Starting phenix.real_space_refine on Sun Jun 29 04:07:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ltj_0974/06_2025/6ltj_0974.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ltj_0974/06_2025/6ltj_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ltj_0974/06_2025/6ltj_0974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ltj_0974/06_2025/6ltj_0974.map" model { file = "/net/cci-nas-00/data/ceres_data/6ltj_0974/06_2025/6ltj_0974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ltj_0974/06_2025/6ltj_0974.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.72, per 1000 atoms: 0.58 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: 8.05 Conformation dependent library (CDL) restraints added in 4.0 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: 11.65 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: 19.04 Time building geometry restraints manager: 9.65 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=" CA SER I 478 " pdb=" CB SER I 478 " ideal model delta sigma weight residual 1.528 1.472 0.057 1.56e-02 4.11e+03 1.33e+01 bond pdb=" C THR I 494 " pdb=" O THR I 494 " ideal model delta sigma weight residual 1.237 1.278 -0.041 1.17e-02 7.31e+03 1.23e+01 bond pdb=" N LEU I 928 " pdb=" CA LEU I 928 " ideal model delta sigma weight residual 1.453 1.493 -0.040 1.18e-02 7.18e+03 1.15e+01 ... (remaining 35397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 47249 2.73 - 5.46: 1367 5.46 - 8.19: 156 8.19 - 10.92: 32 10.92 - 13.65: 7 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=" O3' DC X 122 " pdb=" C3' DC X 122 " pdb=" C2' DC X 122 " ideal model delta sigma weight residual 111.50 98.46 13.04 1.50e+00 4.44e-01 7.56e+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=" O3' DC X 56 " pdb=" C3' DC X 56 " pdb=" C2' DC X 56 " ideal model delta sigma weight residual 111.50 99.95 11.55 1.50e+00 4.44e-01 5.93e+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: 5243 0.138 - 0.276: 211 0.276 - 0.414: 31 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: 34.070 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: 1.300 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 93.050 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.150 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0836 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= 0.477 Angle : 1.079 13.650 48814 Z= 0.657 Chirality : 0.069 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 : 14.05 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.002 TRP J 250 HIS 0.011 0.002 HIS J 105 PHE 0.053 0.003 PHE K 200 TYR 0.040 0.003 TYR I 862 ARG 0.010 0.001 ARG I1009 Details of bonding type rmsd hydrogen bonds : bond 0.13074 ( 1955) hydrogen bonds : angle 6.57912 ( 5458) metal coordination : bond 0.04625 ( 4) metal coordination : angle 6.79404 ( 3) covalent geometry : bond 0.00993 (35402) covalent geometry : angle 1.07768 (48811) *********************** 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 : 3.493 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: 0.1759 (mmm) cc_final: 0.0494 (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: 0.0160 (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: -0.2344 (pm20) REVERT: I 1040 MET cc_start: -0.3201 (ttp) cc_final: -0.3706 (mtm) REVERT: I 1112 MET cc_start: -0.0488 (mmp) cc_final: -0.3704 (mtm) REVERT: I 1182 GLN cc_start: -0.0680 (OUTLIER) cc_final: -0.2080 (tm-30) REVERT: I 1189 ARG cc_start: 0.2501 (OUTLIER) cc_final: 0.1323 (mtt-85) REVERT: I 1305 MET cc_start: 0.2911 (ppp) cc_final: 0.1891 (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: 0.3940 (mmm) cc_final: 0.3343 (mmm) REVERT: K 250 ILE cc_start: -0.3068 (OUTLIER) cc_final: -0.3417 (pt) REVERT: K 283 MET cc_start: 0.0812 (mmp) cc_final: 0.0474 (tpp) REVERT: K 367 PRO cc_start: 0.0527 (Cg_endo) cc_final: -0.0887 (Cg_exo) REVERT: L 2166 MET cc_start: -0.0361 (mtt) cc_final: -0.2535 (tpp) REVERT: M 44 TYR cc_start: 0.1178 (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: 0.5799 time to fit residues: 501.9994 Evaluate side-chains 275 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 260 time to evaluate : 3.436 ------------------------------------------------------------------------------- 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: chunk 320 optimal weight: 6.9990 chunk 288 optimal weight: 0.9990 chunk 159 optimal weight: 40.0000 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 297 optimal weight: 0.0000 chunk 115 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 chunk 221 optimal weight: 0.8980 chunk 345 optimal weight: 0.7980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 106 HIS E 93 GLN F 25 ASN 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 I1182 GLN I1191 HIS I1195 GLN ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 HIS J 251 HIS ** J 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 354 GLN L1997 ASN L2248 HIS N 489 ASN 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 O 938 GLN 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 61 HIS R 70 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.128171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.098273 restraints weight = 144960.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.100788 restraints weight = 66234.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.102288 restraints weight = 39842.600| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3998 r_free = 0.3998 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3998 r_free = 0.3998 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1680 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 35406 Z= 0.179 Angle : 0.757 9.660 48814 Z= 0.404 Chirality : 0.045 0.291 5491 Planarity : 0.005 0.064 5406 Dihedral : 24.492 172.901 6601 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.50 % Favored : 95.47 % Rotamer: Outliers : 2.73 % Allowed : 14.77 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.13), residues: 3552 helix: -0.29 (0.10), residues: 2208 sheet: -1.92 (0.40), residues: 153 loop : -2.29 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP N 620 HIS 0.017 0.002 HIS J 183 PHE 0.032 0.002 PHE L2103 TYR 0.023 0.002 TYR I1008 ARG 0.011 0.001 ARG O 882 Details of bonding type rmsd hydrogen bonds : bond 0.04983 ( 1955) hydrogen bonds : angle 4.90723 ( 5458) metal coordination : bond 0.01210 ( 4) metal coordination : angle 5.14982 ( 3) covalent geometry : bond 0.00390 (35402) covalent geometry : angle 0.75626 (48811) *********************** 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 384 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 297 time to evaluate : 3.222 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: B 84 MET cc_start: 0.2016 (mmm) cc_final: 0.0486 (ptp) REVERT: I 412 PHE cc_start: 0.1098 (t80) cc_final: 0.0450 (t80) REVERT: I 475 TYR cc_start: 0.5128 (m-10) cc_final: 0.4648 (t80) REVERT: I 915 GLN cc_start: -0.0532 (OUTLIER) cc_final: -0.1985 (pm20) REVERT: I 1010 HIS cc_start: 0.1960 (OUTLIER) cc_final: 0.1619 (m-70) REVERT: I 1112 MET cc_start: -0.1498 (mmp) cc_final: -0.3357 (mtm) REVERT: I 1174 PHE cc_start: 0.1043 (OUTLIER) cc_final: -0.0139 (t80) REVERT: I 1189 ARG cc_start: 0.3735 (OUTLIER) cc_final: 0.2630 (mtt180) REVERT: I 1317 MET cc_start: 0.2472 (tpt) cc_final: 0.2129 (ttp) REVERT: J 79 ARG cc_start: 0.1109 (OUTLIER) cc_final: 0.0185 (mmt-90) REVERT: J 294 ASN cc_start: -0.0642 (OUTLIER) cc_final: -0.1656 (m110) REVERT: J 365 ASN cc_start: -0.1461 (OUTLIER) cc_final: -0.1862 (m-40) REVERT: K 30 VAL cc_start: -0.0124 (OUTLIER) cc_final: -0.0335 (p) REVERT: K 84 LYS cc_start: 0.7197 (mttt) cc_final: 0.6585 (ptmm) REVERT: K 190 MET cc_start: 0.4805 (mmm) cc_final: 0.4472 (mmm) REVERT: K 250 ILE cc_start: -0.5137 (OUTLIER) cc_final: -0.5458 (pt) REVERT: K 283 MET cc_start: 0.0575 (mmp) cc_final: 0.0060 (tpp) REVERT: K 287 VAL cc_start: -0.2383 (p) cc_final: -0.2585 (m) REVERT: K 354 GLN cc_start: 0.3120 (pt0) cc_final: 0.2798 (pp30) REVERT: L 2058 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6546 (mm-30) REVERT: L 2166 MET cc_start: -0.0384 (mtt) cc_final: -0.3172 (tpp) REVERT: M 213 MET cc_start: -0.2771 (mtt) cc_final: -0.2971 (mtt) REVERT: M 375 MET cc_start: 0.1062 (mtm) cc_final: -0.0171 (ppp) REVERT: N 444 ARG cc_start: 0.1117 (mtp85) cc_final: 0.0831 (mtp-110) REVERT: N 906 PHE cc_start: 0.5258 (t80) cc_final: 0.4986 (t80) REVERT: N 936 MET cc_start: 0.8503 (mmm) cc_final: 0.7400 (ppp) REVERT: O 631 THR cc_start: -0.4198 (OUTLIER) cc_final: -0.4424 (p) REVERT: O 894 THR cc_start: 0.8895 (t) cc_final: 0.8658 (p) REVERT: O 913 MET cc_start: 0.8047 (ppp) cc_final: 0.7829 (ppp) REVERT: P 333 GLU cc_start: 0.3567 (tt0) cc_final: 0.1856 (tp30) REVERT: Q 188 MET cc_start: 0.2176 (ppp) cc_final: 0.1734 (mpp) REVERT: Q 224 MET cc_start: 0.4456 (mmp) cc_final: 0.3536 (ttm) outliers start: 87 outliers final: 23 residues processed: 370 average time/residue: 0.5038 time to fit residues: 294.7000 Evaluate side-chains 270 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 236 time to evaluate : 3.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain H residue 41 VAL 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 1164 ASN 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 166 TYR Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 250 ILE 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 2132 VAL Chi-restraints excluded: chain L residue 2206 THR Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 365 ILE Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain O residue 631 THR Chi-restraints excluded: chain Q residue 184 ASP Chi-restraints excluded: chain Q residue 190 HIS Chi-restraints excluded: chain Q residue 269 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 346 optimal weight: 0.9990 chunk 99 optimal weight: 0.2980 chunk 178 optimal weight: 5.9990 chunk 11 optimal weight: 0.1980 chunk 161 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 358 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 969 HIS ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 HIS K 115 ASN ** L2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 278 GLN N 925 GLN O 423 HIS ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 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 = 0.4525 r_free = 0.4525 target = 0.127973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.098964 restraints weight = 146683.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.101463 restraints weight = 66456.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.102968 restraints weight = 39734.219| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4024 r_free = 0.4024 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4024 r_free = 0.4024 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1800 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 35406 Z= 0.157 Angle : 0.682 13.168 48814 Z= 0.364 Chirality : 0.042 0.249 5491 Planarity : 0.005 0.058 5406 Dihedral : 24.090 170.458 6587 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.63 % Allowed : 16.78 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3552 helix: 0.35 (0.11), residues: 2222 sheet: -1.55 (0.39), residues: 171 loop : -2.07 (0.17), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP N 620 HIS 0.010 0.001 HIS Q 237 PHE 0.021 0.002 PHE N 906 TYR 0.023 0.002 TYR I1008 ARG 0.014 0.001 ARG O 499 Details of bonding type rmsd hydrogen bonds : bond 0.04460 ( 1955) hydrogen bonds : angle 4.56481 ( 5458) metal coordination : bond 0.02146 ( 4) metal coordination : angle 3.90794 ( 3) covalent geometry : bond 0.00334 (35402) covalent geometry : angle 0.68135 (48811) *********************** 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 351 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 267 time to evaluate : 4.441 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: B 84 MET cc_start: 0.1995 (mmm) cc_final: 0.1054 (mtm) REVERT: G 42 ARG cc_start: 0.2192 (mpt180) cc_final: 0.1310 (mtt180) REVERT: G 83 LEU cc_start: 0.2332 (mm) cc_final: 0.2108 (mt) REVERT: I 475 TYR cc_start: 0.5372 (m-10) cc_final: 0.4982 (t80) REVERT: I 886 MET cc_start: 0.3888 (mtt) cc_final: 0.3624 (mtt) REVERT: I 915 GLN cc_start: -0.0161 (OUTLIER) cc_final: -0.1634 (pm20) REVERT: I 1010 HIS cc_start: 0.2678 (OUTLIER) cc_final: 0.1759 (m-70) REVERT: I 1112 MET cc_start: -0.1227 (mmp) cc_final: -0.2976 (mtm) REVERT: I 1174 PHE cc_start: 0.1182 (OUTLIER) cc_final: -0.0017 (t80) REVERT: I 1189 ARG cc_start: 0.3260 (mpt180) cc_final: 0.2426 (ttm170) REVERT: I 1317 MET cc_start: 0.2451 (tpt) cc_final: 0.2157 (ttp) REVERT: J 43 MET cc_start: -0.4087 (OUTLIER) cc_final: -0.5359 (mmt) REVERT: J 79 ARG cc_start: 0.1427 (OUTLIER) cc_final: 0.0393 (mmt-90) REVERT: J 294 ASN cc_start: -0.0820 (OUTLIER) cc_final: -0.1944 (m110) REVERT: J 365 ASN cc_start: -0.1427 (OUTLIER) cc_final: -0.1790 (m-40) REVERT: J 376 MET cc_start: 0.0674 (ttp) cc_final: 0.0272 (ptm) REVERT: K 84 LYS cc_start: 0.7210 (mttt) cc_final: 0.6575 (ptmm) REVERT: K 132 MET cc_start: 0.1843 (ttt) cc_final: 0.1439 (ttt) REVERT: K 190 MET cc_start: 0.4627 (mmm) cc_final: 0.4229 (mmm) REVERT: K 250 ILE cc_start: -0.5136 (OUTLIER) cc_final: -0.5687 (pt) REVERT: K 354 GLN cc_start: 0.3478 (pt0) cc_final: 0.3045 (pp30) REVERT: L 2004 HIS cc_start: 0.3067 (t-170) cc_final: 0.1845 (t70) REVERT: L 2166 MET cc_start: -0.0015 (mtt) cc_final: -0.2935 (tpp) REVERT: N 896 MET cc_start: 0.5195 (ptt) cc_final: 0.4511 (ppp) REVERT: N 936 MET cc_start: 0.8308 (mmm) cc_final: 0.7494 (ppp) REVERT: O 636 ILE cc_start: 0.3060 (tp) cc_final: 0.2584 (pt) REVERT: O 894 THR cc_start: 0.8853 (t) cc_final: 0.8642 (p) REVERT: O 913 MET cc_start: 0.8087 (ppp) cc_final: 0.7834 (ppp) REVERT: P 297 LEU cc_start: 0.2443 (OUTLIER) cc_final: 0.1485 (mt) REVERT: P 333 GLU cc_start: 0.3293 (tt0) cc_final: 0.1883 (tp30) REVERT: Q 188 MET cc_start: 0.2225 (ppp) cc_final: 0.1832 (mpp) REVERT: Q 224 MET cc_start: 0.4478 (mmp) cc_final: 0.3759 (mtp) REVERT: Q 257 ARG cc_start: 0.8175 (ttp80) cc_final: 0.7970 (ttp80) outliers start: 84 outliers final: 28 residues processed: 333 average time/residue: 0.6188 time to fit residues: 329.0928 Evaluate side-chains 268 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 5.