Starting phenix.real_space_refine on Mon Jul 6 03:26:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wbz_65851/07_2026/9wbz_65851_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wbz_65851/07_2026/9wbz_65851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wbz_65851/07_2026/9wbz_65851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wbz_65851/07_2026/9wbz_65851.map" model { file = "/net/cci-nas-00/data/ceres_data/9wbz_65851/07_2026/9wbz_65851_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wbz_65851/07_2026/9wbz_65851_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 20 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 308 5.49 5 S 88 5.16 5 C 14536 2.51 5 N 4446 2.21 5 O 5195 1.98 5 H 6897 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31470 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 6178 Classifications: {'peptide': 681} Link IDs: {'PTRANS': 20, 'TRANS': 660} Chain breaks: 4 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 717 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3139 Classifications: {'DNA': 154} Link IDs: {'rna3p': 153} Chain: "J" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3175 Classifications: {'DNA': 154} Link IDs: {'rna3p': 153} Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 5816 Classifications: {'peptide': 375} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "N" Number of atoms: 6555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 6555 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain: "O" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 571 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain breaks: 1 Time building chain proxies: 5.09, per 1000 atoms: 0.16 Number of scatterers: 31470 At special positions: 0 Unit cell: (175.365, 138.56, 150.467, 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) S 88 16.00 P 308 15.00 O 5195 8.00 N 4446 7.00 C 14536 6.00 H 6897 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 844.0 milliseconds 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4298 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 27 sheets defined 59.5% alpha, 8.7% beta 149 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 454 through 516 removed outlier: 3.561A pdb=" N LYS A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 488 " --> pdb=" O LYS A 484 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS A 490 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 544 No H-bonds generated for 'chain 'A' and resid 542 through 544' Processing helix chain 'A' and resid 545 through 558 Processing helix chain 'A' and resid 732 through 736 Processing helix chain 'A' and resid 755 through 771 Processing helix chain 'A' and resid 784 through 799 Processing helix chain 'A' and resid 811 through 826 removed outlier: 4.386A pdb=" N SER A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASN A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 844 removed outlier: 3.629A pdb=" N ALA A 843 " --> pdb=" O ALA A 839 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE A 844 " --> pdb=" O ALA A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 851 Processing helix chain 'A' and resid 859 through 866 removed outlier: 3.607A pdb=" N ILE A 863 " --> pdb=" O THR A 859 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A 864 " --> pdb=" O TYR A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 871 Processing helix chain 'A' and resid 883 through 888 removed outlier: 4.278A pdb=" N ASN A 888 " --> pdb=" O ARG A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 901 removed outlier: 3.769A pdb=" N GLN A 895 " --> pdb=" O CYS A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 929 removed outlier: 3.795A pdb=" N TRP A 922 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 939 removed outlier: 3.758A pdb=" N PHE A 939 " --> pdb=" O CYS A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 973 removed outlier: 3.700A pdb=" N ARG A 966 " --> pdb=" O ILE A 962 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 972 " --> pdb=" O LEU A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 985 Processing helix chain 'A' and resid 1001 through 1015 Processing helix chain 'A' and resid 1037 through 1048 Processing helix chain 'A' and resid 1049 through 1053 removed outlier: 3.791A pdb=" N PHE A1052 " --> pdb=" O PRO A1049 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN A1053 " --> pdb=" O TYR A1050 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1049 through 1053' Processing helix chain 'A' and resid 1054 through 1064 removed outlier: 3.763A pdb=" N GLY A1064 " --> pdb=" O SER A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1079 removed outlier: 3.810A pdb=" N TYR A1076 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER A1079 " --> pdb=" O LEU A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1095 Proline residue: A1090 - end of helix Processing helix chain 'A' and resid 1105 through 1120 Processing helix chain 'A' and resid 1133 through 1144 removed outlier: 3.699A pdb=" N MET A1137 " --> pdb=" O GLU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1160 Processing helix chain 'A' and resid 1179 through 1188 removed outlier: 3.693A pdb=" N ASP A1183 " --> pdb=" O ASN A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1222 removed outlier: 4.009A pdb=" N LYS A1213 " --> pdb=" O SER A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1223 through 1229 Processing helix chain 'A' and resid 1241 through 1255 removed outlier: 3.571A pdb=" N ALA A1245 " --> pdb=" O HIS A1241 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A1250 " --> pdb=" O PHE A1246 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU