb=" N ASP K 288 " pdb=" C ASP K 288 " pdb=" CB ASP K 288 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.89e+00 ... (remaining 5488 not shown) Planarity restraints: 5406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR M 355 " 0.027 2.00e-02 2.50e+03 5.35e-02 2.86e+01 pdb=" C THR M 355 " -0.093 2.00e-02 2.50e+03 pdb=" O THR M 355 " 0.035 2.00e-02 2.50e+03 pdb=" N LEU M 356 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 487 " -0.023 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" C LYS I 487 " 0.082 2.00e-02 2.50e+03 pdb=" O LYS I 487 " -0.031 2.00e-02 2.50e+03 pdb=" N GLU I 488 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU I 768 " 0.023 2.00e-02 2.50e+03 4.64e-02 2.16e+01 pdb=" C LEU I 768 " -0.080 2.00e-02 2.50e+03 pdb=" O LEU I 768 " 0.030 2.00e-02 2.50e+03 pdb=" N TYR I 769 " 0.027 2.00e-02 2.50e+03 ... (remaining 5403 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2847 2.72 - 3.26: 34746 3.26 - 3.81: 61067 3.81 - 4.35: 75387 4.35 - 4.90: 116660 Nonbonded interactions: 290707 Sorted by model distance: nonbonded pdb=" OD1 ASP L2157 " pdb=" N ARG L2158 " model vdw 2.173 3.120 nonbonded pdb=" OG SER L1645 " pdb=" OG SER O 669 " model vdw 2.202 3.040 nonbonded pdb=" O SER P 410 " pdb=" OG SER P 413 " model vdw 2.212 3.040 nonbonded pdb=" OG SER L2096 " pdb=" OE1 GLU L2098 " model vdw 2.214 3.040 nonbonded pdb=" O LEU L2017 " pdb=" NH2 ARG L2057 " model vdw 2.214 3.120 ... (remaining 290702 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' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 16 through 109) selection = (chain 'G' and resid 16 through 109) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 33 through 120) } 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=0.21 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: 9.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 45.750 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0848 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 0.102 35406 Z= 0.606 Angle : 1.104 13.650 48814 Z= 0.741 Chirality : 0.071 0.689 5491 Planarity : 0.007 0.073 5406 Dihedral : 22.177 171.156 13939 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.45 % Favored : 93.27 % Rotamer: Outliers : 2.63 % Allowed : 9.75 % Favored : 87.61 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.12), residues: 3552 helix: -2.03 (0.09), residues: 2151 sheet: -2.61 (0.37), residues: 152 loop : -2.90 (0.15), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I1009 TYR 0.040 0.003 TYR I 862 PHE 0.053 0.003 PHE K 200 TRP 0.021 0.002 TRP J 250 HIS 0.011 0.002 HIS J 105 Details of bonding type rmsd/Z covalent geometry : bond 0.01006 / 0.61 (35402) covalent geometry : angle 1.10305 / 0.74 (48811) hydrogen bonds : bond 0.13074 / 8.77 ( 1955) hydrogen bonds : angle 6.57912 / 4.67 ( 5458) metal coordination : bond 0.04625 / 3.28 ( 4) metal coordination : angle 6.79404 / 3.36 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 489 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.1759 (mmm) cc_final: 0.0496 (ptp) REVERT: I 482 HIS cc_start: 0.6824 (OUTLIER) cc_final: 0.6550 (t-90) REVERT: I 880 VAL cc_start: 0.0536 (OUTLIER) cc_final: 0.0158 (p) REVERT: I 893 LEU cc_start: -0.0528 (OUTLIER) cc_final: -0.0892 (tp) REVERT: I 915 GLN cc_start: -0.1225 (OUTLIER) cc_final: -0.2343 (pm20) REVERT: I 1040 MET cc_start: -0.3201 (ttp) cc_final: -0.3522 (mtm) REVERT: I 1112 MET cc_start: -0.0488 (mmp) cc_final: -0.3703 (mtm) REVERT: I 1182 GLN cc_start: -0.0680 (OUTLIER) cc_final: -0.2078 (tm-30) REVERT: I 1189 ARG cc_start: 0.2501 (OUTLIER) cc_final: 0.1325 (mtt-85) REVERT: I 1305 MET cc_start: 0.2911 (ppp) cc_final: 0.1892 (mpp) REVERT: I 1317 MET cc_start: 0.3048 (tpt) cc_final: 0.2579 (ttp) REVERT: J 79 ARG cc_start: 0.0826 (OUTLIER) cc_final: -0.0929 (mmt180) REVERT: J 294 ASN cc_start: 0.0579 (OUTLIER) cc_final: -0.0771 (m110) REVERT: K 84 LYS cc_start: 0.7902 (mttt) cc_final: 0.6469 (ptmm) REVERT: K 190 MET cc_start: 0.3939 (mmm) cc_final: 0.3344 (mmm) REVERT: K 250 ILE cc_start: -0.3068 (OUTLIER) cc_final: -0.3416 (pt) REVERT: K 283 MET cc_start: 0.0812 (mmp) cc_final: 0.0475 (tpp) REVERT: K 367 PRO cc_start: 0.0527 (Cg_endo) cc_final: -0.0886 (Cg_exo) REVERT: L 2166 MET cc_start: -0.0361 (mtt) cc_final: -0.2535 (tpp) REVERT: M 44 TYR cc_start: 0.1179 (m-80) cc_final: 0.0632 (t80) REVERT: N 906 PHE cc_start: 0.4703 (t80) cc_final: 0.4454 (t80) REVERT: P 333 GLU cc_start: 0.2022 (tt0) cc_final: 0.1347 (tp30) REVERT: Q 188 MET cc_start: 0.1784 (ppp) cc_final: 0.1419 (mpp) outliers start: 84 outliers final: 6 residues processed: 569 average time/residue: 0.2535 time to fit residues: 219.9074 Evaluate side-chains 276 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 261 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain I residue 482 HIS Chi-restraints excluded: chain I residue 857 LEU Chi-restraints excluded: chain I residue 880 VAL Chi-restraints excluded: chain I residue 893 LEU Chi-restraints excluded: chain I residue 909 LEU Chi-restraints excluded: chain I residue 915 GLN Chi-restraints excluded: chain I residue 1048 HIS Chi-restraints excluded: chain I residue 1182 GLN Chi-restraints excluded: chain I residue 1189 ARG Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 335 ARG Chi-restraints excluded: chain O residue 521 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.0870 chunk 298 optimal weight: 5.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN A 90 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS C 38 ASN D 44 GLN D 81 ASN D 92 GLN E 93 GLN H 46 HIS ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 473 GLN I 477 ASN ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1048 HIS ** I1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1182 GLN ** I1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1195 GLN ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 HIS J 205 GLN J 251 HIS J 365 ASN J 407 GLN L1835 GLN L1997 ASN L2268 ASN M 322 HIS N 489 ASN N 513 GLN N 638 HIS O 439 HIS ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 632 GLN O 935 HIS P 405 ASN P 432 ASN P 457 GLN Q 232 GLN ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 267 ASN Q 268 ASN ** R 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 HIS R 70 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.128334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.098587 restraints weight = 144536.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.101079 restraints weight = 65859.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.102578 restraints weight = 39555.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.103508 restraints weight = 28691.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.104073 restraints weight = 23523.246| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4033 r_free = 0.4033 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4033 r_free = 0.4033 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.4033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1560 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35406 Z= 0.171 Angle : 0.801 10.827 48814 Z= 0.427 Chirality : 0.050 0.330 5491 Planarity : 0.006 0.074 5406 Dihedral : 24.647 173.270 6601 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.10 % Favored : 94.88 % Rotamer: Outliers : 2.82 % Allowed : 14.64 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.13), residues: 3552 helix: -0.43 (0.10), residues: 2204 sheet: -1.98 (0.39), residues: 155 loop : -2.35 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 931 TYR 0.025 0.002 TYR F 51 PHE 0.030 0.002 PHE L2103 TRP 0.021 0.002 TRP N 620 HIS 0.016 0.001 HIS J 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (35402) covalent geometry : angle 0.79921 / 0.43 (48811) hydrogen bonds : bond 0.05336 / 3.58 ( 1955) hydrogen bonds : angle 5.04703 / 3.56 ( 5458) metal coordination : bond 0.01880 / 1.07 ( 4) metal coordination : angle 6.04582 / 2.88 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 288 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.1998 (mmm) cc_final: 0.0499 (ptp) REVERT: I 475 TYR cc_start: 0.5126 (m-10) cc_final: 0.4476 (t80) REVERT: I 915 GLN cc_start: -0.0538 (OUTLIER) cc_final: -0.2058 (pm20) REVERT: I 1010 HIS cc_start: 0.1674 (OUTLIER) cc_final: 0.1340 (m-70) REVERT: I 1112 MET cc_start: -0.1787 (mmp) cc_final: -0.3706 (mtm) REVERT: I 1174 PHE cc_start: 0.1107 (OUTLIER) cc_final: -0.0140 (t80) REVERT: I 1189 ARG cc_start: 0.3717 (OUTLIER) cc_final: 0.2396 (mtp85) REVERT: I 1305 MET cc_start: 0.1200 (ppp) cc_final: 0.0696 (mmt) REVERT: I 1317 MET cc_start: 0.2419 (tpt) cc_final: 0.2068 (ttp) REVERT: J 79 ARG cc_start: 0.0902 (OUTLIER) cc_final: -0.0091 (mmt180) REVERT: J 92 MET cc_start: -0.4836 (mtt) cc_final: -0.5051 (ttm) REVERT: J 294 ASN cc_start: -0.0821 (OUTLIER) cc_final: -0.1716 (m110) REVERT: J 365 ASN cc_start: -0.1669 (OUTLIER) cc_final: -0.2011 (m-40) REVERT: K 30 VAL cc_start: 0.0102 (OUTLIER) cc_final: -0.0166 (p) REVERT: K 84 LYS cc_start: 0.7159 (mttt) cc_final: 0.6554 (ptmm) REVERT: K 190 MET cc_start: 0.4510 (mmm) cc_final: 0.4102 (mmm) REVERT: K 250 ILE cc_start: -0.5051 (OUTLIER) cc_final: -0.5344 (pt) REVERT: K 283 MET cc_start: 0.0637 (mmp) cc_final: 0.0128 (tpp) REVERT: L 1724 LEU cc_start: 0.1843 (OUTLIER) cc_final: 0.0265 (pp) REVERT: L 2166 MET cc_start: -0.0621 (mtt) cc_final: -0.2530 (tpp) REVERT: M 375 MET cc_start: 0.0975 (mtm) cc_final: -0.0111 (ppp) REVERT: N 896 MET cc_start: 0.4939 (ptt) cc_final: 0.4739 (ptt) REVERT: N 906 PHE cc_start: 0.5215 (t80) cc_final: 0.4937 (t80) REVERT: N 936 MET cc_start: 0.8440 (mmm) cc_final: 0.7385 (ppp) REVERT: O 894 THR cc_start: 0.8873 (t) cc_final: 0.8614 (p) REVERT: O 913 MET cc_start: 0.7943 (ppp) cc_final: 0.7645 (ppp) REVERT: P 333 GLU cc_start: 0.3423 (tt0) cc_final: 0.1713 (tp30) REVERT: P 352 MET cc_start: -0.0461 (tpt) cc_final: -0.1002 (tpt) REVERT: Q 188 MET cc_start: 0.2234 (ppp) cc_final: 0.1835 (mpp) REVERT: Q 224 MET cc_start: 0.4267 (mmp) cc_final: 0.3407 (mtp) REVERT: Q 257 ARG cc_start: 0.8162 (ttp80) cc_final: 0.7736 (ttp80) outliers start: 90 outliers final: 27 residues processed: 363 average time/residue: 0.2312 time to fit residues: 133.2018 Evaluate side-chains 275 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 238 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 857 LEU Chi-restraints excluded: chain I residue 909 LEU Chi-restraints excluded: chain I residue 915 GLN Chi-restraints excluded: chain I residue 924 LEU Chi-restraints excluded: chain I residue 1010 HIS Chi-restraints excluded: chain I residue 1038 THR Chi-restraints excluded: chain I residue 1174 PHE Chi-restraints excluded: chain I residue 1189 ARG Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 365 ASN Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 305 MET Chi-restraints excluded: chain L residue 1724 LEU Chi-restraints excluded: chain L residue 1812 LEU Chi-restraints excluded: chain L residue 1837 PHE Chi-restraints excluded: chain L residue 2058 GLU Chi-restraints excluded: chain L residue 2119 LEU Chi-restraints excluded: chain L residue 2132 VAL Chi-restraints excluded: chain L residue 2206 THR Chi-restraints excluded: chain M residue 60 ARG Chi-restraints excluded: chain M residue 365 ILE Chi-restraints excluded: chain O residue 437 SER Chi-restraints excluded: chain O residue 458 THR Chi-restraints excluded: chain O residue 470 ILE Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 190 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: [52, 87, 372, 249, 218, 37, 64, 345, 31, 94, 194] chunk 52 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 372 optimal weight: 20.0000 chunk 249 optimal weight: 6.9990 chunk 218 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 345 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 94 optimal weight: 0.0570 chunk 194 optimal weight: 5.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN B 25 ASN D 106 HIS ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1054 HIS ** I1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 HIS K 354 GLN ** L2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 423 HIS ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.128362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.099028 restraints weight = 145237.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.101560 restraints weight = 65957.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.103081 restraints weight = 39301.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.104044 restraints weight = 28250.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 74)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.104606 restraints weight = 23060.926| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4052 r_free = 0.4052 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4052 r_free = 0.4052 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.4052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1633 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 35406 Z= 0.154 Angle : 0.720 10.416 48814 Z= 0.384 Chirality : 0.047 0.311 5491 Planarity : 0.005 0.059 5406 Dihedral : 24.346 174.426 6587 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.48 % Allowed : 16.40 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.14), residues: 3552 helix: 0.24 (0.11), residues: 2209 sheet: -1.54 (0.41), residues: 153 loop : -2.15 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 164 TYR 0.025 0.002 TYR P 482 PHE 0.023 0.002 PHE N 906 TRP 0.032 0.002 TRP N 620 HIS 0.011 0.001 HIS Q 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (35402) covalent geometry : angle 0.71980 / 0.38 (48811) hydrogen bonds : bond 0.04796 / 3.20 ( 1955) hydrogen bonds : angle 4.72608 / 3.34 ( 5458) metal coordination : bond 0.02045 / 1.05 ( 4) metal coordination : angle 3.60572 / 1.85 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 263 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.1938 (mmm) cc_final: 0.0977 (mtm) REVERT: D 59 MET cc_start: -0.2258 (tpp) cc_final: -0.2647 (tpp) REVERT: E 120 MET cc_start: 0.3577 (mmt) cc_final: 0.3074 (mtt) REVERT: G 83 LEU cc_start: 0.1759 (mm) cc_final: 0.1145 (mt) REVERT: I 475 TYR cc_start: 0.5122 (m-10) cc_final: 0.4655 (t80) REVERT: I 915 GLN cc_start: -0.0248 (OUTLIER) cc_final: -0.1677 (pm20) REVERT: I 1010 HIS cc_start: 0.2307 (OUTLIER) cc_final: 0.1369 (m-70) REVERT: I 1050 TYR cc_start: -0.2421 (OUTLIER) cc_final: -0.3252 (p90) REVERT: I 1112 MET cc_start: -0.1746 (mmp) cc_final: -0.3148 (mtm) REVERT: I 1164 ASN cc_start: 0.4654 (OUTLIER) cc_final: 0.4108 (t0) REVERT: I 1174 PHE cc_start: 0.1217 (OUTLIER) cc_final: 0.0043 (t80) REVERT: I 1317 MET cc_start: 0.2567 (tpt) cc_final: 0.2209 (ttp) REVERT: J 79 ARG cc_start: 0.0989 (OUTLIER) cc_final: 0.0111 (mmt-90) REVERT: J 294 ASN cc_start: -0.0697 (OUTLIER) cc_final: -0.1617 (m110) REVERT: J 376 MET cc_start: 0.0618 (ttp) cc_final: 0.0356 (ptm) REVERT: K 84 LYS cc_start: 0.7196 (mttt) cc_final: 0.6556 (ptmm) REVERT: K 132 MET cc_start: 0.2174 (ttt) cc_final: 0.1758 (ttt) REVERT: K 190 MET cc_start: 0.4799 (mmm) cc_final: 0.4428 (mmm) REVERT: K 250 ILE cc_start: -0.4954 (OUTLIER) cc_final: -0.5379 (pt) REVERT: M 213 MET cc_start: -0.2693 (mtt) cc_final: -0.2999 (mtt) REVERT: M 375 MET cc_start: 0.0896 (mtm) cc_final: -0.0246 (ppp) REVERT: N 700 PHE cc_start: -0.1700 (OUTLIER) cc_final: -0.2375 (m-80) REVERT: N 936 MET cc_start: 0.8453 (mmm) cc_final: 0.7507 (ppp) REVERT: O 499 ARG cc_start: 0.5247 (OUTLIER) cc_final: 0.4782 (ptm160) REVERT: O 636 ILE cc_start: 0.3021 (tp) cc_final: 0.2732 (pt) REVERT: O 894 THR cc_start: 0.8701 (t) cc_final: 0.8459 (p) REVERT: O 913 MET cc_start: 0.7971 (ppp) cc_final: 0.7736 (ppp) REVERT: P 333 GLU cc_start: 0.3650 (tt0) cc_final: 0.2269 (tp30) REVERT: Q 188 MET cc_start: 0.2332 (ppp) cc_final: 0.1808 (mpp) REVERT: Q 224 MET cc_start: 0.4322 (mmp) cc_final: 0.3571 (mtp) REVERT: Q 257 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7668 (ttp80) outliers start: 79 outliers final: 28 residues processed: 326 average time/residue: 0.2257 time to fit residues: 118.0195 Evaluate side-chains 278 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 240 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 857 LEU Chi-restraints excluded: chain I residue 909 LEU Chi-restraints excluded: chain I residue 915 GLN Chi-restraints excluded: chain I residue 971 VAL Chi-restraints excluded: chain I residue 1010 HIS Chi-restraints excluded: chain I residue 1038 THR Chi-restraints excluded: chain I residue 1050 TYR Chi-restraints excluded: chain I residue 1164 ASN Chi-restraints excluded: chain I residue 1174 PHE Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 109 MET Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 305 MET Chi-restraints excluded: chain L residue 1812 LEU Chi-restraints excluded: chain L residue 1837 PHE Chi-restraints excluded: chain L residue 2007 LEU Chi-restraints excluded: chain L residue 2058 GLU Chi-restraints excluded: chain L residue 2132 VAL Chi-restraints excluded: chain L residue 2206 THR Chi-restraints excluded: chain L residue 2267 MET Chi-restraints excluded: chain M residue 365 ILE Chi-restraints excluded: chain N residue 700 PHE Chi-restraints excluded: chain O residue 437 SER Chi-restraints excluded: chain O residue 499 ARG Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 190 HIS Chi-restraints excluded: chain R residue 71 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: [128, 203, 77, 251, 176, 320, 88, 192, 40, 57, 375] chunk 128 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 251 optimal weight: 0.3980 chunk 176 optimal weight: 20.0000 chunk 320 optimal weight: 9.9990 chunk 88 optimal weight: 0.0270 chunk 192 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 375 optimal weight: 50.0000 overall best weight: 1.