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain I residue 364 VAL 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 971 VAL 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 39 THR 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 365 ASN Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain J residue 405 THR 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 2112 LEU Chi-restraints excluded: chain L residue 2206 THR Chi-restraints excluded: chain M residue 365 ILE Chi-restraints excluded: chain N residue 920 LEU Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain O residue 688 VAL Chi-restraints excluded: chain P residue 297 LEU 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 269 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 337 optimal weight: 8.9990 chunk 361 optimal weight: 10.0000 chunk 281 optimal weight: 2.9990 chunk 330 optimal weight: 0.9980 chunk 130 optimal weight: 0.0020 chunk 224 optimal weight: 0.7980 chunk 354 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 319 optimal weight: 3.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN D 79 HIS ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 GLN J 365 ASN ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2268 ASN M 79 HIS N 513 GLN ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 626 HIS ** O 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** 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 = 0.4531 r_free = 0.4531 target = 0.128008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.099772 restraints weight = 144662.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.102307 restraints weight = 65068.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.103820 restraints weight = 38359.761| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4043 r_free = 0.4043 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4043 r_free = 0.4043 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1811 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 35406 Z= 0.140 Angle : 0.641 9.955 48814 Z= 0.342 Chirality : 0.041 0.240 5491 Planarity : 0.005 0.115 5406 Dihedral : 23.846 171.137 6581 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.70 % Allowed : 17.22 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3552 helix: 0.76 (0.11), residues: 2212 sheet: -1.48 (0.38), residues: 175 loop : -1.86 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 922 HIS 0.012 0.001 HIS Q 237 PHE 0.020 0.002 PHE L2154 TYR 0.021 0.001 TYR I1008 ARG 0.013 0.000 ARG P 334 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 1955) hydrogen bonds : angle 4.33692 ( 5458) metal coordination : bond 0.03609 ( 4) metal coordination : angle 4.14647 ( 3) covalent geometry : bond 0.00293 (35402) covalent geometry : angle 0.63971 (48811) *********************** 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 348 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 262 time to evaluate : 3.267 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: 0.1999 (mmm) cc_final: 0.1076 (mtm) REVERT: G 42 ARG cc_start: 0.1911 (mpt180) cc_final: 0.1103 (mtt180) REVERT: H 91 ILE cc_start: -0.1543 (mm) cc_final: -0.1760 (mm) REVERT: I 475 TYR cc_start: 0.5394 (m-10) cc_final: 0.4994 (t80) REVERT: I 915 GLN cc_start: -0.0122 (OUTLIER) cc_final: -0.1473 (pm20) REVERT: I 1010 HIS cc_start: 0.2815 (OUTLIER) cc_final: 0.1733 (m-70) REVERT: I 1112 MET cc_start: -0.1145 (mmp) cc_final: -0.2961 (mtm) REVERT: I 1174 PHE cc_start: 0.1225 (OUTLIER) cc_final: -0.0381 (t80) REVERT: I 1189 ARG cc_start: 0.3007 (mpt180) cc_final: 0.2311 (ttm170) REVERT: I 1317 MET cc_start: 0.2168 (tpt) cc_final: 0.1848 (ttp) REVERT: J 43 MET cc_start: -0.4195 (OUTLIER) cc_final: -0.5399 (mmt) REVERT: J 79 ARG cc_start: 0.1718 (OUTLIER) cc_final: 0.0698 (mmt-90) REVERT: J 140 MET cc_start: 0.3238 (mmp) cc_final: 0.2177 (tpt) REVERT: J 190 GLN cc_start: 0.4415 (OUTLIER) cc_final: 0.3970 (pm20) REVERT: J 294 ASN cc_start: -0.1078 (OUTLIER) cc_final: -0.2005 (m110) REVERT: J 365 ASN cc_start: -0.1628 (OUTLIER) cc_final: -0.1933 (m-40) REVERT: J 413 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6575 (pttt) REVERT: K 84 LYS cc_start: 0.7238 (mttt) cc_final: 0.6588 (ptmm) REVERT: K 190 MET cc_start: 0.4557 (mmm) cc_final: 0.4154 (mmm) REVERT: L 2166 MET cc_start: -0.0064 (mtt) cc_final: -0.2727 (tpp) REVERT: M 208 MET cc_start: -0.2931 (mtm) cc_final: -0.3750 (tpt) REVERT: N 896 MET cc_start: 0.5228 (ptt) cc_final: 0.4484 (ppp) REVERT: N 936 MET cc_start: 0.8216 (mmm) cc_final: 0.7543 (ppp) REVERT: O 499 ARG cc_start: 0.5711 (ttt180) cc_final: 0.5307 (ptm160) REVERT: O 636 ILE cc_start: 0.3425 (tp) cc_final: 0.2928 (pt) REVERT: O 913 MET cc_start: 0.8059 (ppp) cc_final: 0.7855 (ppp) REVERT: P 149 ASP cc_start: 0.7695 (m-30) cc_final: 0.7219 (m-30) REVERT: P 333 GLU cc_start: 0.3257 (tt0) cc_final: 0.1675 (tp30) REVERT: Q 188 MET cc_start: 0.2402 (ppp) cc_final: 0.1931 (mpp) REVERT: Q 202 LEU cc_start: 0.5390 (mt) cc_final: 0.4984 (mm) REVERT: Q 224 MET cc_start: 0.4574 (mmp) cc_final: 0.3852 (mtp) REVERT: Q 257 ARG cc_start: 0.8079 (ttp80) cc_final: 0.7571 (ttp80) outliers start: 86 outliers final: 40 residues processed: 337 average time/residue: 0.4851 time to fit residues: 260.8454 Evaluate side-chains 284 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 235 time to evaluate : 3.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 492 SER 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 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 1174 PHE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 190 GLN Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 365 ASN Chi-restraints excluded: chain J residue 386 THR 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 175 ILE Chi-restraints excluded: chain K residue 233 SER 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 1954 ILE Chi-restraints excluded: chain L residue 2007 LEU Chi-restraints excluded: chain L residue 2112 LEU Chi-restraints excluded: chain L residue 2206 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 353 LEU Chi-restraints excluded: chain M residue 362 GLU Chi-restraints excluded: chain M residue 365 ILE Chi-restraints excluded: chain N residue 621 ASN Chi-restraints excluded: chain N residue 635 CYS Chi-restraints excluded: chain N residue 920 LEU Chi-restraints excluded: chain N residue 927 LEU Chi-restraints excluded: chain O residue 469 MET Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain P residue 155 ARG Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain Q residue 190 HIS Chi-restraints excluded: chain Q residue 215 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 33 optimal weight: 20.0000 chunk 111 optimal weight: 0.1980 chunk 143 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 163 optimal weight: 40.0000 chunk 65 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 227 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 172 optimal weight: 30.