A1251 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU A1252 " --> pdb=" O GLN A1248 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS A1253 " --> pdb=" O ALA A1249 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A1254 " --> pdb=" O ILE A1250 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU A1255 " --> pdb=" O LEU A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1274 removed outlier: 3.802A pdb=" N GLN A1271 " --> pdb=" O GLU A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1294 removed outlier: 3.575A pdb=" N ARG A1285 " --> pdb=" O ASP A1281 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET A1286 " --> pdb=" O LEU A1282 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A1287 " --> pdb=" O PHE A1283 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU A1288 " --> pdb=" O MET A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1316 removed outlier: 3.905A pdb=" N LYS A1316 " --> pdb=" O SER A1312 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 22 removed outlier: 3.593A pdb=" N LYS B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL B 21 " --> pdb=" O ARG B 17 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 22 " --> pdb=" O HIS B 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 16 through 22' Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.706A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.479A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.545A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.518A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.061A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.575A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.591A 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 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.764A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 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: 4.493A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.504A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.764A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 49 Processing helix chain 'K' and resid 49 through 55 removed outlier: 3.573A pdb=" N ARG K 53 " --> pdb=" O ARG K 49 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN K 55 " --> pdb=" O ILE K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 79 removed outlier: 4.230A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 Processing helix chain 'L' and resid 55 through 61 removed outlier: 3.725A pdb=" N GLN L 59 " --> pdb=" O GLY L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 65 removed outlier: 3.540A pdb=" N LEU L 65 " --> pdb=" O ARG L 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 62 through 65' Processing helix chain 'L' and resid 78 through 92 removed outlier: 3.651A pdb=" N LYS L 84 " --> pdb=" O ASP L 80 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 126 removed outlier: 3.705A pdb=" N ARG L 116 " --> pdb=" O PRO L 112 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET L 123 " --> pdb=" O MET L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 145 removed outlier: 3.503A pdb=" N SER L 145 " --> pdb=" O SER L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 175 removed outlier: 3.687A pdb=" N ILE L 175 " --> pdb=" O PRO L 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 172 through 175' Processing helix chain 'L' and resid 181 through 197 Processing helix chain 'L' and resid 202 through 216 removed outlier: 3.783A pdb=" N GLU L 207 " --> pdb=" O THR L 203 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE L 208 " --> pdb=" O ALA L 204 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS L 215 " --> pdb=" O ASP L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 222 through 233 removed outlier: 3.530A pdb=" N ALA L 228 " --> pdb=" O GLU L 224 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 260 removed outlier: 3.645A pdb=" N CYS L 257 " --> pdb=" O GLU L 253 " (cutoff:3.500A) Proline residue: L 258 - end of helix Processing helix chain 'L' and resid 261 through 262 No H-bonds generated for 'chain 'L' and resid 261 through 262' Processing helix chain 'L' and resid 263 through 268 Processing helix chain 'L' and resid 273 through 284 Processing helix chain 'L' and resid 286 through 296 removed outlier: 4.481A pdb=" N LYS L 291 " --> pdb=" O VAL L 287 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP L 292 " --> pdb=" O ASP L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 301 through 306 removed outlier: 4.156A pdb=" N TYR L 306 " --> pdb=" O THR L 303 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 321 Processing helix chain 'L' and resid 334 through 336 No H-bonds generated for 'chain 'L' and resid 334 through 336' Processing helix chain 'L' and resid 337 through 349 Processing helix chain 'L' and resid 350 through 355 removed outlier: 3.552A pdb=" N GLN L 353 " --> pdb=" O SER L 350 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN L 354 " --> pdb=" O THR L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 366 removed outlier: 3.631A pdb=" N ASP L 363 " --> pdb=" O LYS L 359 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU L 364 " --> pdb=" O GLN L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 368 through 374 removed outlier: 4.175A pdb=" N ARG L 372 " --> pdb=" O SER L 368 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 74 Processing helix chain 'N' and resid 93 through 108 Processing helix chain 'N' and resid 112 through 116 removed outlier: 3.538A pdb=" N HIS N 116 " --> pdb=" O ALA N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 127 through 141 removed outlier: 