Starting phenix.real_space_refine on Wed Aug 7 07:35:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlq_41371/08_2024/8tlq_41371.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlq_41371/08_2024/8tlq_41371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlq_41371/08_2024/8tlq_41371.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlq_41371/08_2024/8tlq_41371.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlq_41371/08_2024/8tlq_41371.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlq_41371/08_2024/8tlq_41371.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 P 29 5.49 5 S 82 5.16 5 C 12496 2.51 5 N 3256 2.21 5 O 3351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1356": "OD1" <-> "OD2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E ASP 94": "OD1" <-> "OD2" Residue "F GLU 400": "OE1" <-> "OE2" Residue "F GLU 481": "OE1" <-> "OE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 19219 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 9541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1283, 9541 Classifications: {'peptide': 1283} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 59, 'TRANS': 1223} Chain breaks: 9 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 934 Unresolved non-hydrogen angles: 1190 Unresolved non-hydrogen dihedrals: 708 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 18, 'ASP:plan': 50, 'PHE:plan': 3, 'GLU:plan': 58, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 537 Chain: "D" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1399 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain breaks: 5 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 11, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "E" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1705 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 15, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 146 Chain: "F" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3260 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 25, 'TRANS': 431} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 410 Unresolved non-hydrogen angles: 528 Unresolved non-hydrogen dihedrals: 324 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 24, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 260 Chain: "G" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 882 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1818 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain breaks: 1 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 1, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 8, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 135 Chain: "P" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 212 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 322 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 69 Unusual residues: {' CA': 1, 'DCP': 1, 'SF4': 1} Classifications: {'undetermined': 3, 'water': 32} Link IDs: {None: 34} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9297 SG CYS A1473 40.113 60.169 92.457 1.00 56.04 S ATOM 9119 SG CYS A1449 43.892 54.936 92.487 1.00 53.21 S ATOM 9257 SG CYS A1468 37.481 54.051 94.304 1.00 49.71 S ATOM 9097 SG CYS A1446 38.578 55.227 88.079 1.00 52.81 S Time building chain proxies: 10.92, per 1000 atoms: 0.57 Number of scatterers: 19219 At special positions: 0 Unit cell: (87.658, 143.246, 180.661, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 82 16.00 P 29 15.00 O 3351 8.00 N 3256 7.00 C 12496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.20 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1603 " pdb="FE3 SF4 A1603 " - pdb=" SG CYS A1468 " pdb="FE2 SF4 A1603 " - pdb=" SG CYS A1449 " pdb="FE4 SF4 A1603 " - pdb=" SG CYS A1446 " pdb="FE1 SF4 A1603 " - pdb=" SG CYS A1473 " Number of angles added : 12 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4828 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 21 sheets defined 40.2% alpha, 14.0% beta 10 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 6.57 Creating SS restraints... Processing helix chain 'A' and resid 95 through 117 removed outlier: 3.521A pdb=" N GLN A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 194 through 203 Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 235 through 246 Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 306 through 322 removed outlier: 4.215A pdb=" N ARG A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 531 through 541 removed outlier: 4.146A pdb=" N ASN A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.527A pdb=" N ASP A 557 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 623 Processing helix chain 'A' and resid 725 through 735 Processing helix chain 'A' and resid 744 through 760 Processing helix chain 'A' and resid 773 through 784 Processing helix chain 'A' and resid 788 through 794 removed outlier: 3.570A pdb=" N GLU A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 813 Processing helix chain 'A' and resid 825 through 834 Processing helix chain 'A' and resid 840 through 848 