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** J 190 GLN J 370 GLN ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2004 HIS ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 638 HIS ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.128252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.099830 restraints weight = 147550.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.102338 restraints weight = 67057.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.103824 restraints weight = 39774.261| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4051 r_free = 0.4051 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4051 r_free = 0.4051 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1902 moved from start: 0.4766 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= 0.144 Angle : 0.636 14.129 48814 Z= 0.337 Chirality : 0.041 0.394 5491 Planarity : 0.004 0.054 5406 Dihedral : 23.704 171.576 6579 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.32 % Allowed : 18.31 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3552 helix: 0.91 (0.11), residues: 2220 sheet: -1.55 (0.38), residues: 185 loop : -1.76 (0.17), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 922 HIS 0.011 0.001 HIS Q 237 PHE 0.023 0.002 PHE J 141 TYR 0.015 0.001 TYR F 51 ARG 0.007 0.000 ARG L2116 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 1955) hydrogen bonds : angle 4.24379 ( 5458) metal coordination : bond 0.03234 ( 4) metal coordination : angle 3.86723 ( 3) covalent geometry : bond 0.00300 (35402) covalent geometry : angle 0.63494 (48811) *********************** 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 335 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 261 time to evaluate : 3.526 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: 0.2211 (mmm) cc_final: 0.1242 (mtm) REVERT: G 42 ARG cc_start: 0.1838 (mpt180) cc_final: 0.1353 (mtt180) REVERT: I 475 TYR cc_start: 0.5552 (m-10) cc_final: 0.5138 (t80) REVERT: I 886 MET cc_start: 0.3549 (mtt) cc_final: 0.0572 (ttt) REVERT: I 915 GLN cc_start: -0.0002 (OUTLIER) cc_final: -0.1421 (pm20) REVERT: I 1010 HIS cc_start: 0.2673 (OUTLIER) cc_final: 0.1609 (m-70) REVERT: I 1112 MET cc_start: -0.1212 (mmp) cc_final: -0.2906 (mtm) REVERT: I 1174 PHE cc_start: 0.0488 (OUTLIER) cc_final: -0.0660 (t80) REVERT: I 1189 ARG cc_start: 0.3015 (mpt180) cc_final: 0.2357 (ttm170) REVERT: I 1317 MET cc_start: 0.2153 (tpt) cc_final: 0.1852 (ttp) REVERT: J 43 MET cc_start: -0.4073 (OUTLIER) cc_final: -0.5119 (mmt) REVERT: J 79 ARG cc_start: 0.1575 (OUTLIER) cc_final: 0.0614 (mmt-90) REVERT: J 335 MET cc_start: 0.3043 (ptp) cc_final: 0.2479 (ptp) REVERT: J 376 MET cc_start: -0.0802 (ttp) cc_final: -0.2394 (ptm) REVERT: K 84 LYS cc_start: 0.7249 (mttt) cc_final: 0.6634 (pttp) REVERT: K 190 MET cc_start: 0.4605 (mmm) cc_final: 0.4191 (mmm) REVERT: K 355 MET cc_start: -0.0598 (ttm) cc_final: -0.1895 (ppp) REVERT: L 2166 MET cc_start: 0.0303 (mtt) cc_final: -0.2544 (tpp) REVERT: M 208 MET cc_start: -0.2776 (mtm) cc_final: -0.3562 (tpt) REVERT: N 896 MET cc_start: 0.5296 (ptt) cc_final: 0.4539 (ppp) REVERT: N 936 MET cc_start: 0.8225 (mmm) cc_final: 0.7689 (ppp) REVERT: O 499 ARG cc_start: 0.5639 (ttt180) cc_final: 0.5196 (ptm160) REVERT: O 626 HIS cc_start: 0.5532 (m90) cc_final: 0.5320 (m90) REVERT: P 149 ASP cc_start: 0.7401 (m-30) cc_final: 0.6885 (m-30) REVERT: P 431 ILE cc_start: 0.1667 (OUTLIER) cc_final: 0.1443 (tt) REVERT: Q 188 MET cc_start: 0.2292 (ppp) cc_final: 0.1817 (mpp) REVERT: Q 224 MET cc_start: 0.4570 (mmp) cc_final: 0.3852 (mtp) REVERT: Q 257 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7880 (ttp80) outliers start: 74 outliers final: 42 residues processed: 320 average time/residue: 0.4916 time to fit residues: 251.8598 Evaluate side-chains 286 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 76 THR 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 416 LEU Chi-restraints excluded: chain I residue 492 SER 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 971 VAL 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 39 THR 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 175 ILE Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 233 SER 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 1954 ILE Chi-restraints excluded: chain L residue 2007 LEU Chi-restraints excluded: chain L residue 2093 VAL Chi-restraints excluded: chain L residue 2112 LEU Chi-restraints excluded: chain L residue 2152 VAL Chi-restraints excluded: chain L residue 2206 THR Chi-restraints excluded: chain M residue 353 LEU Chi-restraints excluded: chain M residue 362 GLU Chi-restraints excluded: chain M residue 365 ILE Chi-restraints excluded: chain N residue 621 ASN Chi-restraints excluded: chain N residue 920 LEU Chi-restraints excluded: chain N residue 927 LEU Chi-restraints excluded: chain O residue 469 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 163 optimal weight: 40.0000 chunk 203 optimal weight: 0.4980 chunk 160 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 345 optimal weight: 0.3980 chunk 333 optimal weight: 9.9990 chunk 222 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 334 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** I1304 GLN ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 513 GLN ** O 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 344 GLN P 359 GLN ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.128043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.100264 restraints weight = 146035.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.102800 restraints weight = 66138.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.104331 restraints weight = 38960.779| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4065 r_free = 0.4065 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 = 0.4065 r_free = 0.4065 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1923 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35406 Z= 0.134 Angle : 0.631 10.594 48814 Z= 0.332 Chirality : 0.041 0.332 5491 Planarity : 0.004 0.094 5406 Dihedral : 23.597 172.427 6576 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.32 % Allowed : 19.25 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3552 helix: 1.00 (0.11), residues: 2230 sheet: -1.39 (0.38), residues: 185 loop : -1.65 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 922 HIS 0.010 0.001 HIS Q 237 PHE 0.028 0.002 PHE M 25 TYR 0.018 0.001 TYR M 26 ARG 0.010 0.000 ARG O 917 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 1955) hydrogen bonds : angle 4.17452 ( 5458) metal coordination : bond 0.02076 ( 4) metal coordination : angle 3.33600 ( 3) covalent geometry : bond 0.00286 (35402) covalent geometry : angle 0.63038 (48811) *********************** 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 323 