3.839A pdb=" N GLU N 136 " --> pdb=" O GLU N 132 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU N 137 " --> pdb=" O LYS N 133 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET N 138 " --> pdb=" O LEU N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 160 Processing helix chain 'N' and resid 187 through 190 Processing helix chain 'N' and resid 196 through 212 Processing helix chain 'N' and resid 217 through 219 No H-bonds generated for 'chain 'N' and resid 217 through 219' Processing helix chain 'N' and resid 245 through 265 removed outlier: 3.515A pdb=" N LEU N 265 " --> pdb=" O GLN N 261 " (cutoff:3.500A) Processing helix chain 'N' and resid 273 through 280 Processing helix chain 'N' and resid 297 through 302 removed outlier: 3.607A pdb=" N ILE N 302 " --> pdb=" O GLU N 298 " (cutoff:3.500A) Processing helix chain 'N' and resid 303 through 308 removed outlier: 4.096A pdb=" N PHE N 307 " --> pdb=" O PRO N 303 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 312 Processing helix chain 'N' and resid 322 through 334 removed outlier: 3.573A pdb=" N CYS N 334 " --> pdb=" O SER N 330 " (cutoff:3.500A) Processing helix chain 'N' and resid 338 through 345 removed outlier: 3.529A pdb=" N LEU N 342 " --> pdb=" O ILE N 338 " (cutoff:3.500A) Processing helix chain 'N' and resid 350 through 355 removed outlier: 4.031A pdb=" N ILE N 355 " --> pdb=" O ASN N 352 " (cutoff:3.500A) Processing helix chain 'N' and resid 357 through 370 Processing helix chain 'N' and resid 383 through 389 removed outlier: 3.506A pdb=" N ARG N 387 " --> pdb=" O THR N 383 " (cutoff:3.500A) Processing helix chain 'N' and resid 389 through 401 removed outlier: 3.528A pdb=" N GLY N 395 " --> pdb=" O SER N 391 " (cutoff:3.500A) Processing helix chain 'N' and resid 402 through 408 removed outlier: 3.651A pdb=" N GLN N 405 " --> pdb=" O GLY N 402 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN N 406 " --> pdb=" O THR N 403 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP N 408 " --> pdb=" O GLN N 405 " (cutoff:3.500A) Processing helix chain 'N' and resid 411 through 418 Processing helix chain 'N' and resid 420 through 426 removed outlier: 3.665A pdb=" N ARG N 424 " --> pdb=" O GLN N 420 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 22 removed outlier: 3.572A pdb=" N ILE O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 776 through 777 removed outlier: 6.505A pdb=" N MET A 878 " --> pdb=" O LEU A 907 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU A 909 " --> pdb=" O MET A 878 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL A 880 " --> pdb=" O LEU A 909 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU A 807 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ASP A 881 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE A 809 " --> pdb=" O ASP A 881 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 832 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 992 through 996 removed outlier: 6.607A pdb=" N LEU A1124 " --> pdb=" O LEU A1153 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N SER A1155 " --> pdb=" O LEU A1124 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N LEU A1126 " --> pdb=" O SER A1155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1017 through 1018 Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.509A pdb=" N ARG B 45 " --> pdb=" O ILE K 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.065A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.956A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.006A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB3, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.272A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB5, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.710A pdb=" N LEU L 8 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N THR L 106 " --> pdb=" O LEU L 8 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 35 through 36 Processing sheet with id=AB7, first strand: chain 'L' and resid 71 through 72 Processing sheet with id=AB8, first strand: chain 'L' and resid 169 through 170 removed outlier: 3.840A pdb=" N TYR L 166 " --> pdb=" O TYR L 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 169 through 170 removed outlier: 3.840A pdb=" N TYR L 166 " --> pdb=" O TYR L 169 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR L 297 " --> pdb=" O ILE L 330 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 238 through 241 Processing sheet with id=AC2, first strand: chain 'N' and resid 33 through 36 removed outlier: 3.515A pdb=" N ALA N 23 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE N 35 " --> pdb=" O VAL N 21 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU N 12 " --> pdb=" O LEU N 119 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N SER N 121 " --> pdb=" O LEU N 12 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE N 14 " --> pdb=" O SER N 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 65 through 67 removed outlier: 3.512A pdb=" N ILE N 83 " --> pdb=" O ILE N 39 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 86 through 87 Processing sheet with id=AC5, first strand: chain 'N' and resid 184 through 185 removed outlier: 3.763A pdb=" N VAL N 191 " --> pdb=" O ALA N 177 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 184 through 185 removed outlier: 7.734A pdb=" N ILE N 347 " --> pdb=" O THR N 164 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU N 166 " --> pdb=" O ILE N 347 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ALA N 349 " --> pdb=" O LEU N 166 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU N 168 " --> pdb=" O ALA N 349 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL N 346 " --> pdb=" O ILE N 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 221 through 225 removed outlier: 6.517A pdb=" N LYS N 236 " --> pdb=" O ALA N 222 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS N 224 " --> pdb=" O ASN N 234 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ASN N 234 " --> pdb=" O LYS N 224 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 283 through 286 Processing sheet with id=AC9, first strand: chain 'O' and resid 31 through 37 937 hydrogen bonds defined for protein. 