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1182 GLN ** J 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1650 GLN ** L2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2248 HIS N 925 GLN ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 626 HIS ** O 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.128133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.099099 restraints weight = 145859.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.101619 restraints weight = 65945.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.103138 restraints weight = 39131.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.104089 restraints weight = 28058.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.104652 restraints weight = 22837.197| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4067 r_free = 0.4067 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4067 r_free = 0.4067 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.4067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1779 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 35406 Z= 0.160 Angle : 0.699 16.704 48814 Z= 0.372 Chirality : 0.046 0.313 5491 Planarity : 0.005 0.089 5406 Dihedral : 24.215 179.007 6583 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.57 % Allowed : 16.56 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.14), residues: 3552 helix: 0.53 (0.11), residues: 2221 sheet: -1.36 (0.38), residues: 176 loop : -2.03 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG P 334 TYR 0.023 0.002 TYR I1008 PHE 0.021 0.002 PHE L2103 TRP 0.023 0.001 TRP I 922 HIS 0.015 0.001 HIS J 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (35402) covalent geometry : angle 0.69653 / 0.37 (48811) hydrogen bonds : bond 0.04600 / 3.07 ( 1955) hydrogen bonds : angle 4.54507 / 3.22 ( 5458) metal coordination : bond 0.06063 / 3.24 ( 4) metal coordination : angle 8.16842 / 4.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 259 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.1774 (mmm) cc_final: 0.0950 (mtm) REVERT: D 59 MET cc_start: -0.2208 (tpp) cc_final: -0.2473 (tpp) REVERT: G 83 LEU cc_start: 0.1859 (mm) cc_final: 0.1427 (mt) REVERT: I 475 TYR cc_start: 0.5263 (m-10) cc_final: 0.4825 (t80) REVERT: I 915 GLN cc_start: -0.0208 (OUTLIER) cc_final: -0.1677 (pm20) REVERT: I 1010 HIS cc_start: 0.2545 (OUTLIER) cc_final: 0.1565 (m-70) REVERT: I 1050 TYR cc_start: -0.2912 (OUTLIER) cc_final: -0.3515 (p90) REVERT: I 1112 MET cc_start: -0.1350 (mmp) cc_final: -0.2718 (mtm) REVERT: I 1164 ASN cc_start: 0.4813 (OUTLIER) cc_final: 0.4556 (t0) REVERT: I 1174 PHE cc_start: 0.1201 (OUTLIER) cc_final: -0.0169 (t80) REVERT: I 1189 ARG cc_start: 0.3179 (mpt180) cc_final: 0.2181 (ttm170) REVERT: I 1317 MET cc_start: 0.2369 (tpt) cc_final: 0.2046 (ttp) REVERT: J 43 MET cc_start: -0.4036 (OUTLIER) cc_final: -0.5275 (mmt) REVERT: J 79 ARG cc_start: 0.1448 (OUTLIER) cc_final: 0.0486 (mmt-90) REVERT: J 294 ASN cc_start: -0.0815 (OUTLIER) cc_final: -0.1824 (m110) REVERT: J 335 MET cc_start: 0.2084 (mtp) cc_final: 0.1784 (mtm) REVERT: J 376 MET cc_start: 0.0348 (ttp) cc_final: -0.0104 (ptm) REVERT: J 413 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6684 (pttt) REVERT: K 84 LYS cc_start: 0.7223 (mttt) cc_final: 0.6561 (ptmm) REVERT: K 190 MET cc_start: 0.4624 (mmm) cc_final: 0.4224 (mmm) REVERT: K 250 ILE cc_start: -0.5209 (OUTLIER) cc_final: -0.5730 (pt) REVERT: L 2166 MET cc_start: -0.0998 (mtt) cc_final: -0.2486 (tpp) REVERT: M 213 MET cc_start: -0.2500 (mtt) cc_final: -0.2811 (mtt) REVERT: N 700 PHE cc_start: -0.1867 (OUTLIER) cc_final: -0.2486 (m-80) REVERT: N 896 MET cc_start: 0.5313 (ptm) cc_final: 0.4884 (ppp) REVERT: N 936 MET cc_start: 0.8315 (mmm) cc_final: 0.7488 (ppp) REVERT: O 499 ARG cc_start: 0.5392 (OUTLIER) cc_final: 0.5135 (ptt180) REVERT: O 894 THR cc_start: 0.8700 (t) cc_final: 0.8459 (p) REVERT: P 297 LEU cc_start: 0.2625 (mt) cc_final: 0.1657 (mt) REVERT: P 333 GLU cc_start: 0.3530 (tt0) cc_final: 0.2055 (tp30) REVERT: Q 188 MET cc_start: 0.2255 (ppp) cc_final: 0.1804 (mpp) REVERT: Q 224 MET cc_start: 0.4348 (mmp) cc_final: 0.3654 (mtp) REVERT: Q 257 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7574 (ttp80) outliers start: 82 outliers final: 34 residues processed: 325 average time/residue: 0.2207 time to fit residues: 115.2963 Evaluate side-chains 278 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 232 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 762 LEU Chi-restraints excluded: chain I residue 857 LEU Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 915 GLN Chi-restraints excluded: chain I residue 1010 HIS Chi-restraints excluded: chain I residue 1038 THR Chi-restraints excluded: chain I residue 1050 TYR Chi-restraints excluded: chain I residue 1164 ASN Chi-restraints excluded: chain I residue 1174 PHE Chi-restraints excluded: chain I residue 1182 GLN Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain J residue 413 LYS Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 305 MET Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 1812 LEU Chi-restraints excluded: chain L residue 1837 PHE Chi-restraints excluded: chain L residue 2007 LEU Chi-restraints excluded: chain L residue 2152 VAL Chi-restraints excluded: chain L residue 2206 THR Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 353 LEU Chi-restraints excluded: chain M residue 365 ILE Chi-restraints excluded: chain N residue 700 PHE Chi-restraints excluded: chain N residue 920 LEU Chi-restraints excluded: chain O residue 469 MET Chi-restraints excluded: chain O residue 499 ARG Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain O residue 688 VAL Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 190 HIS Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 269 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: [2, 248, 72, 202, 224, 220, 141, 205, 377, 199, 178] chunk 2 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 202 optimal weight: 10.0000 chunk 224 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 205 optimal weight: 0.6980 chunk 377 optimal weight: 30.0000 chunk 199 optimal weight: 0.0070 chunk 178 optimal weight: 0.6980 overall best weight: 1.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS I 356 GLN ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 ASN K 354 GLN ** L1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 621 ASN ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 638 HIS O 935 HIS ** O 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.128322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.100694 restraints weight = 147492.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.103262 restraints weight = 68296.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.103989 restraints weight = 41843.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.104444 restraints weight = 27629.