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 249 time to evaluate : 3.353 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: 0.2215 (mmm) cc_final: 0.1272 (mtm) REVERT: G 42 ARG cc_start: 0.1745 (mpt180) cc_final: 0.1231 (mtt180) REVERT: I 475 TYR cc_start: 0.5516 (m-10) cc_final: 0.5136 (t80) REVERT: I 886 MET cc_start: 0.3524 (mtt) cc_final: 0.0260 (ttt) REVERT: I 915 GLN cc_start: -0.0228 (OUTLIER) cc_final: -0.1555 (pm20) REVERT: I 1010 HIS cc_start: 0.2756 (OUTLIER) cc_final: 0.1608 (m-70) REVERT: I 1112 MET cc_start: -0.1211 (mmp) cc_final: -0.2985 (mtm) REVERT: I 1164 ASN cc_start: 0.4616 (OUTLIER) cc_final: 0.4330 (t0) REVERT: I 1174 PHE cc_start: 0.0708 (OUTLIER) cc_final: -0.0634 (t80) REVERT: I 1189 ARG cc_start: 0.2859 (mpt180) cc_final: 0.2137 (ttm170) REVERT: I 1317 MET cc_start: 0.2179 (tpt) cc_final: 0.1862 (ttp) REVERT: J 43 MET cc_start: -0.4113 (OUTLIER) cc_final: -0.5136 (mmt) REVERT: J 79 ARG cc_start: 0.1491 (OUTLIER) cc_final: 0.0485 (mmt-90) REVERT: J 195 SER cc_start: -0.4079 (OUTLIER) cc_final: -0.4290 (m) REVERT: J 294 ASN cc_start: -0.1032 (OUTLIER) cc_final: -0.1922 (m110) REVERT: K 84 LYS cc_start: 0.7234 (mttt) cc_final: 0.6613 (pttp) REVERT: K 190 MET cc_start: 0.4556 (mmm) cc_final: 0.4148 (mmm) REVERT: K 355 MET cc_start: -0.0642 (ttm) cc_final: -0.2046 (ppp) REVERT: L 2166 MET cc_start: 0.0357 (mtt) cc_final: -0.2580 (tpp) REVERT: M 208 MET cc_start: -0.2717 (mtm) cc_final: -0.3458 (tpt) REVERT: N 896 MET cc_start: 0.5272 (ptt) cc_final: 0.4514 (ppp) REVERT: N 936 MET cc_start: 0.8229 (mmm) cc_final: 0.7543 (ppp) REVERT: O 469 MET cc_start: 0.4231 (OUTLIER) cc_final: 0.3580 (mmt) REVERT: O 499 ARG cc_start: 0.5625 (ttt180) cc_final: 0.5187 (ptm160) REVERT: O 917 ARG cc_start: 0.6949 (mpt180) cc_final: 0.6592 (mpt180) REVERT: P 149 ASP cc_start: 0.7428 (m-30) cc_final: 0.6936 (m-30) REVERT: P 431 ILE cc_start: 0.1881 (OUTLIER) cc_final: 0.1638 (tt) REVERT: Q 188 MET cc_start: 0.2135 (ppp) cc_final: 0.1706 (mpp) REVERT: Q 201 ARG cc_start: 0.5230 (mmt90) cc_final: 0.4261 (tmm160) REVERT: Q 202 LEU cc_start: 0.5908 (tt) cc_final: 0.5441 (pp) REVERT: Q 224 MET cc_start: 0.4526 (mmp) cc_final: 0.3852 (mtp) REVERT: Q 257 ARG cc_start: 0.8119 (ttp80) cc_final: 0.7875 (ttp80) outliers start: 74 outliers final: 44 residues processed: 308 average time/residue: 0.4934 time to fit residues: 242.8145 Evaluate side-chains 291 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 237 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 THR 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 416 LEU Chi-restraints excluded: chain I residue 762 LEU Chi-restraints excluded: chain I residue 857 LEU Chi-restraints excluded: chain I residue 875 TRP 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 971 VAL 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 39 THR Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 195 SER 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 305 MET Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 1812 LEU Chi-restraints excluded: chain L residue 1954 ILE Chi-restraints excluded: chain L residue 2007 LEU Chi-restraints excluded: chain L residue 2093 VAL Chi-restraints excluded: chain L residue 2112 LEU Chi-restraints excluded: chain L residue 2152 VAL Chi-restraints excluded: chain L residue 2206 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 353 LEU 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 469 MET Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain O residue 677 VAL Chi-restraints excluded: chain O residue 925 GLN 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 Chi-restraints excluded: chain R residue 71 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 369 optimal weight: 30.0000 chunk 174 optimal weight: 9.9990 chunk 192 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 333 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 chunk 93 optimal weight: 0.0270 chunk 262 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 343 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** 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** L2018 HIS L2173 ASN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 GLN ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 500 GLN ** Q 252 HIS ** 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 = 0.4547 r_free = 0.4547 target = 0.128219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.100990 restraints weight = 151595.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.103468 restraints weight = 69550.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.104968 restraints weight = 41148.050| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4093 r_free = 0.4093 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 = 0.4093 r_free = 0.4093 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2210 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 35406 Z= 0.166 Angle : 0.693 10.919 48814 Z= 0.361 Chirality : 0.042 0.325 5491 Planarity : 0.005 0.067 5406 Dihedral : 23.543 173.055 6576 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.23 % Allowed : 19.16 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.14), residues: 3552 helix: 0.77 (0.11), residues: 2235 sheet: -1.05 (0.41), residues: 165 loop : -1.67 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 86 HIS 0.011 0.001 HIS L2004 PHE 0.024 0.002 PHE L2103 TYR 0.018 0.002 TYR N 465 ARG 0.010 0.001 ARG N 444 Details of bonding type rmsd hydrogen bonds : bond 0.04249 ( 1955) hydrogen bonds : angle 4.34776 ( 5458) metal coordination : bond 0.01896 ( 4) metal coordination : angle 6.51847 ( 3) covalent geometry : bond 0.00363 (35402) covalent geometry : angle 0.69109 (48811) *********************** 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 325 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 254 time to evaluate : 3.499 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: 0.2572 (mmm) cc_final: 0.1115 (ptp) REVERT: E 69 ARG cc_start: 0.7817 (mmm160) cc_final: 0.7563 (mmt180) REVERT: I 475 TYR cc_start: 0.5702 (m-10) cc_final: 0.5285 (t80) REVERT: I 865 LYS cc_start: 0.5217 (mptt) cc_final: 0.4869 (ttmm) REVERT: I 886 MET cc_start: 0.3565 (mtt) cc_final: 0.0300 (ttt) REVERT: I 915 GLN cc_start: -0.0143 (OUTLIER) cc_final: -0.1533 (pm20) REVERT: I 1010 HIS cc_start: 0.3047 (OUTLIER) cc_final: 0.1782 (m-70) REVERT: I 1112 MET cc_start: -0.1164 (mmp) cc_final: -0.2801 (mtm) REVERT: I 1174 PHE cc_start: 0.0700 (OUTLIER) cc_final: -0.0530 (t80) REVERT: I 1189 ARG cc_start: 0.2992 (mpt180) cc_final: 0.2213 (ttm170) REVERT: I 1317 MET cc_start: 0.1978 (tpt) cc_final: 0.1660 (ttp) REVERT: J 43 MET cc_start: -0.3824 (OUTLIER) cc_final: -0.4727 (mmt) REVERT: J 79 ARG cc_start: 0.1313 (OUTLIER) cc_final: 0.0291 (mmp-170) REVERT: J 140 MET cc_start: 0.2661 (mmt) cc_final: 0.1080 (tpt) REVERT: J 294 ASN cc_start: -0.0914 (OUTLIER) cc_final: -0.1960 (m110) REVERT: K 84 LYS cc_start: 0.7243 (mttt) cc_final: 0.6647 (pttp) REVERT: K 123 MET cc_start: -0.2396 (tpp) cc_final: -0.2735 (tpp) REVERT: K 190 MET cc_start: 0.4565 (mmm) cc_final: 0.4163 (mmm) REVERT: K 269 MET cc_start: 0.3339 (tpt) cc_final: 0.2876 (mtt) REVERT: K 355 MET cc_start: -0.0674 (ttm) cc_final: -0.0930 (ttp) REVERT: L 1983 CYS cc_start: 0.7147 (p) cc_final: 0.6882 (p) REVERT: L 2132 VAL cc_start: 0.5455 (t) cc_final: 0.5226 (t) REVERT: L 2166 MET cc_start: 0.0942 (mtt) cc_final: -0.2445 (tpp) REVERT: M 208 MET cc_start: -0.2440 (mtm) cc_final: -0.3166 (tpt) REVERT: N 444 ARG cc_start: 0.4401 (mtp-110) cc_final: 0.3967 (mtp-110) REVERT: N 896 MET cc_start: 0.5387 (ptt) cc_final: 0.4587 (ppp) REVERT: N 936 MET cc_start: 0.8189 (mmm) cc_final: 0.7651 (ppp) REVERT: O 469 MET cc_start: 0.4519 (OUTLIER) cc_final: 0.3871 (mmm) REVERT: O 499 ARG cc_start: 0.5961 (ttt180) cc_final: 0.5324 (ptm160) REVERT: P 148 MET cc_start: 0.6303 (ppp) cc_final: 0.6013 (ppp) REVERT: P 149 ASP cc_start: 0.7481 (m-30) cc_final: 0.7189 (m-30) REVERT: P 431 ILE cc_start: 0.2747 (OUTLIER) cc_final: 0.2495 (tt) REVERT: Q 188 MET cc_start: 0.2307 (ppp) cc_final: 0.2013 (mpp) REVERT: Q 201 ARG cc_start: 0.5474 (mmt90) cc_final: 0.4463 (tmm160) REVERT: Q 202 LEU cc_start: 0.6212 (tt) cc_final: 0.5584 (pp) REVERT: Q 224 MET cc_start: 0.4387 (mmp) cc_final: 0.3882 (mtp) REVERT: Q 257 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7916 (ttp80) outliers start: 71 outliers final: 40 residues processed: 313 average time/residue: 0.4983 time to fit residues: 249.7373 Evaluate side-chains 280 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 232 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 416 LEU 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 971 VAL 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 I residue 1366 MET Chi-restraints excluded: chain J residue 39 THR 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 175 ILE Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 305 MET Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 2001 MET Chi-restraints excluded: chain L residue 2010 ILE Chi-restraints excluded: chain L residue 2056 LEU Chi-restraints excluded: chain L residue 2093 VAL Chi-restraints excluded: chain L residue 2112 LEU Chi-restraints excluded: chain L residue 2152 VAL Chi-restraints excluded: chain L residue 2206 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 353 LEU 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 214 optimal weight: 0.8980 chunk 345 optimal weight: 0.9990 chunk 368 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 190 optimal weight: 0.0870 chunk 2 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 329 optimal weight: 3.9990 chunk 312 optimal weight: 0.8980 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 82 GLN ** 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** ** J 162 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** L2004 HIS ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 632 GLN ** O 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.128196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.101016 restraints weight = 150509.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.103476 restraints weight = 69251.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.104965 restraints weight = 41425.435| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4097 r_free = 0.4097 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 = 0.4097 r_free = 0.4097 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2165 moved from start: 0.6138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35406 Z= 0.136 Angle : 0.638 17.001 48814 Z= 0.334 Chirality : 0.041 0.260 5491 Planarity : 0.004 0.060 5406 Dihedral : 23.479 175.021 6576 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.98 % Allowed : 19.85 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3552 helix: 0.95 (0.11), residues: 2234 sheet: -0.82 (0.43), residues: 160 loop : -1.56 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP M 281 HIS 0.008 0.001 HIS Q 237 PHE 0.030 0.002 PHE M 25 TYR 0.012 0.001 TYR B 72 ARG 0.019 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 1955) hydrogen bonds : angle 4.16369 ( 5458) metal coordination : bond 0.01761 ( 4) metal coordination : angle 3.38112 ( 3) covalent geometry : bond 0.00293 (35402) covalent geometry : angle 0.63774 (48811) *********************** 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 307 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 244 time to evaluate : 3.588 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: B 84 MET cc_start: 0.2561 (mmm) cc_final: 0.1112 (ptp) REVERT: E 69 ARG cc_start: 0.7755 (mmm160) cc_final: 0.7533 (mmm160) REVERT: I 475 TYR cc_start: 0.5624 (m-10) cc_final: 0.5269 (t80) REVERT: I 865 LYS cc_start: 0.5210 (mptt) cc_final: 0.4922 (ttmt) REVERT: I 886 MET cc_start: 0.3460 (mtt) cc_final: 0.0219 (ttt) REVERT: I 915 GLN cc_start: -0.0114 (OUTLIER) cc_final: -0.1454 (pm20) REVERT: I 1010 HIS cc_start: 0.3069 (OUTLIER) cc_final: 0.1833 (m-70) REVERT: I 1112 MET cc_start: -0.1169 (mmp) cc_final: -0.3037 (ttt) REVERT: I 1174 PHE cc_start: 0.0814 (OUTLIER) cc_final: -0.0314 (t80) REVERT: I 1189 ARG cc_start: 0.2936 (mpt180) cc_final: 0.2089 (ttm170) REVERT: I 1317 MET cc_start: 0.2112 (tpt) cc_final: 0.1800 (ttp) REVERT: J 43 MET cc_start: -0.3926 (OUTLIER) cc_final: -0.4759 (mmt) REVERT: J 79 ARG cc_start: 0.1342 (OUTLIER) cc_final: 0.0317 (mmp-170) REVERT: J 294 ASN cc_start: -0.0910 (OUTLIER) cc_final: -0.1948 (m110) REVERT: K 84 LYS cc_start: 0.7221 (mttt) cc_final: 0.6605 (pttp) REVERT: K 190 MET cc_start: 0.4676 (mmm) cc_final: 0.4285 (mmm) REVERT: K 355 MET cc_start: -0.0427 (ttm) cc_final: -0.1446 (ppp) REVERT: L 1958 GLU cc_start: -0.0347 (OUTLIER) cc_final: -0.0616 (mt-10) REVERT: L 2132 VAL cc_start: 0.5460 (t) cc_final: 0.5213 (t) REVERT: M 53 ARG cc_start: 0.3137 (ttp-170) cc_final: 0.2087 (ptp90) REVERT: M 208 MET cc_start: -0.2663 (mtm) cc_final: -0.3166 (tpt) REVERT: N 439 HIS cc_start: 0.2881 (t-90) cc_final: 0.2521 (t-90) REVERT: N 896 MET cc_start: 0.5401 (ptt) cc_final: 0.4575 (ppp) REVERT: N 936 MET cc_start: 0.8256 (mmm) cc_final: 0.7691 (ppp) REVERT: O 469 MET cc_start: 0.4413 (OUTLIER) cc_final: 0.3831 (mmm) REVERT: O 499 ARG cc_start: 0.5930 (ttt180) cc_final: 0.5308 (ptm160) REVERT: O 917 ARG cc_start: 0.7145 (mmt180) cc_final: 0.6836 (mpt180) REVERT: P 431 ILE cc_start: 0.2763 (OUTLIER) cc_final: 0.2553 (tt) REVERT: Q 188 MET cc_start: 0.2481 (ppp) cc_final: 0.2110 (mpp) REVERT: Q 201 ARG cc_start: 0.5544 (mmt90) cc_final: 0.4527 (tmm160) REVERT: Q 202 LEU cc_start: 0.6091 (tt) cc_final: 0.5541 (pp) REVERT: Q 224 MET cc_start: 0.4557 (mmp) cc_final: 0.4026 (mtp) REVERT: Q 257 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7943 (ttp80) outliers start: 63 outliers final: 40 residues processed: 293 average time/residue: 0.4998 time to fit residues: 234.2344 Evaluate side-chains 278 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 3.