Processing helix chain 'A' and resid 857 through 865 Processing helix chain 'A' and resid 870 through 896 removed outlier: 3.569A pdb=" N LEU A 874 " --> pdb=" O SER A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 909 Processing helix chain 'A' and resid 911 through 917 removed outlier: 3.758A pdb=" N VAL A 915 " --> pdb=" O ASP A 911 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR A 916 " --> pdb=" O PHE A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 933 removed outlier: 3.888A pdb=" N LYS A 923 " --> pdb=" O GLY A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 949 Processing helix chain 'A' and resid 978 through 988 Processing helix chain 'A' and resid 990 through 992 No H-bonds generated for 'chain 'A' and resid 990 through 992' Processing helix chain 'A' and resid 1018 through 1023 Processing helix chain 'A' and resid 1044 through 1067 Processing helix chain 'A' and resid 1071 through 1095 Processing helix chain 'A' and resid 1106 through 1131 removed outlier: 3.593A pdb=" N ASP A1131 " --> pdb=" O ILE A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1173 removed outlier: 4.259A pdb=" N SER A1160 " --> pdb=" O ILE A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1241 Processing helix chain 'A' and resid 1243 through 1261 removed outlier: 3.651A pdb=" N ILE A1247 " --> pdb=" O ASP A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1299 removed outlier: 3.635A pdb=" N VAL A1290 " --> pdb=" O PRO A1286 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A1291 " --> pdb=" O ALA A1287 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A1298 " --> pdb=" O ARG A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1327 removed outlier: 3.913A pdb=" N ARG A1326 " --> pdb=" O LEU A1322 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS A1327 " --> pdb=" O LEU A1323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1322 through 1327' Processing helix chain 'A' and resid 1329 through 1336 Processing helix chain 'A' and resid 1342 through 1360 removed outlier: 3.651A pdb=" N LEU A1351 " --> pdb=" O ILE A1347 " (cutoff:3.500A) Proline residue: A1353 - end of helix Processing helix chain 'A' and resid 1365 through 1373 removed outlier: 4.386A pdb=" N TRP A1369 " --> pdb=" O ASN A1365 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A1373 " --> pdb=" O TRP A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1455 removed outlier: 3.877A pdb=" N LEU A1426 " --> pdb=" O SER A1422 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG A1452 " --> pdb=" O THR A1448 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N TYR A1453 " --> pdb=" O CYS A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1468 Processing helix chain 'A' and resid 1473 through 1488 removed outlier: 3.791A pdb=" N TYR A1477 " --> pdb=" O CYS A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1502 removed outlier: 3.585A pdb=" N VAL A1492 " --> pdb=" O ASP A1488 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 24 removed outlier: 3.800A pdb=" N VAL D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 68 removed outlier: 3.525A pdb=" N LYS D 68 " --> pdb=" O ASP D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.610A pdb=" N VAL D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS D 130 " --> pdb=" O MET D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 243 removed outlier: 4.124A pdb=" N SER D 243 " --> pdb=" O ILE D 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 24 removed outlier: 3.593A pdb=" N LYS E 7 " --> pdb=" O ARG E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 68 removed outlier: 3.522A pdb=" N LYS E 68 " --> pdb=" O ASP E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 130 removed outlier: 3.832A pdb=" N LYS E 130 " --> pdb=" O MET E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 159 removed outlier: 3.794A pdb=" N ASP E 157 " --> pdb=" O HIS E 154 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG E 158 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN E 159 " --> pdb=" O LEU E 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 154 through 159' Processing helix chain 'E' and resid 164 through 175 removed outlier: 3.590A pdb=" N SER E 175 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 0 through 9 Processing helix chain 'F' and resid 53 through 76 Processing helix chain 'F' and resid 92 through 96 removed outlier: 4.118A pdb=" N ILE F 96 " --> pdb=" O VAL F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 125 Processing helix chain 'F' and resid 131 through 137 Processing helix chain 'F' and resid 159 through 164 Processing helix chain 'F' and resid 227 through 241 Processing helix chain 'F' and resid 247 through 253 removed outlier: 3.631A pdb=" N LEU F 253 " --> pdb=" O ASP F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 291 removed outlier: 3.602A pdb=" N LEU F 276 " --> pdb=" O ASN F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 325 Processing helix chain 'F' and resid 357 through 365 Processing helix chain 'F' and resid 391 