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.104704 restraints weight = 23847.575| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4067 r_free = 0.4067 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4067 r_free = 0.4067 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1847 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 35406 Z= 0.144 Angle : 0.680 12.738 48814 Z= 0.360 Chirality : 0.045 0.313 5491 Planarity : 0.005 0.086 5406 Dihedral : 24.101 174.067 6581 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.88 % Allowed : 17.37 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 3552 helix: 0.71 (0.11), residues: 2220 sheet: -1.36 (0.39), residues: 172 loop : -1.90 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG O 947 TYR 0.016 0.001 TYR I 769 PHE 0.041 0.002 PHE O 503 TRP 0.015 0.001 TRP L1973 HIS 0.011 0.001 HIS O 935 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (35402) covalent geometry : angle 0.67865 / 0.36 (48811) hydrogen bonds : bond 0.04407 / 2.94 ( 1955) hydrogen bonds : angle 4.42341 / 3.13 ( 5458) metal coordination : bond 0.05473 / 2.88 ( 4) metal coordination : angle 5.56094 / 2.39 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 250 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.1898 (mmm) cc_final: 0.0960 (mtm) REVERT: D 59 MET cc_start: -0.2117 (tpp) cc_final: -0.2386 (tpp) REVERT: G 83 LEU cc_start: 0.2045 (mm) cc_final: 0.1693 (mt) REVERT: I 475 TYR cc_start: 0.5302 (m-10) cc_final: 0.4880 (t80) REVERT: I 886 MET cc_start: 0.3601 (mtt) cc_final: 0.0768 (ttt) REVERT: I 915 GLN cc_start: -0.0227 (OUTLIER) cc_final: -0.1551 (pm20) REVERT: I 1010 HIS cc_start: 0.2709 (OUTLIER) cc_final: 0.1552 (m-70) REVERT: I 1050 TYR cc_start: -0.3175 (OUTLIER) cc_final: -0.3702 (p90) REVERT: I 1112 MET cc_start: -0.1060 (mmp) cc_final: -0.2576 (mtm) REVERT: I 1164 ASN cc_start: 0.4743 (OUTLIER) cc_final: 0.4407 (t0) REVERT: I 1174 PHE cc_start: 0.0714 (OUTLIER) cc_final: -0.0499 (t80) REVERT: I 1182 GLN cc_start: -0.0253 (OUTLIER) cc_final: -0.1550 (pt0) REVERT: I 1189 ARG cc_start: 0.2851 (mpt180) cc_final: 0.1930 (ttm170) REVERT: I 1317 MET cc_start: 0.2334 (tpt) cc_final: 0.1943 (ttp) REVERT: J 43 MET cc_start: -0.4134 (OUTLIER) cc_final: -0.5354 (mmt) REVERT: J 79 ARG cc_start: 0.1687 (OUTLIER) cc_final: 0.0659 (mmt-90) REVERT: J 294 ASN cc_start: -0.0707 (OUTLIER) cc_final: -0.1732 (m110) REVERT: J 376 MET cc_start: 0.0472 (ttp) cc_final: 0.0086 (ttp) REVERT: K 84 LYS cc_start: 0.7251 (mttt) cc_final: 0.6512 (ptmm) REVERT: K 190 MET cc_start: 0.4552 (mmm) cc_final: 0.4121 (mmm) REVERT: K 250 ILE cc_start: -0.4999 (OUTLIER) cc_final: -0.5648 (pt) REVERT: L 2057 ARG cc_start: 0.8755 (mmp80) cc_final: 0.6291 (ptp-110) REVERT: M 213 MET cc_start: -0.2606 (mtt) cc_final: -0.2968 (mtt) REVERT: N 444 ARG cc_start: 0.3165 (mtp-110) cc_final: 0.2386 (mtm110) REVERT: N 896 MET cc_start: 0.5357 (ptm) cc_final: 0.4871 (ppp) REVERT: N 936 MET cc_start: 0.8244 (mmm) cc_final: 0.7592 (ppp) REVERT: O 499 ARG cc_start: 0.5709 (OUTLIER) cc_final: 0.5368 (ptt180) REVERT: O 894 THR cc_start: 0.8738 (t) cc_final: 0.8503 (p) REVERT: O 913 MET cc_start: 0.7828 (ppp) cc_final: 0.7547 (ppp) REVERT: P 149 ASP cc_start: 0.7669 (m-30) cc_final: 0.7169 (m-30) REVERT: P 333 GLU cc_start: 0.3492 (tt0) cc_final: 0.1837 (tp30) REVERT: Q 188 MET cc_start: 0.2361 (ppp) cc_final: 0.1886 (mpp) REVERT: Q 224 MET cc_start: 0.4590 (mmp) cc_final: 0.3860 (mtp) REVERT: Q 257 ARG cc_start: 0.8185 (ttp80) cc_final: 0.7639 (ttp80) outliers start: 92 outliers final: 42 residues processed: 325 average time/residue: 0.2114 time to fit residues: 111.1071 Evaluate side-chains 283 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 230 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 492 SER Chi-restraints excluded: chain I residue 493 VAL Chi-restraints excluded: chain I residue 762 LEU Chi-restraints excluded: chain I residue 857 LEU Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 915 GLN Chi-restraints excluded: chain I residue 924 LEU Chi-restraints excluded: chain I residue 1010 HIS Chi-restraints excluded: chain I residue 1038 THR Chi-restraints excluded: chain I residue 1050 TYR Chi-restraints excluded: chain I residue 1164 ASN Chi-restraints excluded: chain I residue 1174 PHE Chi-restraints excluded: chain I residue 1182 GLN Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 109 MET Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 132 MET Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 305 MET Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 1812 LEU Chi-restraints excluded: chain L residue 1837 PHE Chi-restraints excluded: chain L residue 2007 LEU Chi-restraints excluded: chain L residue 2093 VAL Chi-restraints excluded: chain L residue 2152 VAL Chi-restraints excluded: chain L residue 2206 THR Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 353 LEU Chi-restraints excluded: chain M residue 358 ASP Chi-restraints excluded: chain M residue 362 GLU Chi-restraints excluded: chain M residue 365 ILE Chi-restraints excluded: chain N residue 920 LEU Chi-restraints excluded: chain O residue 437 SER Chi-restraints excluded: chain O residue 499 ARG Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain O residue 688 VAL Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 190 HIS Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain R residue 71 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: [291, 99, 364, 23, 236, 41, 136, 30, 31, 19, 147] chunk 291 optimal weight: 0.9990 chunk 99 optimal weight: 30.0000 chunk 364 optimal weight: 30.0000 chunk 23 optimal weight: 3.9990 chunk 236 optimal weight: 0.0050 chunk 41 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 147 optimal weight: 30.0000 overall best weight: 2.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1191 HIS ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 ASN ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 HIS ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 513 GLN O 925 GLN ** O 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 344 GLN P 425 HIS P 500 GLN ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.128204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.100242 restraints weight = 148449.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.102760 restraints weight = 67480.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.104261 restraints weight = 39993.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.105202 restraints weight = 28515.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.105765 restraints weight = 23137.044| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4105 r_free = 0.4105 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4105 r_free = 0.4105 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.4105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2122 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 35406 Z= 0.182 Angle : 0.742 12.471 48814 Z= 0.388 Chirality : 0.046 0.291 5491 Planarity : 0.005 0.071 5406 Dihedral : 24.048 171.239 6581 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.67 % Allowed : 19.19 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.14), residues: 3552 helix: 0.48 (0.11), residues: 2229 sheet: -1.27 (0.41), residues: 164 loop : -1.82 (0.17), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG O 443 TYR 0.017 0.002 TYR O 941 PHE 0.032 0.002 PHE L2103 TRP 0.034 0.002 TRP L1973 HIS 0.009 0.002 HIS N 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (35402) covalent geometry : angle 0.74048 / 0.39 (48811) hydrogen bonds : bond 0.04821 / 3.25 ( 1955) hydrogen bonds : angle 4.55152 / 3.23 ( 5458) metal coordination : bond 0.07314 / 4.07 ( 4) metal coordination : angle 6.68314 / 3.