2685 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 382 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 149 basepair parallelities 264 stacking parallelities Total time for adding SS restraints: 9.18 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6882 1.03 - 1.23: 149 1.23 - 1.42: 11248 1.42 - 1.62: 14134 1.62 - 1.81: 153 Bond restraints: 32566 Sorted by residual: bond pdb=" N MET L 1 " pdb=" H2 MET L 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N MET L 1 " pdb=" H3 MET L 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C3' DG J 103 " pdb=" C2' DG J 103 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DT J 7 " pdb=" C2' DT J 7 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 ... (remaining 32561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.20: 51695 15.20 - 30.40: 1 30.40 - 45.60: 0 45.60 - 60.80: 0 60.80 - 76.00: 1 Bond angle restraints: 51697 Sorted by residual: angle pdb=" H1 MET L 1 " pdb=" N MET L 1 " pdb=" H3 MET L 1 " ideal model delta sigma weight residual 109.47 33.47 76.00 3.00e+00 1.11e-01 6.42e+02 angle pdb=" H1 MET L 1 " pdb=" N MET L 1 " pdb=" H2 MET L 1 " ideal model delta sigma weight residual 109.47 130.66 -21.19 3.00e+00 1.11e-01 4.99e+01 angle pdb=" O4' DA J 117 " pdb=" C4' DA J 117 " pdb=" C3' DA J 117 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.24e+01 angle pdb=" N3 DT I 104 " pdb=" C4 DT I 104 " pdb=" O4 DT I 104 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT J 50 " pdb=" C4 DT J 50 " pdb=" O4 DT J 50 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 ... (remaining 51692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.72: 15318 34.72 - 69.44: 1638 69.44 - 104.16: 45 104.16 - 138.88: 1 138.88 - 173.60: 3 Dihedral angle restraints: 17005 sinusoidal: 9914 harmonic: 7091 Sorted by residual: dihedral pdb=" CA ARG K 53 " pdb=" C ARG K 53 " pdb=" N TYR K 54 " pdb=" CA TYR K 54 " ideal model delta harmonic sigma weight residual -180.00 -158.07 -21.93 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual 220.00 46.40 173.60 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 46.94 173.06 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 17002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2618 0.031 - 0.061: 886 0.061 - 0.092: 277 0.092 - 0.122: 240 0.122 - 0.153: 16 Chirality restraints: 4037 Sorted by residual: chirality pdb=" C3' DC I 54 " pdb=" C4' DC I 54 " pdb=" O3' DC I 54 " pdb=" C2' DC I 54 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" C3' DA I 43 " pdb=" C4' DA I 43 " pdb=" O3' DA I 43 " pdb=" C2' DA I 43 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" C3' DC I 66 " pdb=" C4' DC I 66 " pdb=" O3' DC I 66 " pdb=" C2' DC I 66 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 4034 not shown) Planarity restraints: 4366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS N 426 " 0.050 5.00e-02 4.00e+02 7.39e-02 8.73e+00 pdb=" N PRO N 427 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO N 427 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO N 427 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " -0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO D 103 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET N 280 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO N 281 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO N 281 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO N 281 " -0.021 5.00e-02 4.00e+02 ... (remaining 4363 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1292 2.23 - 2.82: 34906 2.82 - 3.41: 56525 3.41 - 4.01: 87798 4.01 - 4.60: 128766 Nonbonded interactions: 309287 Sorted by model distance: nonbonded pdb=" HG1 THR N 175 " pdb=" O LEU N 195 " model vdw 1.636 2.450 nonbonded pdb="HH21 ARG L 37 " pdb=" OD1 ASP L 81 " model vdw 1.639 2.450 nonbonded pdb=" H LEU L 8 " pdb=" O PRO L 102 " model vdw 1.644 2.450 nonbonded pdb="HH21 ARG N 205 " pdb=" OD1 ASN N 254 " model vdw 1.644 2.450 nonbonded pdb=" H LEU N 168 " pdb=" O ILE N 347 " model vdw 1.646 2.450 ... (remaining 309282 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 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 117 or (resid 118 and (name N or \ name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 32 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 56 or (resid 57 through 58 and (na \ me N or name CA or name C or name O or name CB )) or resid 59 through 124)) } ncs_group { reference = chain 'E' selection = (chain 'K' and resid 40 through 134) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.250 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 32.270 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 25669 Z= 0.381 Angle : 0.575 6.348 35989 Z= 0.482 Chirality : 0.041 0.153 4037 Planarity : 0.003 0.074 3523 Dihedral : 22.802 173.597 10398 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.18), residues: 2260 helix: 1.80 (0.16), residues: 1197 sheet: 0.48 (0.39), residues: 186 loop : -0.21 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 299 TYR 0.010 0.001 TYR B 51 PHE 0.020 0.001 PHE A 975 TRP 0.016 0.001 TRP O 