through 405 Processing helix chain 'F' and resid 411 through 416 Processing helix chain 'G' and resid 4 through 15 Processing helix chain 'G' and resid 22 through 30 Processing helix chain 'G' and resid 32 through 45 removed outlier: 3.751A pdb=" N LYS G 45 " --> pdb=" O PHE G 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 154 removed outlier: 3.535A pdb=" N PHE B 136 " --> pdb=" O ARG B 132 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 191 Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 229 through 239 removed outlier: 4.273A pdb=" N VAL B 233 " --> pdb=" O PRO B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 899 removed outlier: 4.398A pdb=" N GLY B 899 " --> pdb=" O ALA B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 921 Processing helix chain 'B' and resid 923 through 941 Processing helix chain 'B' and resid 950 through 961 Processing helix chain 'B' and resid 962 through 967 removed outlier: 4.411A pdb=" N ASN B 967 " --> pdb=" O ILE B 963 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213 removed outlier: 6.117A pdb=" N LEU A 27 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ALA A 64 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLN A 70 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ILE A 268 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A 72 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE A 270 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N HIS A 74 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 189 removed outlier: 7.362A pdb=" N ILE A 938 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE A 146 " --> pdb=" O ILE A 938 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 177 through 179 removed outlier: 5.963A pdb=" N ALA D 143 " --> pdb=" O TYR A 523 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR D 140 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE D 79 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU D 142 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE D 77 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL D 144 " --> pdb=" O PHE D 75 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE D 75 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASN D 146 " --> pdb=" O TYR D 73 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN D 81 " --> pdb=" O CYS D 87 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N CYS D 87 " --> pdb=" O ASN D 81 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN D 214 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 563 through 565 removed outlier: 4.274A pdb=" N TYR A 563 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 584 through 585 Processing sheet with id=AA6, first strand: chain 'E' and resid 177 through 179 removed outlier: 5.861A pdb=" N ALA E 143 " --> pdb=" O TYR A 606 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN E 214 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 739 through 742 removed outlier: 8.152A pdb=" N MET A 740 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 714 " --> pdb=" O MET A 740 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N TYR A 742 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE A 716 " --> pdb=" O TYR A 742 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N SER A 692 " --> pdb=" O VAL A 717 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N HIS A 675 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A 694 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLU A 673 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TRP A 696 " --> pdb=" O THR A 671 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR A 671 " --> pdb=" O TRP A 696 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU A 670 " --> pdb=" O SER A 765 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 965 through 967 removed outlier: 3.611A pdb=" N ALA A 965 " --> pdb=" O LEU A1190 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A1190 " --> pdb=" O ALA A 965 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP A 975 " --> pdb=" O LYS A1180 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A1180 " --> pdb=" O ASP A 975 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1138 through 1141 removed outlier: 6.239A pdb=" N VAL A1138 " --> pdb=" O TYR A1149 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR A1149 " --> pdb=" O VAL A1138 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR A1140 " --> pdb=" O PHE A1147 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR A1185 " --> pdb=" O TYR A1201 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N TYR A1201 " --> pdb=" O TYR A1185 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ARG A1195 " --> pdb=" O ILE A1191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 994 through 997 removed outlier: 6.811A pdb=" N MET A 994 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA A1037 " --> pdb=" O MET A 994 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 996 " --> pdb=" O VAL A1035 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1006 