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 235 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.2238 (mmm) cc_final: 0.1346 (mtm) REVERT: G 83 LEU cc_start: 0.2581 (mm) cc_final: 0.2092 (mt) REVERT: I 475 TYR cc_start: 0.5515 (m-10) cc_final: 0.5079 (t80) REVERT: I 886 MET cc_start: 0.3799 (mtt) cc_final: 0.0665 (ttt) REVERT: I 915 GLN cc_start: 0.0028 (OUTLIER) cc_final: -0.1428 (pm20) REVERT: I 1010 HIS cc_start: 0.2814 (OUTLIER) cc_final: 0.1765 (m-70) REVERT: I 1050 TYR cc_start: -0.3100 (OUTLIER) cc_final: -0.3469 (p90) REVERT: I 1112 MET cc_start: -0.1354 (mmp) cc_final: -0.2672 (mtm) REVERT: I 1164 ASN cc_start: 0.4500 (OUTLIER) cc_final: 0.4292 (t0) REVERT: I 1174 PHE cc_start: 0.0702 (OUTLIER) cc_final: -0.0633 (t80) REVERT: I 1189 ARG cc_start: 0.3189 (mpt180) cc_final: 0.2211 (mtp85) REVERT: I 1317 MET cc_start: 0.2161 (tpt) cc_final: 0.1853 (ttp) REVERT: J 43 MET cc_start: -0.4054 (OUTLIER) cc_final: -0.5328 (mmt) REVERT: J 79 ARG cc_start: 0.1737 (OUTLIER) cc_final: 0.0584 (mmp-170) REVERT: J 294 ASN cc_start: -0.1018 (OUTLIER) cc_final: -0.2009 (m110) REVERT: J 376 MET cc_start: -0.0705 (ttp) cc_final: -0.0920 (ttp) REVERT: K 84 LYS cc_start: 0.7227 (mttt) cc_final: 0.6595 (pttp) REVERT: K 190 MET cc_start: 0.4618 (mmm) cc_final: 0.4210 (mmm) REVERT: K 250 ILE cc_start: -0.6100 (OUTLIER) cc_final: -0.6523 (pt) REVERT: L 1702 MET cc_start: 0.0318 (mmt) cc_final: -0.0332 (ptp) REVERT: L 2004 HIS cc_start: 0.3429 (t70) cc_final: 0.3096 (t-90) REVERT: L 2257 ARG cc_start: 0.3470 (mmp-170) cc_final: 0.3243 (mmp-170) REVERT: M 213 MET cc_start: -0.1889 (mtt) cc_final: -0.2578 (mtt) REVERT: N 444 ARG cc_start: 0.4238 (mtp-110) cc_final: 0.3778 (mtp-110) REVERT: N 896 MET cc_start: 0.5489 (ptm) cc_final: 0.5039 (ppp) REVERT: N 936 MET cc_start: 0.8243 (mmm) cc_final: 0.7953 (ppp) REVERT: O 432 TRP cc_start: 0.0272 (p-90) cc_final: -0.0687 (p-90) REVERT: O 913 MET cc_start: 0.7937 (ppp) cc_final: 0.7671 (ppp) REVERT: P 149 ASP cc_start: 0.7702 (m-30) cc_final: 0.7494 (m-30) REVERT: P 333 GLU cc_start: 0.3780 (tt0) cc_final: 0.1894 (tp30) REVERT: P 431 ILE cc_start: 0.2018 (OUTLIER) cc_final: 0.1751 (tt) REVERT: P 483 PHE cc_start: 0.4602 (m-80) cc_final: 0.4136 (m-80) REVERT: Q 188 MET cc_start: 0.2371 (ppp) cc_final: 0.1851 (mpp) REVERT: Q 224 MET cc_start: 0.4360 (mmp) cc_final: 0.3690 (mtp) REVERT: Q 257 ARG cc_start: 0.8132 (ttp80) cc_final: 0.7614 (ttp80) outliers start: 85 outliers final: 43 residues processed: 306 average time/residue: 0.2139 time to fit residues: 106.3090 Evaluate side-chains 267 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 214 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 493 VAL Chi-restraints excluded: chain I residue 762 LEU Chi-restraints excluded: chain I residue 857 LEU Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 910 THR Chi-restraints excluded: chain I residue 915 GLN Chi-restraints excluded: chain I residue 924 LEU Chi-restraints excluded: chain I residue 1010 HIS Chi-restraints excluded: chain I residue 1050 TYR Chi-restraints excluded: chain I residue 1164 ASN Chi-restraints excluded: chain I residue 1174 PHE Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 109 MET Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 305 MET Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 1713 LEU Chi-restraints excluded: chain L residue 1720 PHE Chi-restraints excluded: chain L residue 1837 PHE Chi-restraints excluded: chain L residue 2093 VAL Chi-restraints excluded: chain L residue 2152 VAL Chi-restraints excluded: chain L residue 2206 THR Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 353 LEU Chi-restraints excluded: chain M residue 365 ILE Chi-restraints excluded: chain N residue 920 LEU Chi-restraints excluded: chain O residue 437 SER Chi-restraints excluded: chain O residue 469 MET Chi-restraints excluded: chain O residue 499 ARG Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain O residue 677 VAL Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain P residue 431 ILE Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 190 HIS Chi-restraints excluded: chain Q residue 215 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: [208, 95, 172, 118, 102, 260, 338, 311, 249, 16, 303] chunk 208 optimal weight: 0.9980 chunk 95 optimal weight: 40.0000 chunk 172 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 260 optimal weight: 10.0000 chunk 338 optimal weight: 6.9990 chunk 311 optimal weight: 20.0000 chunk 249 optimal weight: 0.0060 chunk 16 optimal weight: 10.0000 chunk 303 optimal weight: 0.8980 overall best weight: 3.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 445 GLN I 472 HIS ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 327 HIS ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 ASN ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1858 HIS L1986 ASN ** L2004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2247 ASN L2268 ASN M 179 ASN ** M 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 949 GLN ** P 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 321 GLN P 359 GLN P 432 ASN Q 190 HIS ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 70 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.128306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.101916 restraints weight = 155537.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.104455 restraints weight = 70811.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.105949 restraints weight = 41533.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.106864 restraints weight = 29444.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.107484 restraints weight = 23732.279| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4159 r_free = 0.4159 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4159 r_free = 0.4159 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2468 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.144 35406 Z= 0.248 Angle : 0.874 18.389 48814 Z= 0.453 Chirality : 0.051 0.609 5491 Planarity : 0.006 0.070 5406 Dihedral : 24.141 173.860 6580 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.10 % Favored : 94.88 % Rotamer: Outliers : 3.45 % Allowed : 18.56 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.13), residues: 3552 helix: -0.03 (0.10), residues: 2211 sheet: -1.30 (0.42), residues: 165 loop : -1.97 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L1721 TYR 0.028 0.002 TYR N 465 PHE 0.049 0.003 PHE M 25 TRP 0.025 0.003 TRP L1670 HIS 0.011 0.002 HIS L2004 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.25 (35402) covalent geometry : angle 0.86794 / 0.45 (48811) hydrogen bonds : bond 0.05368 / 3.64 ( 1955) hydrogen bonds : angle 4.98774 / 3.55 ( 5458) metal coordination : bond 0.08883 / 4.85 ( 4) metal coordination : angle 13.26295 / 5.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 254 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.2576 (mmm) cc_final: 0.1599 (mtm) REVERT: G 83 LEU cc_start: 0.2351 (mm) cc_final: 0.2150 (mt) REVERT: I 777 LEU cc_start: 0.1407 (OUTLIER) cc_final: 0.1006 (pt) REVERT: I 857 LEU cc_start: -0.3846 (OUTLIER) cc_final: -0.4446 (pp) REVERT: I 865 LYS cc_start: 0.5217 (mptt) cc_final: 0.4918 (ttmm) REVERT: I 886 MET cc_start: 0.3755 (mtt) cc_final: 0.0584 (ttt) REVERT: I 915 GLN cc_start: 0.0551 (OUTLIER) cc_final: -0.1228 (pm20) REVERT: I 1010 HIS cc_start: 0.2954 (OUTLIER) cc_final: 0.1590 (m-70) REVERT: I 1050 TYR cc_start: -0.2627 (OUTLIER) cc_final: -0.3355 (p90) REVERT: I 1112 MET cc_start: -0.1058 (mmp) cc_final: -0.2788 (mtm) REVERT: I 1174 PHE cc_start: 0.0847 (OUTLIER) cc_final: -0.0428 (t80) REVERT: I 1189 ARG cc_start: 0.3192 (mpt180) cc_final: 0.2294 (ttm170) REVERT: I 1317 MET cc_start: 0.2005 (tpt) cc_final: 0.1682 (ttp) REVERT: J 43 MET cc_start: -0.3938 (OUTLIER) cc_final: -0.5107 (mmt) REVERT: J 79 ARG cc_start: 0.1335 (OUTLIER) cc_final: 0.0344 (mmp-170) REVERT: J 140 MET cc_start: 0.2860 (mmt) cc_final: 0.1157 (tpt) REVERT: J 294 ASN cc_start: -0.0738 (OUTLIER) cc_final: -0.1976 (m110) REVERT: K 84 LYS cc_start: 0.7205 (mttt) cc_final: 0.6573 (pttp) REVERT: K 190 MET cc_start: 0.4782 (mmm) cc_final: 0.4432 (mmm) REVERT: L 1702 MET cc_start: 0.0086 (mmt) cc_final: -0.1218 (ptt) REVERT: L 1958 GLU cc_start: 0.0138 (OUTLIER) cc_final: -0.1282 (mt-10) REVERT: L 2025 LYS cc_start: 0.4838 (tptt) cc_final: 0.4320 (mmmt) REVERT: M 53 ARG cc_start: 0.3173 (ttp-170) cc_final: 0.2002 (tpm170) REVERT: N 498 MET cc_start: -0.0643 (mtp) cc_final: -0.1630 (tpt) REVERT: N 625 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.5100 (pp20) REVERT: N 896 MET cc_start: 0.5597 (ptm) cc_final: 0.5203 (ppp) REVERT: N 936 MET cc_start: 0.8332 (mmm) cc_final: 0.8008 (ppp) REVERT: O 913 MET cc_start: 0.7941 (ppp) cc_final: 0.7687 (ppp) REVERT: O 949 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.6724 (pp30) REVERT: P 354 PHE cc_start: 0.3983 (OUTLIER) cc_final: 0.0795 (m-80) REVERT: P 483 PHE cc_start: 0.5026 (m-80) cc_final: 0.4567 (m-80) REVERT: Q 188 MET cc_start: 0.2697 (ppp) cc_final: 0.2136 (mpp) REVERT: Q 224 MET cc_start: 0.4133 (mmp) cc_final: 0.3842 (mtp) REVERT: Q 257 ARG cc_start: 0.8174 (ttp80) cc_final: 0.7801 (ttp80) outliers start: 110 outliers final: 48 residues processed: 