31 HIS 0.006 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.38 (25669) covalent geometry : angle 0.57487 / 0.48 (35989) hydrogen bonds : bond 0.17717 / 11.64 ( 1316) hydrogen bonds : angle 6.17789 / 4.50 ( 3429) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 922 TRP cc_start: 0.7337 (t60) cc_final: 0.7073 (t60) REVERT: A 927 PHE cc_start: 0.7663 (t80) cc_final: 0.7461 (t80) REVERT: A 1333 MET cc_start: 0.6419 (pmm) cc_final: 0.5846 (pmm) REVERT: L 1 MET cc_start: 0.3194 (tmm) cc_final: 0.2393 (tmm) REVERT: L 325 MET cc_start: -0.2948 (mmt) cc_final: -0.3167 (mpp) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.9891 time to fit residues: 192.8439 Evaluate side-chains 131 residues out of total 1970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 247 optimal weight: 20.0000 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 ASN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1230 GLN G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.181420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.102159 restraints weight = 106141.346| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 6.98 r_work: 0.2954 rms_B_bonded: 6.26 restraints_weight: 2.0000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25669 Z= 0.175 Angle : 0.541 9.914 35989 Z= 0.317 Chirality : 0.039 0.212 4037 Planarity : 0.003 0.045 3523 Dihedral : 26.792 176.626 5869 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.66 % Allowed : 5.37 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.18), residues: 2260 helix: 1.89 (0.15), residues: 1223 sheet: 0.53 (0.39), residues: 180 loop : -0.25 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 841 TYR 0.012 0.001 TYR A 475 PHE 0.011 0.001 PHE A 975 TRP 0.008 0.001 TRP O 31 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (25669) covalent geometry : angle 0.54138 / 0.32 (35989) hydrogen bonds : bond 0.06393 / 4.19 ( 1316) hydrogen bonds : angle 4.81750 / 3.48 ( 3429) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 922 TRP cc_start: 0.7355 (t60) cc_final: 0.7087 (t60) REVERT: A 1105 MET cc_start: 0.5577 (pmm) cc_final: 0.5371 (pmm) REVERT: L 1 MET cc_start: 0.3273 (tmm) cc_final: 0.2570 (tmm) REVERT: L 325 MET cc_start: -0.2746 (mmt) cc_final: -0.2976 (mpp) outliers start: 13 outliers final: 3 residues processed: 143 average time/residue: 0.9936 time to fit residues: 160.7854 Evaluate side-chains 129 residues out of total 1970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain N residue 174 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 87 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 205 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 chunk 108 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 HIS A1164 ASN G 73 ASN ** N 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.181214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.101050 restraints weight = 106047.301| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 7.67 r_work: 0.2943 rms_B_bonded: 6.71 restraints_weight: 2.0000 r_work: 0.3084 rms_B_bonded: 5.56 restraints_weight: 4.0000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25669 Z= 0.166 Angle : 0.500 6.993 35989 Z= 0.292 Chirality : 0.038 0.202 4037 Planarity : 0.003 0.047 3523 Dihedral : 26.855 175.607 5869 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.97 % Allowed : 6.64 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.18), residues: 2260 helix: 2.02 (0.15), residues: 1224 sheet: 0.07 (0.36), residues: 196 loop : -0.30 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 842 TYR 0.014 0.001 TYR A 475 PHE 0.013 0.001 PHE A 927 TRP 0.011 0.001 TRP O 31 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 (25669) covalent geometry : angle 0.49952 / 0.29 (35989) hydrogen bonds : bond 0.05419 / 3.57 ( 1316) hydrogen bonds : angle 4.29683 / 3.10 ( 3429) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 922 TRP cc_start: 0.7305 (t60) cc_final: 0.6983 (t60) REVERT: A 1040 MET cc_start: 0.6136 (OUTLIER) cc_final: 0.5602 (ttm) REVERT: H 71 GLU cc_start: 0.8326 (pt0) cc_final: 0.8111 (pt0) REVERT: L 1 MET cc_start: 0.3657 (tmm) cc_final: 0.3062 (tmm) REVERT: L 325 MET cc_start: -0.2569 (mmt) cc_final: -0.2791 (mpp) REVERT: N 333 MET cc_start: 0.2278 (OUTLIER) cc_final: 0.2018 (ptm) outliers start: 19 outliers final: 5 residues processed: 141 average time/residue: 0.9949 time to fit residues: 159.4291 Evaluate side-chains 135 residues out of total 1970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1040 MET Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain N residue 174 HIS Chi-restraints excluded: chain N residue 333 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 122 optimal weight: 0.5980 chunk 228 optimal weight: 0.0570 chunk 110 optimal weight: 0.0770 chunk 187 optimal weight: 8.9990 chunk 138 optimal weight: 8.9990 chunk 239 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 148 optimal weight: 20.0000 chunk 252 optimal weight: 30.0000 overall best weight: 2.