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 416 LEU 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 971 VAL 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 39 THR 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 380 LEU 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 305 MET Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 1958 GLU Chi-restraints excluded: chain L residue 2010 ILE Chi-restraints excluded: chain L residue 2056 LEU Chi-restraints excluded: chain L residue 2093 VAL Chi-restraints excluded: chain L residue 2112 LEU Chi-restraints excluded: chain L residue 2152 VAL Chi-restraints excluded: chain L residue 2206 THR Chi-restraints excluded: chain L residue 2267 MET 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 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 469 MET Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain O residue 631 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 315 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 74 optimal weight: 0.0030 chunk 211 optimal weight: 1.9990 chunk 284 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 149 optimal weight: 0.0170 chunk 333 optimal weight: 0.9990 chunk 230 optimal weight: 3.9990 chunk 206 optimal weight: 0.7980 overall best weight: 0.4628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 889 HIS ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 935 HIS Q 232 GLN ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.128475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.101078 restraints weight = 150561.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.103560 restraints weight = 69493.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.105005 restraints weight = 41687.995| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4096 r_free = 0.4096 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 = 0.4096 r_free = 0.4096 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2093 moved from start: 0.6300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 35406 Z= 0.128 Angle : 0.633 18.220 48814 Z= 0.329 Chirality : 0.040 0.229 5491 Planarity : 0.004 0.055 5406 Dihedral : 23.351 176.900 6576 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.63 % Allowed : 20.57 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3552 helix: 1.10 (0.11), residues: 2236 sheet: -0.65 (0.44), residues: 160 loop : -1.52 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 281 HIS 0.008 0.001 HIS Q 237 PHE 0.021 0.001 PHE M 25 TYR 0.022 0.001 TYR M 26 ARG 0.011 0.000 ARG P 155 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 1955) hydrogen bonds : angle 4.08581 ( 5458) metal coordination : bond 0.01152 ( 4) metal coordination : angle 2.01682 ( 3) covalent geometry : bond 0.00276 (35402) covalent geometry : angle 0.63294 (48811) *********************** 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 307 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 255 time to evaluate : 3.785 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: 0.1922 (mmm) cc_final: 0.0819 (mtm) REVERT: I 475 TYR cc_start: 0.5760 (m-10) cc_final: 0.5407 (t80) REVERT: I 865 LYS cc_start: 0.5180 (mptt) cc_final: 0.4899 (ttmt) REVERT: I 886 MET cc_start: 0.3321 (mtt) cc_final: 0.0050 (ttt) REVERT: I 915 GLN cc_start: -0.0129 (OUTLIER) cc_final: -0.1466 (pm20) REVERT: I 1010 HIS cc_start: 0.2956 (OUTLIER) cc_final: 0.1706 (m-70) REVERT: I 1112 MET cc_start: -0.1174 (mmp) cc_final: -0.3067 (ttt) REVERT: I 1174 PHE cc_start: 0.0846 (OUTLIER) cc_final: -0.0367 (t80) REVERT: I 1189 ARG cc_start: 0.2710 (mpt180) cc_final: 0.2052 (ttm170) REVERT: I 1317 MET cc_start: 0.2119 (tpt) cc_final: 0.1818 (ttp) REVERT: J 43 MET cc_start: -0.3586 (OUTLIER) cc_final: -0.4358 (mmt) REVERT: J 79 ARG cc_start: 0.1427 (OUTLIER) cc_final: 0.0419 (mmp-170) REVERT: K 84 LYS cc_start: 0.7241 (mttt) cc_final: 0.6639 (pttp) REVERT: K 190 MET cc_start: 0.4627 (mmm) cc_final: 0.4237 (mmm) REVERT: K 269 MET cc_start: 0.2669 (tpt) cc_final: 0.2029 (mtt) REVERT: L 1958 GLU cc_start: -0.0471 (OUTLIER) cc_final: -0.0787 (mt-10) REVERT: L 2166 MET cc_start: 0.0681 (mtt) cc_final: -0.2441 (tpp) REVERT: M 53 ARG cc_start: 0.3222 (ttp-170) cc_final: 0.2142 (ptp90) REVERT: M 78 ASP cc_start: 0.4596 (p0) cc_final: 0.4347 (p0) REVERT: M 208 MET cc_start: -0.2719 (mtm) cc_final: -0.3139 (tpt) REVERT: N 439 HIS cc_start: 0.2671 (t-90) cc_final: 0.2381 (t-90) REVERT: N 469 MET cc_start: -0.3313 (mtt) cc_final: -0.4469 (tmm) REVERT: N 896 MET cc_start: 0.5398 (ptt) cc_final: 0.4586 (ppp) REVERT: N 936 MET cc_start: 0.8226 (mmm) cc_final: 0.7665 (ppp) REVERT: O 432 TRP cc_start: -0.0490 (p-90) cc_final: -0.0802 (p-90) REVERT: O 499 ARG cc_start: 0.5780 (ttt180) cc_final: 0.5351 (ptm160) REVERT: O 917 ARG cc_start: 0.7087 (mmt180) cc_final: 0.6573 (mpt180) REVERT: P 149 ASP cc_start: 0.7568 (m-30) cc_final: 0.7267 (m-30) REVERT: Q 188 MET cc_start: 0.2425 (ppp) cc_final: 0.2076 (mpp) REVERT: Q 201 ARG cc_start: 0.5696 (mmt90) cc_final: 0.4666 (tmm160) REVERT: Q 202 LEU cc_start: 0.5958 (tt) cc_final: 0.5535 (pp) REVERT: Q 224 MET cc_start: 0.4499 (mmp) cc_final: 0.4079 (mtp) REVERT: Q 257 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7912 (ttp80) outliers start: 52 outliers final: 37 residues processed: 299 average time/residue: 0.7450 time to fit residues: 362.2594 Evaluate side-chains 279 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 236 time to evaluate : 3.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain I residue 416 LEU 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 971 VAL 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 39 THR Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 380 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 305 MET Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 1958 GLU Chi-restraints excluded: chain L residue 2007 LEU Chi-restraints excluded: chain L residue 2093 VAL Chi-restraints excluded: chain L residue 2112 LEU Chi-restraints excluded: chain L residue 2152 VAL Chi-restraints excluded: chain M residue 25 PHE 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 362 GLU Chi-restraints excluded: chain M residue 365 ILE Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain O residue 631 THR Chi-restraints excluded: chain O residue 673 VAL Chi-restraints excluded: chain O residue 677 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 256 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 230 optimal weight: 0.0070 chunk 246 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 363 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 chunk 357 optimal weight: 0.0770 chunk 138 optimal weight: 9.9990 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 888 ASN ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.128273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.100859 restraints weight = 151783.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.103349 restraints weight = 69158.