338 average time/residue: 0.2192 time to fit residues: 118.4670 Evaluate side-chains 278 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 217 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 492 SER Chi-restraints excluded: chain I residue 493 VAL Chi-restraints excluded: chain I residue 762 LEU Chi-restraints excluded: chain I residue 777 LEU Chi-restraints excluded: chain I residue 857 LEU Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 910 THR Chi-restraints excluded: chain I residue 915 GLN Chi-restraints excluded: chain I residue 924 LEU Chi-restraints excluded: chain I residue 1010 HIS Chi-restraints excluded: chain I residue 1050 TYR Chi-restraints excluded: chain I residue 1174 PHE Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 109 MET Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain K residue 86 TRP Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 305 MET Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 1713 LEU Chi-restraints excluded: chain L residue 1720 PHE Chi-restraints excluded: chain L residue 1837 PHE Chi-restraints excluded: chain L residue 1958 GLU Chi-restraints excluded: chain L residue 2053 LEU Chi-restraints excluded: chain L residue 2152 VAL Chi-restraints excluded: chain L residue 2206 THR Chi-restraints excluded: chain L residue 2231 MET Chi-restraints excluded: chain L residue 2267 MET Chi-restraints excluded: chain L residue 2278 VAL Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain M residue 217 MET Chi-restraints excluded: chain M residue 261 ARG Chi-restraints excluded: chain M residue 353 LEU Chi-restraints excluded: chain M residue 358 ASP Chi-restraints excluded: chain M residue 362 GLU Chi-restraints excluded: chain N residue 625 GLU Chi-restraints excluded: chain N residue 920 LEU Chi-restraints excluded: chain N residue 927 LEU Chi-restraints excluded: chain O residue 437 SER Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain O residue 677 VAL Chi-restraints excluded: chain O residue 949 GLN Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain P residue 354 PHE Chi-restraints excluded: chain P residue 361 LEU Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 190 HIS Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 269 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: [365, 336, 75, 53, 202, 371, 60, 214, 105, 25, 344] chunk 365 optimal weight: 40.0000 chunk 336 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 371 optimal weight: 30.0000 chunk 60 optimal weight: 0.7980 chunk 214 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 344 optimal weight: 7.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 472 HIS ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2173 ASN M 260 GLN ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 530 HIS O 632 GLN ** O 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 362 HIS ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.128300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.101753 restraints weight = 154224.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.104306 restraints weight = 71163.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.105808 restraints weight = 41829.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.106741 restraints weight = 29513.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.107344 restraints weight = 23762.363| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4157 r_free = 0.4157 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4157 r_free = 0.4157 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.4157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2434 moved from start: 0.6508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 35406 Z= 0.170 Angle : 0.747 18.098 48814 Z= 0.387 Chirality : 0.046 0.296 5491 Planarity : 0.005 0.065 5406 Dihedral : 24.068 174.268 6578 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.38 % Allowed : 19.97 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.14), residues: 3552 helix: 0.22 (0.11), residues: 2213 sheet: -1.05 (0.44), residues: 164 loop : -1.88 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O 882 TYR 0.020 0.002 TYR O 462 PHE 0.028 0.002 PHE L2103 TRP 0.019 0.002 TRP N 620 HIS 0.010 0.001 HIS P 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (35402) covalent geometry : angle 0.74483 / 0.39 (48811) hydrogen bonds : bond 0.04686 / 3.15 ( 1955) hydrogen bonds : angle 4.76633 / 3.39 ( 5458) metal coordination : bond 0.02408 / 1.29 ( 4) metal coordination : angle 6.75344 / 2.74 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 236 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: -0.0243 (mmt) cc_final: -0.0701 (mpp) REVERT: B 84 MET cc_start: 0.2395 (mmm) cc_final: 0.1409 (mtm) REVERT: D 97 LEU cc_start: 0.1833 (OUTLIER) cc_final: 0.1496 (pp) REVERT: I 777 LEU cc_start: 0.1296 (OUTLIER) cc_final: 0.0897 (pt) REVERT: I 857 LEU cc_start: -0.3850 (OUTLIER) cc_final: -0.4439 (pp) REVERT: I 865 LYS cc_start: 0.5132 (mptt) cc_final: 0.4777 (ttmt) REVERT: I 886 MET cc_start: 0.3406 (mtt) cc_final: 0.0341 (ttt) REVERT: I 915 GLN cc_start: 0.0657 (OUTLIER) cc_final: -0.1204 (pm20) REVERT: I 1010 HIS cc_start: 0.2861 (OUTLIER) cc_final: 0.1597 (m-70) REVERT: I 1050 TYR cc_start: -0.2725 (OUTLIER) cc_final: -0.3435 (p90) REVERT: I 1112 MET cc_start: -0.1202 (mmp) cc_final: -0.2927 (mtm) REVERT: I 1150 PHE cc_start: 0.1505 (t80) cc_final: -0.0357 (m-80) REVERT: I 1174 PHE cc_start: 0.0901 (OUTLIER) cc_final: -0.0403 (t80) REVERT: I 1189 ARG cc_start: 0.3122 (mpt180) cc_final: 0.2128 (ttm170) REVERT: I 1317 MET cc_start: 0.2158 (tpt) cc_final: 0.1828 (ttp) REVERT: J 43 MET cc_start: -0.3843 (OUTLIER) cc_final: -0.5043 (mmt) REVERT: J 79 ARG cc_start: 0.1442 (OUTLIER) cc_final: 0.0392 (mmp-170) REVERT: J 294 ASN cc_start: -0.0754 (OUTLIER) cc_final: -0.1974 (m110) REVERT: K 84 LYS cc_start: 0.7205 (mttt) cc_final: 0.6590 (pttp) REVERT: K 190 MET cc_start: 0.4725 (mmm) cc_final: 0.4334 (mmm) REVERT: L 1650 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7831 (tm-30) REVERT: L 1702 MET cc_start: -0.0438 (mmt) cc_final: -0.1378 (ptt) REVERT: L 1983 CYS cc_start: 0.7491 (p) cc_final: 0.7110 (p) REVERT: L 2055 MET cc_start: 0.5385 (tmm) cc_final: 0.5071 (tmm) REVERT: M 53 ARG cc_start: 0.3095 (ttp-170) cc_final: 0.1990 (tpm170) REVERT: N 498 MET cc_start: -0.1028 (mtp) cc_final: -0.1667 (tpt) REVERT: N 896 MET cc_start: 0.5611 (ptm) cc_final: 0.5212 (ppp) REVERT: N 936 MET cc_start: 0.8142 (mmm) cc_final: 0.7815 (ppp) REVERT: O 432 TRP cc_start: -0.0238 (p-90) cc_final: -0.0570 (p-90) REVERT: P 483 PHE cc_start: 0.5087 (m-80) cc_final: 0.4600 (m-80) REVERT: Q 188 MET cc_start: 0.2435 (ppp) cc_final: 0.1610 (mpp) REVERT: Q 224 MET cc_start: 0.4292 (mmp) cc_final: 0.3896 (mtp) REVERT: Q 257 ARG cc_start: 0.8180 (ttp80) cc_final: 0.7777 (ttp80) outliers start: 76 outliers final: 47 residues processed: 296 average time/residue: 0.2094 time to fit residues: 99.8676 Evaluate side-chains 281 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 472 HIS Chi-restraints excluded: chain I residue 493 VAL Chi-restraints excluded: chain I residue 762 LEU Chi-restraints excluded: chain I residue 777 LEU Chi-restraints excluded: chain I residue 857 LEU Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 910 THR Chi-restraints excluded: chain I residue 915 GLN Chi-restraints excluded: chain I residue 924 LEU Chi-restraints excluded: chain I residue 1010 HIS Chi-restraints excluded: chain I residue 1050 TYR Chi-restraints excluded: chain I residue 1174 PHE Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain K residue 86 TRP Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 305 MET Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 1720 PHE Chi-restraints excluded: chain L residue 1814 VAL Chi-restraints excluded: chain L residue 2053 LEU Chi-restraints excluded: chain L residue 2152 VAL Chi-restraints excluded: chain L residue 2206 THR Chi-restraints excluded: chain L residue 2231 MET Chi-restraints excluded: chain L residue 2267 MET Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain M residue 353 LEU Chi-restraints excluded: chain M residue 358 ASP Chi-restraints excluded: chain M residue 362 GLU Chi-restraints excluded: chain N residue 920 LEU Chi-restraints excluded: chain O residue 437 SER Chi-restraints excluded: chain O residue 469 MET Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain O residue 673 VAL Chi-restraints excluded: chain O residue 677 VAL Chi-restraints excluded: chain O residue 707 VAL Chi-restraints excluded: chain P residue 441 MET Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 215 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: [104, 20, 82, 134, 225, 279, 171, 94, 338, 69, 280] chunk 104 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 225 optimal weight: 4.9990 chunk 279 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 94 optimal weight: 8.9990 chunk 338 optimal weight: 0.0770 chunk 69 optimal weight: 5.9990 chunk 280 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1304 GLN ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 938 GLN P 432 ASN ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.127844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.101136 restraints weight = 150746.