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.180489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.100198 restraints weight = 104791.088| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 7.23 r_work: 0.2887 rms_B_bonded: 5.83 restraints_weight: 2.0000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25669 Z= 0.239 Angle : 0.562 13.801 35989 Z= 0.316 Chirality : 0.041 0.226 4037 Planarity : 0.004 0.054 3523 Dihedral : 27.047 175.806 5869 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.18 % Allowed : 7.92 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.18), residues: 2260 helix: 1.96 (0.15), residues: 1224 sheet: -0.06 (0.35), residues: 196 loop : -0.32 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 42 TYR 0.015 0.001 TYR A 475 PHE 0.011 0.001 PHE F 61 TRP 0.037 0.001 TRP A 764 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.24 (25669) covalent geometry : angle 0.56240 / 0.32 (35989) hydrogen bonds : bond 0.05675 / 3.76 ( 1316) hydrogen bonds : angle 4.25301 / 3.06 ( 3429) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 797 MET cc_start: 0.2804 (OUTLIER) cc_final: 0.2513 (tpt) REVERT: A 922 TRP cc_start: 0.7363 (t60) cc_final: 0.6984 (t60) REVERT: E 129 ARG cc_start: 0.9252 (OUTLIER) cc_final: 0.8808 (tpt-90) REVERT: K 129 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8644 (tpt-90) REVERT: L 1 MET cc_start: 0.3379 (tmm) cc_final: 0.2630 (tmm) REVERT: L 325 MET cc_start: -0.2676 (mmt) cc_final: -0.2903 (mpp) REVERT: N 333 MET cc_start: 0.2171 (OUTLIER) cc_final: 0.1874 (ptm) outliers start: 23 outliers final: 8 residues processed: 138 average time/residue: 0.9983 time to fit residues: 156.3521 Evaluate side-chains 131 residues out of total 1970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 797 MET Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain N residue 174 HIS Chi-restraints excluded: chain N residue 333 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 129 optimal weight: 0.6980 chunk 146 optimal weight: 50.0000 chunk 168 optimal weight: 0.6980 chunk 155 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 142 optimal weight: 10.9990 chunk 213 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 185 optimal weight: 20.0000 chunk 251 optimal weight: 20.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.183981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.106784 restraints weight = 103352.869| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 5.50 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25669 Z= 0.127 Angle : 0.478 8.448 35989 Z= 0.279 Chirality : 0.037 0.193 4037 Planarity : 0.003 0.034 3523 Dihedral : 26.939 176.215 5869 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.82 % Allowed : 9.15 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.18), residues: 2260 helix: 2.21 (0.15), residues: 1231 sheet: -0.07 (0.36), residues: 196 loop : -0.33 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 71 TYR 0.014 0.001 TYR A 475 PHE 0.011 0.001 PHE F 61 TRP 0.046 0.001 TRP A 764 HIS 0.003 0.000 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 (25669) covalent geometry : angle 0.47751 / 0.28 (35989) hydrogen bonds : bond 0.04792 / 3.15 ( 1316) hydrogen bonds : angle 3.97845 / 2.87 ( 3429) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 797 MET cc_start: 0.2902 (OUTLIER) cc_final: 0.2568 (tpt) REVERT: A 922 TRP cc_start: 0.7493 (t60) cc_final: 0.7069 (t60) REVERT: K 129 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7869 (tpt-90) REVERT: L 1 MET cc_start: 0.3185 (tmm) cc_final: 0.2308 (tmm) REVERT: L 325 MET cc_start: -0.2830 (mmt) cc_final: -0.3064 (mpp) REVERT: N 333 MET cc_start: 0.2012 (OUTLIER) cc_final: 0.1686 (ptm) outliers start: 16 outliers final: 6 residues processed: 136 average time/residue: 1.0323 time to fit residues: 159.6202 Evaluate side-chains 135 residues out of total 1970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 797 MET Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain N residue 174 HIS Chi-restraints excluded: chain N residue 333 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 202 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 221 optimal weight: 30.0000 chunk 78 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 171 optimal weight: 40.0000 chunk 227 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.179736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.097273 restraints weight = 104148.088| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 7.24 r_work: 0.2870 rms_B_bonded: 6.35 restraints_weight: 2.0000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 25669 Z= 0.327 Angle : 0.617 11.191 35989 Z= 0.340 Chirality : 0.044 0.244 4037 Planarity : 0.004 0.046 3523 Dihedral : 27.226 175.887 5869 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.18 % Allowed : 9.71 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.18), residues: 2260 helix: 1.90 (0.15), residues: 1236 sheet: -0.02 (0.36), residues: 188 loop : -0.44 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 42 TYR 0.016 0.001 TYR H 42 PHE 0.012 0.001 PHE D 65 TRP 0.031 0.001 TRP A 764 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.33 (25669) covalent geometry : angle 0.61727 / 0.34 (35989) hydrogen bonds : bond 0.06331 / 4.21 ( 1316) hydrogen bonds : angle 4.22646 / 3.03 ( 3429) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 797 MET cc_start: 0.2940 (OUTLIER) cc_final: 0.2681 (tpt) REVERT: A 922 TRP cc_start: 0.7360 (t60) cc_final: 0.6963 (t60) REVERT: A 1305 MET cc_start: 0.5191 (tmm) cc_final: 0.4954 (mpt) REVERT: C 91 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8229 (tm-30) REVERT: E 129 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8817 (tpt-90) REVERT: F 84 MET cc_start: 0.9429 (mmm) cc_final: 0.9154 (mmm) REVERT: L 1 MET cc_start: 0.3714 (tmm) cc_final: 0.3082 (tmm) REVERT: L 325 MET cc_start: -0.2536 (mmt) cc_final: -0.2761 (mpp) REVERT: N 333 MET cc_start: 0.2178 (OUTLIER) cc_final: 0.1903 (ptm) outliers start: 23 outliers final: 12 residues processed: 132 average time/residue: 1.0332 time to fit residues: 154.5476 Evaluate side-chains 134 residues out of total 1970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 797 MET Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 73 GLU Chi-restraints