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.104858 restraints weight = 41344.513| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4093 r_free = 0.4093 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 = 0.4093 r_free = 0.4093 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2124 moved from start: 0.6496 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= 0.129 Angle : 0.639 14.241 48814 Z= 0.331 Chirality : 0.040 0.255 5491 Planarity : 0.004 0.055 5406 Dihedral : 23.268 178.427 6576 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.69 % Allowed : 20.76 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3552 helix: 1.17 (0.11), residues: 2234 sheet: -0.54 (0.44), residues: 160 loop : -1.46 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP N 620 HIS 0.010 0.001 HIS O 626 PHE 0.023 0.001 PHE Q 266 TYR 0.022 0.001 TYR F 88 ARG 0.010 0.000 ARG I 905 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 1955) hydrogen bonds : angle 4.05551 ( 5458) metal coordination : bond 0.01151 ( 4) metal coordination : angle 2.31893 ( 3) covalent geometry : bond 0.00277 (35402) covalent geometry : angle 0.63857 (48811) ********************** 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 306 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 252 time to evaluate : 3.256 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: 0.2298 (mmm) cc_final: 0.1238 (mtm) REVERT: I 475 TYR cc_start: 0.5939 (m-10) cc_final: 0.5478 (t80) REVERT: I 865 LYS cc_start: 0.5194 (mptt) cc_final: 0.4905 (ttmm) REVERT: I 886 MET cc_start: 0.3326 (mtt) cc_final: 0.0061 (ttt) REVERT: I 915 GLN cc_start: -0.0176 (OUTLIER) cc_final: -0.1467 (pm20) REVERT: I 1010 HIS cc_start: 0.3049 (OUTLIER) cc_final: 0.1761 (m-70) REVERT: I 1112 MET cc_start: -0.1138 (mmp) cc_final: -0.2921 (ttt) REVERT: I 1174 PHE cc_start: 0.0901 (OUTLIER) cc_final: -0.0264 (t80) REVERT: I 1189 ARG cc_start: 0.2724 (mpt180) cc_final: 0.2045 (ttm170) REVERT: I 1317 MET cc_start: 0.2028 (tpt) cc_final: 0.1739 (ttp) REVERT: J 79 ARG cc_start: 0.1437 (OUTLIER) cc_final: 0.0409 (mmp-170) REVERT: J 338 ILE cc_start: 0.2571 (tp) cc_final: 0.2187 (tt) REVERT: K 84 LYS cc_start: 0.7207 (mttt) cc_final: 0.6615 (pttp) REVERT: K 190 MET cc_start: 0.4657 (mmm) cc_final: 0.4280 (mmm) REVERT: K 325 MET cc_start: -0.2251 (tpp) cc_final: -0.2459 (mmm) REVERT: L 1958 GLU cc_start: -0.0583 (OUTLIER) cc_final: -0.0845 (mt-10) REVERT: L 2166 MET cc_start: 0.0764 (mtt) cc_final: -0.2297 (tpp) REVERT: M 53 ARG cc_start: 0.3225 (ttp-170) cc_final: 0.1903 (tpm170) REVERT: M 78 ASP cc_start: 0.4677 (p0) cc_final: 0.4438 (p0) REVERT: M 208 MET cc_start: -0.2823 (mtm) cc_final: -0.3185 (tpt) REVERT: N 896 MET cc_start: 0.5500 (ptt) cc_final: 0.4699 (ppp) REVERT: N 936 MET cc_start: 0.8227 (mmm) cc_final: 0.7680 (ppp) REVERT: O 432 TRP cc_start: -0.0700 (p-90) cc_final: -0.0923 (p-90) REVERT: O 499 ARG cc_start: 0.5882 (ttt180) cc_final: 0.5414 (ptm160) REVERT: O 615 MET cc_start: -0.2192 (OUTLIER) cc_final: -0.2945 (ttt) REVERT: O 917 ARG cc_start: 0.6965 (mmt180) cc_final: 0.6372 (mmt180) REVERT: P 149 ASP cc_start: 0.7619 (m-30) cc_final: 0.7220 (m-30) REVERT: P 400 LEU cc_start: 0.7176 (tp) cc_final: 0.6805 (tp) REVERT: Q 188 MET cc_start: 0.2428 (ppp) cc_final: 0.2135 (mpp) REVERT: Q 201 ARG cc_start: 0.5693 (mmt90) cc_final: 0.4678 (tmm160) REVERT: Q 202 LEU cc_start: 0.6007 (tt) cc_final: 0.5534 (pp) REVERT: Q 224 MET cc_start: 0.4441 (mmp) cc_final: 0.3965 (mtp) REVERT: Q 257 ARG cc_start: 0.8260 (ttp80) cc_final: 0.8011 (ttp80) outliers start: 54 outliers final: 39 residues processed: 297 average time/residue: 0.5102 time to fit residues: 242.7017 Evaluate side-chains 279 residues out of total 3191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 234 time to evaluate : 3.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain I residue 416 LEU 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 971 VAL 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 39 THR Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 380 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 305 MET Chi-restraints excluded: chain K residue 330 ILE Chi-restraints excluded: chain L residue 1958 GLU Chi-restraints excluded: chain L residue 2007 LEU Chi-restraints excluded: chain L residue 2093 VAL Chi-restraints excluded: chain L residue 2112 LEU Chi-restraints excluded: chain L residue 2152 VAL 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 362 GLU Chi-restraints excluded: chain M residue 365 ILE Chi-restraints excluded: chain N residue 441 ILE Chi-restraints excluded: chain N residue 927 LEU Chi-restraints excluded: chain O residue 521 THR Chi-restraints excluded: chain O residue 615 MET Chi-restraints excluded: chain O residue 631 THR Chi-restraints excluded: chain O residue 673 VAL Chi-restraints excluded: chain O residue 677 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 193 THR 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: chunk 334 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 292 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 180 optimal weight: 30.0000 chunk 195 optimal weight: 0.7980 chunk 175 optimal weight: 20.0000 chunk 324 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 445 GLN I 470 GLN ** 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** L1835 GLN ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2273 GLN M 179 ASN ** M 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 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 321 GLN P 362 HIS ** 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 = 0.128380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.102165 restraints weight = 156295.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.104666 restraints weight = 72496.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.106174 restraints weight = 43054.316| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4132 r_free = 0.4132 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 = 0.4132 r_free = 0.4132 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2437 moved from start: 0.7274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 35406 Z= 0.177 Angle : 0.739 14.448 48814 Z= 0.383 Chirality : 0.044 0.376 5491 Planarity : 0.006 0.143 5406 Dihedral : 23.320 178.079 6576 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.47 % Allowed : 20.95 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3552 helix: 0.73 (0.11), residues: 2232 sheet: -0.68 (0.44), residues: 159 loop : -1.52 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP M 281 HIS 0.008 0.001 HIS P 332 PHE 0.032 0.002 PHE J 360 TYR 0.031 0.002 TYR M 26 ARG 0.033 0.001 ARG O 945 Details of bonding type rmsd hydrogen bonds : bond 0.04446 ( 1955) hydrogen bonds : angle 4.43603 ( 5458) metal coordination : bond 0.02665 ( 4) metal coordination : angle 8.42742 ( 3) covalent geometry : bond 0.00393 (35402) covalent geometry : angle 0.73615 (48811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15773.23 seconds wall clock time: 275 minutes 14.58 seconds (16514.58 seconds total)