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.103726 restraints weight = 68793.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.105297 restraints weight = 40315.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.106272 restraints weight = 28333.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.106855 restraints weight = 22723.187| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4144 r_free = 0.4144 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4144 r_free = 0.4144 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2308 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35406 Z= 0.141 Angle : 0.708 15.530 48814 Z= 0.367 Chirality : 0.045 0.308 5491 Planarity : 0.005 0.115 5406 Dihedral : 23.954 173.793 6578 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.94 % Allowed : 20.73 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 3552 helix: 0.49 (0.11), residues: 2220 sheet: -0.96 (0.43), residues: 160 loop : -1.71 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 945 TYR 0.031 0.002 TYR N 941 PHE 0.023 0.002 PHE N 906 TRP 0.020 0.002 TRP P 320 HIS 0.054 0.001 HIS I 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (35402) covalent geometry : angle 0.70706 / 0.37 (48811) hydrogen bonds : bond 0.04334 / 2.88 ( 1955) hydrogen bonds : angle 4.52866 / 3.24 ( 5458) metal coordination : bond 0.01953 / 1.04 ( 4) metal coordination : angle 4.14090 / 1.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 248 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.2316 (mmm) cc_final: 0.1305 (mtm) REVERT: I 777 LEU cc_start: 0.1280 (OUTLIER) cc_final: 0.0868 (pt) REVERT: I 797 MET cc_start: -0.4373 (mtm) cc_final: -0.4623 (mtt) REVERT: I 857 LEU cc_start: -0.3718 (OUTLIER) cc_final: -0.4225 (pp) REVERT: I 865 LYS cc_start: 0.5231 (mptt) cc_final: 0.4908 (ttmt) REVERT: I 886 MET cc_start: 0.3344 (mtt) cc_final: 0.0229 (ttt) REVERT: I 915 GLN cc_start: 0.0237 (OUTLIER) cc_final: -0.1478 (pm20) REVERT: I 1010 HIS cc_start: 0.2795 (OUTLIER) cc_final: 0.1480 (m-70) REVERT: I 1050 TYR cc_start: -0.2785 (OUTLIER) cc_final: -0.3436 (p90) REVERT: I 1112 MET cc_start: -0.1105 (mmp) cc_final: -0.2986 (mtm) REVERT: I 1150 PHE cc_start: 0.1407 (t80) cc_final: -0.0440 (m-80) REVERT: I 1174 PHE cc_start: 0.1249 (OUTLIER) cc_final: -0.0195 (t80) REVERT: I 1189 ARG cc_start: 0.2865 (mpt180) cc_final: 0.2032 (ttm170) REVERT: I 1317 MET cc_start: 0.2049 (tpt) cc_final: 0.1693 (ttp) REVERT: J 43 MET cc_start: -0.3719 (OUTLIER) cc_final: -0.4954 (mmt) REVERT: J 79 ARG cc_start: 0.1596 (OUTLIER) cc_final: 0.0710 (mmt-90) REVERT: J 294 ASN cc_start: -0.0755 (OUTLIER) cc_final: -0.1923 (m110) REVERT: K 84 LYS cc_start: 0.7239 (mttt) cc_final: 0.6597 (pttp) REVERT: K 190 MET cc_start: 0.4621 (mmm) cc_final: 0.4207 (mmm) REVERT: L 1702 MET cc_start: -0.0209 (mmt) cc_final: -0.1084 (ptt) REVERT: L 1958 GLU cc_start: 0.0031 (OUTLIER) cc_final: -0.1127 (mt-10) REVERT: L 2055 MET cc_start: 0.5326 (tmm) cc_final: 0.4927 (tmm) REVERT: M 53 ARG cc_start: 0.3082 (ttp-170) cc_final: 0.2217 (ptp90) REVERT: N 444 ARG cc_start: 0.4118 (mtp-110) cc_final: 0.3912 (mtp-110) REVERT: N 469 MET cc_start: -0.3275 (mtt) cc_final: -0.4453 (tmm) REVERT: N 498 MET cc_start: -0.1195 (mtp) cc_final: -0.1715 (tpt) REVERT: N 896 MET cc_start: 0.5572 (ptm) cc_final: 0.4992 (ppp) REVERT: N 936 MET cc_start: 0.8069 (mmm) cc_final: 0.7784 (ppp) REVERT: O 432 TRP cc_start: -0.0174 (p-90) cc_final: -0.0393 (p-90) REVERT: O 916 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7401 (mm-30) REVERT: P 149 ASP cc_start: 0.7809 (m-30) cc_final: 0.7443 (m-30) REVERT: P 483 PHE cc_start: 0.4825 (m-80) cc_final: 0.4317 (m-80) REVERT: Q 188 MET cc_start: 0.2206 (ppp) cc_final: 0.1458 (mpp) REVERT: Q 201 ARG cc_start: 0.5632 (mmt90) cc_final: 0.4552 (ttp80) REVERT: Q 224 MET cc_start: 0.4469 (mmp) cc_final: 0.4178 (mtp) REVERT: Q 257 ARG cc_start: 0.8152 (ttp80) cc_final: 0.7890 (ttp80) outliers start: 62 outliers final: 42 residues processed: 297 average time/residue: 0.2185 time to fit residues: 104.4353 Evaluate side-chains 281 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 229 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain I residue 493 VAL Chi-restraints excluded: chain I residue 762 LEU Chi-restraints excluded: chain I residue 777 LEU Chi-restraints excluded: chain I residue 857 LEU Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 910 THR Chi-restraints excluded: chain I residue 915 GLN Chi-restraints excluded: chain I residue 924 LEU Chi-restraints excluded: chain I residue 1010 HIS Chi-restraints excluded: chain I residue 1050 TYR Chi-restraints excluded: chain I residue 1174 PHE Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain K residue 86 TRP Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 305 MET Chi-restraints excluded: chain L residue 1713 LEU Chi-restraints excluded: chain L residue 1720 PHE Chi-restraints excluded: chain L residue 1814 VAL Chi-restraints excluded: chain L residue 1958 GLU Chi-restraints excluded: chain L residue 2053 LEU Chi-restraints excluded: chain L residue 2152 VAL Chi-restraints excluded: chain L residue 2267 MET Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain M residue 322 HIS Chi-restraints excluded: chain M residue 353 LEU Chi-restraints excluded: chain M residue 358 ASP Chi-restraints excluded: chain M residue 362 GLU Chi-restraints excluded: chain M residue 365 ILE Chi-restraints excluded: chain N residue 920 LEU Chi-restraints excluded: chain N residue 927 LEU Chi-restraints excluded: chain O residue 437 SER Chi-restraints excluded: chain O residue 469 MET Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain O residue 673 VAL Chi-restraints excluded: chain O residue 677 VAL Chi-restraints excluded: chain O residue 707 VAL Chi-restraints excluded: chain P residue 441 MET Chi-restraints excluded: chain Q residue 190 HIS Chi-restraints excluded: chain Q residue 215 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: [283, 212, 319, 117, 26, 320, 351, 11, 220, 339, 206] chunk 283 optimal weight: 0.9980 chunk 212 optimal weight: 0.9980 chunk 319 optimal weight: 30.0000 chunk 117 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 320 optimal weight: 0.7980 chunk 351 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 220 optimal weight: 0.9980 chunk 339 optimal weight: 0.3980 chunk 206 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 470 GLN I 472 HIS ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 HIS ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.128247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.101424 restraints weight = 152979.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.103982 restraints weight = 70359.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.105516 restraints weight = 41707.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.106476 restraints weight = 29614.