excluded: chain N residue 174 HIS Chi-restraints excluded: chain N residue 333 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 140 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 171 optimal weight: 30.0000 chunk 141 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 154 optimal weight: 7.9990 chunk 29 optimal weight: 0.2980 chunk 115 optimal weight: 0.6980 chunk 239 optimal weight: 40.0000 chunk 39 optimal weight: 0.0060 chunk 72 optimal weight: 0.6980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 508 HIS ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.184205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.106168 restraints weight = 103731.156| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 5.62 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25669 Z= 0.110 Angle : 0.485 11.048 35989 Z= 0.279 Chirality : 0.037 0.192 4037 Planarity : 0.003 0.034 3523 Dihedral : 27.048 176.384 5869 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.82 % Allowed : 10.12 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.18), residues: 2260 helix: 2.24 (0.15), residues: 1239 sheet: -0.03 (0.36), residues: 188 loop : -0.32 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 842 TYR 0.014 0.001 TYR A 475 PHE 0.010 0.001 PHE F 61 TRP 0.030 0.001 TRP A 764 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.11 (25669) covalent geometry : angle 0.48525 / 0.28 (35989) hydrogen bonds : bond 0.04717 / 3.11 ( 1316) hydrogen bonds : angle 3.86146 / 2.78 ( 3429) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 797 MET cc_start: 0.2952 (OUTLIER) cc_final: 0.2640 (tpt) REVERT: A 922 TRP cc_start: 0.7428 (t60) cc_final: 0.6960 (t60) REVERT: A 1040 MET cc_start: 0.4058 (OUTLIER) cc_final: 0.3789 (ttm) REVERT: A 1305 MET cc_start: 0.5130 (tmm) cc_final: 0.4830 (mpt) REVERT: L 1 MET cc_start: 0.3352 (tmm) cc_final: 0.2491 (tmm) REVERT: L 325 MET cc_start: -0.2732 (mmt) cc_final: -0.2968 (mpp) REVERT: N 333 MET cc_start: 0.1872 (OUTLIER) cc_final: 0.1518 (ptm) outliers start: 16 outliers final: 7 residues processed: 136 average time/residue: 0.9827 time to fit residues: 151.9466 Evaluate side-chains 136 residues out of total 1970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 797 MET Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1040 MET Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 174 HIS Chi-restraints excluded: chain N residue 333 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 107 optimal weight: 0.0020 chunk 206 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 218 optimal weight: 10.0000 chunk 235 optimal weight: 20.0000 chunk 230 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 202 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 overall best weight: 3.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.182693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.105623 restraints weight = 102743.252| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 5.92 r_work: 0.2907 rms_B_bonded: 5.51 restraints_weight: 2.0000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 25669 Z= 0.310 Angle : 0.608 10.237 35989 Z= 0.334 Chirality : 0.043 0.241 4037 Planarity : 0.004 0.050 3523 Dihedral : 27.262 176.085 5869 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.07 % Allowed : 10.22 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.18), residues: 2260 helix: 1.98 (0.15), residues: 1239 sheet: -0.07 (0.36), residues: 188 loop : -0.43 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 842 TYR 0.016 0.001 TYR H 42 PHE 0.011 0.001 PHE F 61 TRP 0.031 0.001 TRP A 764 HIS 0.004 0.001 HIS A 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.31 (25669) covalent geometry : angle 0.60773 / 0.33 (35989) hydrogen bonds : bond 0.06093 / 4.05 ( 1316) hydrogen bonds : angle 4.10576 / 2.94 ( 3429) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 749 MET cc_start: 0.4331 (OUTLIER) cc_final: 0.4014 (ppp) REVERT: A 797 MET cc_start: 0.3174 (OUTLIER) cc_final: 0.2804 (tpt) REVERT: A 922 TRP cc_start: 0.7444 (t60) cc_final: 0.7061 (t60) REVERT: A 932 ILE cc_start: 0.6683 (OUTLIER) cc_final: 0.6325 (mm) REVERT: A 1272 MET cc_start: 0.5957 (OUTLIER) cc_final: 0.5328 (tmm) REVERT: A 1305 MET cc_start: 0.5312 (tmm) cc_final: 0.4966 (mtm) REVERT: E 129 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8768 (tpt-90) REVERT: F 84 MET cc_start: 0.9406 (mmm) cc_final: 0.9124 (mmm) REVERT: L 1 MET cc_start: 0.3147 (tmm) cc_final: 0.2232 (tmm) REVERT: L 82 MET cc_start: 0.0070 (tpt) cc_final: -0.0768 (ttt) REVERT: L 325 MET cc_start: -0.3013 (mmt) cc_final: -0.3268 (mpp) REVERT: N 333 MET cc_start: 0.1963 (OUTLIER) cc_final: 0.1612 (ptm) outliers start: 21 outliers final: 9 residues processed: 131 average time/residue: 0.9807 time to fit residues: 145.9354 Evaluate side-chains 132 residues out of total 1970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 797 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1272 MET Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain N residue 174 HIS Chi-restraints excluded: chain N residue 333 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 187 optimal weight: 20.0000 chunk 152 optimal weight: 7.9990 chunk 92 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 228 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 224 optimal weight: 50.0000 chunk 189 optimal weight: 20.