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.107058 restraints weight = 23793.822| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4147 r_free = 0.4147 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4147 r_free = 0.4147 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.4147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2310 moved from start: 0.6748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 35406 Z= 0.140 Angle : 0.706 13.894 48814 Z= 0.365 Chirality : 0.044 0.310 5491 Planarity : 0.005 0.064 5406 Dihedral : 23.833 173.158 6578 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.63 % Allowed : 21.17 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3552 helix: 0.67 (0.11), residues: 2221 sheet: -0.80 (0.43), residues: 166 loop : -1.64 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG P 334 TYR 0.020 0.001 TYR L2076 PHE 0.026 0.002 PHE M 25 TRP 0.021 0.002 TRP P 320 HIS 0.013 0.001 HIS O 935 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (35402) covalent geometry : angle 0.70511 / 0.37 (48811) hydrogen bonds : bond 0.04195 / 2.80 ( 1955) hydrogen bonds : angle 4.45826 / 3.19 ( 5458) metal coordination : bond 0.01629 / 0.87 ( 4) metal coordination : angle 3.62624 / 1.60 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 243 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: -0.0159 (mmt) cc_final: -0.0539 (mpp) REVERT: B 84 MET cc_start: 0.2465 (mmm) cc_final: 0.0908 (ptp) REVERT: D 59 MET cc_start: -0.2105 (tpp) cc_final: -0.2583 (tpp) REVERT: I 777 LEU cc_start: 0.1193 (OUTLIER) cc_final: 0.0802 (pt) REVERT: I 857 LEU cc_start: -0.3588 (OUTLIER) cc_final: -0.4179 (pp) REVERT: I 865 LYS cc_start: 0.5175 (mptt) cc_final: 0.4890 (ttmm) REVERT: I 886 MET cc_start: 0.3566 (mtt) cc_final: 0.0351 (ttt) REVERT: I 915 GLN cc_start: 0.0077 (OUTLIER) cc_final: -0.1515 (pm20) REVERT: I 1010 HIS cc_start: 0.2823 (OUTLIER) cc_final: 0.1549 (m-70) REVERT: I 1050 TYR cc_start: -0.2737 (OUTLIER) cc_final: -0.3393 (p90) REVERT: I 1112 MET cc_start: -0.1171 (mmp) cc_final: -0.3033 (ttt) REVERT: I 1150 PHE cc_start: 0.1553 (t80) cc_final: -0.0226 (m-80) REVERT: I 1174 PHE cc_start: 0.1106 (OUTLIER) cc_final: -0.0162 (t80) REVERT: I 1189 ARG cc_start: 0.2830 (mpt180) cc_final: 0.2011 (ttm170) REVERT: I 1317 MET cc_start: 0.2020 (tpt) cc_final: 0.1692 (ttp) REVERT: J 43 MET cc_start: -0.3732 (OUTLIER) cc_final: -0.4946 (mmt) REVERT: J 79 ARG cc_start: 0.1587 (OUTLIER) cc_final: 0.0562 (mmp-170) REVERT: K 84 LYS cc_start: 0.7242 (mttt) cc_final: 0.6626 (pttp) REVERT: K 153 MET cc_start: -0.3278 (mtp) cc_final: -0.3547 (ttm) REVERT: K 190 MET cc_start: 0.4608 (mmm) cc_final: 0.4210 (mmm) REVERT: L 1702 MET cc_start: -0.0103 (mmt) cc_final: -0.0967 (ptt) REVERT: L 1746 ASP cc_start: 0.7075 (m-30) cc_final: 0.6832 (t70) REVERT: L 1958 GLU cc_start: -0.0042 (OUTLIER) cc_final: -0.0315 (mt-10) REVERT: L 1979 LYS cc_start: 0.7937 (mttm) cc_final: 0.7666 (mttm) REVERT: L 2025 LYS cc_start: 0.4938 (tptt) cc_final: 0.4405 (mmmt) REVERT: L 2055 MET cc_start: 0.5373 (tmm) cc_final: 0.4981 (tmm) REVERT: L 2230 MET cc_start: 0.1570 (tpp) cc_final: 0.0693 (tmm) REVERT: L 2257 ARG cc_start: 0.2891 (mmp80) cc_final: 0.2519 (tpp-160) REVERT: M 53 ARG cc_start: 0.3414 (ttp-170) cc_final: 0.2175 (tpm170) REVERT: N 444 ARG cc_start: 0.4079 (mtp-110) cc_final: 0.3400 (mtp-110) REVERT: N 896 MET cc_start: 0.5656 (ptm) cc_final: 0.5104 (ppp) REVERT: N 936 MET cc_start: 0.8046 (mmm) cc_final: 0.7706 (ppp) REVERT: O 469 MET cc_start: 0.4624 (OUTLIER) cc_final: 0.4400 (mmm) REVERT: O 661 TYR cc_start: 0.6433 (OUTLIER) cc_final: 0.3219 (m-80) REVERT: O 915 ARG cc_start: 0.9300 (mmp80) cc_final: 0.9085 (mmm160) REVERT: O 916 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7619 (mm-30) REVERT: P 483 PHE cc_start: 0.4818 (m-80) cc_final: 0.4317 (m-80) REVERT: Q 188 MET cc_start: 0.2168 (ppp) cc_final: 0.1478 (mpp) REVERT: Q 224 MET cc_start: 0.4323 (mmp) cc_final: 0.3929 (mtp) REVERT: Q 257 ARG cc_start: 0.8244 (ttp80) cc_final: 0.7970 (ttp80) outliers start: 52 outliers final: 39 residues processed: 286 average time/residue: 0.2070 time to fit residues: 95.0179 Evaluate side-chains 279 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain I residue 493 VAL Chi-restraints excluded: chain I residue 762 LEU Chi-restraints excluded: chain I residue 777 LEU Chi-restraints excluded: chain I residue 857 LEU Chi-restraints excluded: chain I residue 902 VAL Chi-restraints excluded: chain I residue 910 THR Chi-restraints excluded: chain I residue 915 GLN Chi-restraints excluded: chain I residue 924 LEU Chi-restraints excluded: chain I residue 1010 HIS Chi-restraints excluded: chain I residue 1050 TYR Chi-restraints excluded: chain I residue 1174 PHE Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain K residue 86 TRP Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 305 MET Chi-restraints excluded: chain L residue 1713 LEU Chi-restraints excluded: chain L residue 1720 PHE Chi-restraints excluded: chain L residue 1954 ILE Chi-restraints excluded: chain L residue 1958 GLU Chi-restraints excluded: chain L residue 2053 LEU Chi-restraints excluded: chain L residue 2152 VAL Chi-restraints excluded: chain L residue 2267 MET Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 205 THR Chi-restraints excluded: chain M residue 322 HIS Chi-restraints excluded: chain M residue 353 LEU Chi-restraints excluded: chain M residue 358 ASP Chi-restraints excluded: chain M residue 362 GLU Chi-restraints excluded: chain N residue 920 LEU Chi-restraints excluded: chain N residue 927 LEU Chi-restraints excluded: chain O residue 437 SER Chi-restraints excluded: chain O residue 469 MET Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain O residue 661 TYR Chi-restraints excluded: chain O residue 673 VAL Chi-restraints excluded: chain O residue 677 VAL Chi-restraints excluded: chain O residue 707 VAL Chi-restraints excluded: chain P residue 441 MET Chi-restraints excluded: chain Q residue 215 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: [159, 79, 369, 167, 220, 104, 125, 92, 141, 49, 42] chunk 159 optimal weight: 20.0000 chunk 79 optimal weight: 4.9990 chunk 369 optimal weight: 50.0000 chunk 167 optimal weight: 50.0000 chunk 220 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 141 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 60 ASN H 64 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 464 GLN ** I 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 888 ASN I 889 HIS I1004 GLN ** I1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 GLN J 384 ASN ** L1650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2070 GLN ** L2194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 323 GLN ** M 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 380 ASN N 489 ASN N 935 HIS ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 432 ASN ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.128243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.104183 restraints weight = 168023.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.106602 restraints weight = 80441.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.108051 restraints weight = 48073.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.108951 restraints weight = 33989.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.109520 restraints weight = 27166.815| |-----------------------------------------------------------------------------| r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4230 r_free = 0.4230 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4230 r_free = 0.4230 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2976 moved from start: 0.8267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.306 35406 Z= 0.362 Angle : 1.160 22.334 48814 Z= 0.597 Chirality : 0.060 0.545 5491 Planarity : 0.010 0.182 5406 Dihedral : 24.203 177.286 6576 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 34.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.31 % Favored : 93.64 % Rotamer: Outliers : 2.32 % Allowed : 21.01 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.03 (0.13), residues: 3552 helix: -0.78 (0.10), residues: 2197 sheet: -1.15 (0.43), residues: 155 loop : -2.28 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.002 ARG P 351 TYR 0.076 0.004 TYR N 465 PHE 0.060 0.005 PHE L2103 TRP 0.057 0.005 TRP L2091 HIS 0.019 0.003 HIS P 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00819 / 0.36 (35402) covalent geometry : angle 1.15415 / 0.60 (48811) hydrogen bonds : bond 0.07902 / 5.37 ( 1955) hydrogen bonds : angle 5.83237 / 4.17 ( 5458) metal coordination : bond 0.05422 / 3.03 ( 4) metal coordination : angle 15.48444 / 7.54 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8866.46 seconds wall clock time: 152 minutes 27.52 seconds (9147.52 seconds total)