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.183983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.105822 restraints weight = 102999.323| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 6.10 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25669 Z= 0.146 Angle : 0.511 10.453 35989 Z= 0.290 Chirality : 0.038 0.213 4037 Planarity : 0.003 0.033 3523 Dihedral : 27.162 176.334 5869 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.92 % Allowed : 10.48 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.18), residues: 2260 helix: 2.23 (0.15), residues: 1234 sheet: -0.07 (0.36), residues: 188 loop : -0.36 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 842 TYR 0.014 0.001 TYR A 475 PHE 0.011 0.001 PHE F 61 TRP 0.045 0.002 TRP L 86 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (25669) covalent geometry : angle 0.51057 / 0.29 (35989) hydrogen bonds : bond 0.04784 / 3.15 ( 1316) hydrogen bonds : angle 3.86868 / 2.78 ( 3429) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 749 MET cc_start: 0.4375 (OUTLIER) cc_final: 0.4037 (ppp) REVERT: A 797 MET cc_start: 0.3076 (OUTLIER) cc_final: 0.2781 (tpt) REVERT: A 922 TRP cc_start: 0.7409 (t60) cc_final: 0.6954 (t60) REVERT: A 1305 MET cc_start: 0.4965 (tmm) cc_final: 0.4715 (mtm) REVERT: L 1 MET cc_start: 0.3574 (tmm) cc_final: 0.2812 (tmm) REVERT: L 82 MET cc_start: 0.0615 (tpt) cc_final: 0.0260 (ttt) REVERT: L 325 MET cc_start: -0.2688 (mmt) cc_final: -0.2936 (mpp) REVERT: N 333 MET cc_start: 0.1865 (OUTLIER) cc_final: 0.1526 (ptm) outliers start: 18 outliers final: 10 residues processed: 131 average time/residue: 0.9906 time to fit residues: 147.5455 Evaluate side-chains 134 residues out of total 1970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 797 MET Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain N residue 174 HIS Chi-restraints excluded: chain N residue 280 MET Chi-restraints excluded: chain N residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 242 optimal weight: 5.9990 chunk 102 optimal weight: 0.1980 chunk 208 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 249 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 250 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 247 optimal weight: 5.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.180559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.101085 restraints weight = 105286.460| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 6.53 r_work: 0.2901 rms_B_bonded: 6.01 restraints_weight: 2.0000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25669 Z= 0.202 Angle : 0.536 10.346 35989 Z= 0.300 Chirality : 0.039 0.221 4037 Planarity : 0.003 0.039 3523 Dihedral : 27.154 176.570 5869 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.77 % Allowed : 10.78 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.18), residues: 2260 helix: 2.22 (0.15), residues: 1227 sheet: -0.06 (0.36), residues: 188 loop : -0.35 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 842 TYR 0.014 0.001 TYR K 54 PHE 0.011 0.001 PHE F 61 TRP 0.054 0.002 TRP L 86 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 (25669) covalent geometry : angle 0.53563 / 0.30 (35989) hydrogen bonds : bond 0.05112 / 3.38 ( 1316) hydrogen bonds : angle 3.88887 / 2.79 ( 3429) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 749 MET cc_start: 0.4243 (OUTLIER) cc_final: 0.3860 (ppp) REVERT: A 797 MET cc_start: 0.3096 (OUTLIER) cc_final: 0.2763 (tpt) REVERT: A 922 TRP cc_start: 0.7358 (t60) cc_final: 0.6934 (t60) REVERT: A 932 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6312 (mm) REVERT: A 1305 MET cc_start: 0.5341 (tmm) cc_final: 0.4991 (mtm) REVERT: L 1 MET cc_start: 0.3312 (tmm) cc_final: 0.2466 (tmm) REVERT: L 82 MET cc_start: 0.0571 (tpt) cc_final: 0.0158 (ttt) REVERT: L 325 MET cc_start: -0.2907 (mmt) cc_final: -0.3161 (mpp) REVERT: N 333 MET cc_start: 0.1916 (OUTLIER) cc_final: 0.1565 (ptm) outliers start: 15 outliers final: 10 residues processed: 128 average time/residue: 0.9904 time to fit residues: 143.8811 Evaluate side-chains 133 residues out of total 1970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 797 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1050 TYR Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain N residue 174 HIS Chi-restraints excluded: chain N residue 280 MET Chi-restraints excluded: chain N residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 165 optimal weight: 1.9990 chunk 201 optimal weight: 7.9990 chunk 236 optimal weight: 30.0000 chunk 110 optimal weight: 0.5980 chunk 190 optimal weight: 5.9990 chunk 112 optimal weight: 0.0670 chunk 185 optimal weight: 30.0000 chunk 205 optimal weight: 2.9990 chunk 144 optimal weight: 20.0000 chunk 87 optimal weight: 0.7980 chunk 103 optimal weight: 0.4980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.181359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.103141 restraints weight = 105588.179| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 5.79 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25669 Z= 0.118 Angle : 0.497 11.252 35989 Z= 0.282 Chirality : 0.037 0.203 4037 Planarity : 0.003 0.033 3523 Dihedral : 27.107 176.714 5869 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.72 % Allowed : 10.78 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.18), residues: 2260 helix: 2.35 (0.15), residues: 1227 sheet: -0.07 (0.36), residues: 188 loop : -0.30 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 842 TYR 0.013 0.001 TYR A 475 PHE 0.008 0.001 PHE F 61 TRP 0.041 0.001 TRP L 86 HIS 0.003 0.001 HIS A 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.12 (25669) covalent geometry : angle 0.49742 / 0.28 (35989) hydrogen bonds : bond 0.04611 / 3.03 ( 1316) hydrogen bonds : angle 3.75998 / 2.70 ( 3429) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15445.11 seconds wall clock time: 261 minutes 35.32 seconds (15695.32 seconds total)