through 1008 removed outlier: 3.606A pdb=" N ASN A1006 " --> pdb=" O PHE A1013 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A1013 " --> pdb=" O ASN A1006 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A1011 " --> pdb=" O LEU A1008 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1270 through 1274 removed outlier: 4.305A pdb=" N LYS A1272 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU A1308 " --> pdb=" O VAL A1274 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 32 through 33 Processing sheet with id=AB5, first strand: chain 'E' and resid 32 through 34 Processing sheet with id=AB6, first strand: chain 'F' and resid 23 through 24 removed outlier: 5.934A pdb=" N ARG F 23 " --> pdb=" O LYS G 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 88 through 89 removed outlier: 8.529A pdb=" N PHE F 185 " --> pdb=" O ARG F 154 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU F 156 " --> pdb=" O PHE F 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 88 through 89 removed outlier: 3.667A pdb=" N GLY F 106 " --> pdb=" O VAL F 173 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 113 through 114 Processing sheet with id=AC1, first strand: chain 'F' and resid 336 through 338 removed outlier: 3.552A pdb=" N ASN F 337 " --> pdb=" O VAL F 296 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER F 295 " --> pdb=" O GLY F 255 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS F 213 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LEU F 258 " --> pdb=" O LYS F 213 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA F 215 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE G 57 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE G 85 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N CYS G 59 " --> pdb=" O CYS G 83 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N CYS G 83 " --> pdb=" O CYS G 59 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL G 20 " --> pdb=" O PHE G 88 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 343 through 347 removed outlier: 3.526A pdb=" N TYR F 343 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASP F 351 " --> pdb=" O VAL F 435 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ILE F 437 " --> pdb=" O ASP F 351 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU F 353 " --> pdb=" O ILE F 437 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ALA F 439 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL F 355 " --> pdb=" O ALA F 439 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N GLN F 441 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN F 440 " --> pdb=" O VAL F 461 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY F 445 " --> pdb=" O SER F 460 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 194 through 196 removed outlier: 6.475A pdb=" N ILE B 171 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 210 " --> pdb=" O VAL B 227 " (cutoff:3.500A) 858 hydrogen bonds defined for protein. 2478 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 9.11 Time building geometry restraints manager: 8.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 7977 1.40 - 1.59: 11515 1.59 - 1.77: 54 1.77 - 1.96: 107 1.96 - 2.14: 12 Bond restraints: 19665 Sorted by residual: bond pdb=" S1 SF4 A1603 " pdb="FE4 SF4 A1603 " ideal model delta sigma weight residual 2.280 2.104 0.176 3.00e-02 1.11e+03 3.45e+01 bond pdb=" S1 SF4 A1603 " pdb="FE3 SF4 A1603 " ideal model delta sigma weight residual 2.280 2.124 0.156 3.00e-02 1.11e+03 2.69e+01 bond pdb=" S3 SF4 A1603 " pdb="FE2 SF4 A1603 " ideal model delta sigma weight residual 2.280 2.125 0.155 3.00e-02 1.11e+03 2.68e+01 bond pdb=" S2 SF4 A1603 " pdb="FE4 SF4 A1603 " ideal model delta sigma weight residual 2.280 2.125 0.155 3.00e-02 1.11e+03 2.68e+01 bond pdb=" S4 SF4 A1603 " pdb="FE2 SF4 A1603 " ideal model delta sigma weight residual 2.280 2.125 0.155 3.00e-02 1.11e+03 2.67e+01 ... (remaining 19660 not shown) Histogram of bond angle deviations from ideal: 89.39 - 99.48: 24 99.48 - 109.56: 1991 109.56 - 119.65: 14797 119.65 - 129.74: 9907 129.74 - 139.82: 135 Bond angle restraints: 26854 Sorted by residual: angle pdb="FE3 SF4 A1603 " pdb=" S1 SF4 A1603 " pdb="FE4 SF4 A1603 " ideal model delta sigma weight residual 73.70 90.62 -16.92 1.50e+00 4.44e-01 1.27e+02 angle pdb="FE2 SF4 A1603 " pdb=" S1 SF4 A1603 " pdb="FE4 SF4 A1603 " ideal model delta sigma weight residual 73.70 90.49 -16.79 1.50e+00 4.44e-01 1.25e+02 angle pdb="FE1 SF4 A1603 " pdb=" S2 SF4 A1603 " pdb="FE4 SF4 A1603 " ideal model delta sigma weight residual 73.70 90.43 -16.73 1.50e+00 4.44e-01 1.24e+02 angle pdb="FE1 SF4 A1603 " pdb=" S3 SF4 A1603 " pdb="FE4 SF4 A1603 " ideal model delta sigma weight residual 73.70 90.39 -16.69 1.50e+00 4.44e-01 1.24e+02 angle pdb="FE1 SF4 A1603 " pdb=" S4 SF4 A1603 " pdb="FE3 SF4 A1603 " ideal model delta sigma weight residual 73.70 90.34 -16.64 1.50e+00 4.44e-01 1.23e+02 ... (remaining 26849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 9999 17.80 - 35.61: 1127 35.61 - 53.41: 399 53.41 - 71.21: 67 71.21 - 89.02: 13 Dihedral angle restraints: 11605 sinusoidal: 4185 harmonic: 7420 Sorted by residual: dihedral pdb=" CG ARG A1324 " pdb=" CD ARG A1324 " pdb=" NE ARG A1324 " pdb=" CZ ARG A1324 " ideal model delta sinusoidal sigma weight residual 180.00 -135.95 -44.05 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CB GLU E 6 " pdb=" CG GLU E 6 " pdb=" CD GLU E 6 " pdb=" OE1 GLU E 6 " ideal model delta sinusoidal sigma weight residual 0.00 87.23 -87.23 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA HIS F 316 " pdb=" C HIS F 316 " pdb=" N LYS F 317 " pdb=" CA LYS F 317 " ideal model delta harmonic sigma weight residual 180.00 164.39 15.61 0 5.00e+00 4.00e-02 9.75e+00 ... (remaining 11602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.047: 3137 4.047 - 8.095: 0 8.095 - 12.142: 0 12.142 - 16.190: 0 16.190 - 20.237: 4 Chirality restraints: 3141 Sorted by residual: chirality pdb="FE3 SF4 A1603 " pdb=" S1 SF4 A1603 " pdb=" S2 SF4 A1603 " pdb=" S4 SF4 A1603 " both_signs ideal model delta sigma weight residual False -10.55 9.68 -20.24 2.00e-01 2.50e+01 1.02e+04 chirality pdb="FE1 SF4 A1603 " pdb=" S2 SF4 A1603 " pdb=" S3 SF4 A1603 " pdb=" S4 SF4 A1603 " both_signs ideal model delta sigma weight residual False -10.55 9.61 -20.16 2.00e-01 2.50e+01 1.02e+04 chirality pdb="FE2 SF4 A1603 " pdb=" S1 SF4 A1603 " pdb=" S3 SF4 A1603 " pdb=" S4 SF4 A1603 " both_signs ideal model delta sigma weight residual False 10.55 -9.60 20.15 2.00e-01 2.50e+01 1.02e+04 ... (remaining 3138 not shown) Planarity restraints: 3258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 28 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO D 29 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 29 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 29 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 922 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C ASN B 922 " 0.028 2.00e-02 2.50e+03 pdb=" O ASN B 922 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG B 923 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1352 " -0.026 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO A1353 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A1353 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1353 " -0.021 5.00e-02 4.00e+02 ... (remaining 3255 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4072 2.78 - 3.31: 17544 3.31 - 3.84: 31863 3.84 - 4.37: 34104 4.37 - 4.90: 61923 Nonbonded interactions: 149506 Sorted by model distance: nonbonded pdb=" OH TYR A 613 " pdb=" OD1 ASP E 136 " model vdw 2.253 3.040 nonbonded pdb=" OD2 ASP A1144 " pdb="CA CA A1601 " model vdw 2.307 2.510 nonbonded pdb=" OH TYR B 130 " pdb=" OE1 GLU B 138 " model vdw 2.331 3.040 nonbonded pdb="CA CA A1601 " pdb=" O2G DCP A1602 " model vdw 2.343 2.510 nonbonded pdb=" O PHE A 976 " pdb="CA CA A1601 " model vdw 2.348 2.510 ... (remaining 149501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.650 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 61.530 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.080 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 74.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 0.176 19665 Z= 0.229 Angle : 0.635 16.920 26854 Z= 0.384 Chirality : 0.720 20.237 3141 Planarity : 0.003 0.062 3258 Dihedral : 17.379 89.016 6777 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.13 % Allowed : 24.43 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.18), residues: 2468 helix: 2.54 (0.17), residues: 933 sheet: 0.45 (0.30), residues: 324 loop : -0.78 (0.18), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 103 HIS 0.002 0.000 HIS A 669 PHE 0.009 0.001 PHE A 39 TYR 0.018 0.001 TYR B 973 ARG 0.003 0.000 ARG A 884 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 223 time to evaluate : 2.155 Fit side-chains REVERT: G 12 LYS cc_start: 0.8567 (tptm) cc_final: 0.8063 (tppt) outliers start: 2 outliers final: 0 residues processed: 224 average time/residue: 0.2623 time to fit residues: 98.3623 Evaluate side-chains 217 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 211 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 103 GLN ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 ASN D 214 GLN E 99 GLN F 117 ASN F 316 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.274 19665 Z= 0.614 Angle : 1.309 51.152 26854 Z= 0.829 Chirality : 0.226 6.434 3141 Planarity : 0.005 0.063 3258 Dihedral : 10.148 83.473 2974 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.24 % Favored : 93.72 % Rotamer: Outliers : 3.80 % Allowed : 21.90 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.17), residues: 2468 helix: 1.83 (0.17), residues: 936 sheet: -0.24 (0.29), residues: 335 loop : -0.89 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 604 HIS 0.008 0.002 HIS A 74 PHE 0.028 0.002 PHE F 345 TYR 0.021 0.002 TYR D 16 ARG 0.006 0.001 ARG D 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 213 time to evaluate : 2.246 Fit side-chains REVERT: A 760 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7820 (m-30) REVERT: E 184 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7488 (tt0) REVERT: G 65 ILE cc_start: 0.9227 (mm) cc_final: 0.8873 (mt) REVERT: B 913 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8433 (ttmm) outliers start: 60 outliers final: 35 residues processed: 259 average time/residue: 0.2670 time to fit residues: 113.8011 Evaluate side-chains 233 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 196 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1499 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 126 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 189 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 62 optimal weight: 0.2980 chunk 228 optimal weight: 7.9990 chunk 246 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 226 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1082 GLN D 214 GLN E 214 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.250 19665 Z= 0.348 Angle : 1.209 50.422 26854 Z= 0.783 Chirality : 0.230 6.356 3141 Planarity : 0.003 0.051 3258 Dihedral : 9.869 88.697 2974 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.66 % Allowed : 23.23 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2468 helix: 2.27 (0.17), residues: 933 sheet: -0.32 (0.29), residues: 330 loop : -0.85 (0.18), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 103 HIS 0.018 0.001 HIS F 316 PHE 0.016 0.001 PHE E 215 TYR 0.019 0.001 TYR A 353 ARG 0.004 0.000 ARG B 936 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 217 time to evaluate : 2.294 Fit side-chains REVERT: A 1050 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8633 (mm) REVERT: E 27 TYR cc_start: 0.8792 (m-80) cc_final: 0.8540 (m-10) REVERT: F 399 MET cc_start: 0.8530 (mmt) cc_final: 0.7609 (mtt) REVERT: G 65 ILE cc_start: 0.9243 (mm) cc_final: 0.8911 (mt) outliers start: 42 outliers final: 20 residues processed: 249 average time/residue: 0.2762 time to fit residues: 113.2171 Evaluate side-chains 224 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 203 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 245 ASN Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain B residue 226 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 225 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 229 optimal weight: 7.9990 chunk 242 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 chunk 217 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 ASN ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 HIS G 53 ASN B 948 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.247 19665 Z= 0.826 Angle : 1.385 50.910 26854 Z= 0.863 Chirality : 0.232 6.434 3141 Planarity : 0.006 0.064 3258 Dihedral : 10.889 83.989 2974 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.62 % Favored : 92.30 % Rotamer: Outliers : 5.95 % Allowed : 22.66 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.17), residues: 2468 helix: 1.04 (0.17), residues: 942 sheet: -0.99 (0.28), residues: 318 loop : -1.35 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 103 HIS 0.009 0.002 HIS A 822 PHE 0.036 0.003 PHE D 40 TYR 0.028 0.003 TYR D 16 ARG 0.006 0.001 ARG D 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 187 time to evaluate : 2.281 Fit side-chains revert: symmetry clash REVERT: A 182 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.5645 (m-10) REVERT: A 760 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.7944 (m-30) REVERT: A 1050 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8808 (mm) REVERT: F 399 MET cc_start: 0.8844 (mmt) cc_final: 0.8014 (mtt) REVERT: G 65 ILE cc_start: 0.9231 (mm) cc_final: 0.8956 (mt) outliers start: 94 outliers final: 70 residues processed: 268 average time/residue: 0.2587 time to fit residues: 114.1709 Evaluate side-chains 249 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 176 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1156 ILE Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1260 ILE Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1296 ILE Chi-restraints excluded: chain A residue 1303 GLU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1489 ASN Chi-restraints excluded: chain A residue 1499 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain F residue 53 TYR Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 202 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 217 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 19665 Z= 0.364 Angle : 1.224 50.513 26854 Z= 0.790 Chirality : 0.230 6.350 3141 Planarity : 0.004 0.051 3258 Dihedral : 10.255 79.011 2974 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.42 % Allowed : 24.68 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.17), residues: 2468 helix: 1.70 (0.17), residues: 949 sheet: -0.92 (0.28), residues: 327 loop : -1.15 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 103 HIS 0.005 0.001 HIS B 948 PHE 0.015 0.001 PHE E 215 TYR 0.018 0.001 TYR D 34 ARG 0.005 0.000 ARG B 936 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 199 time to evaluate : 2.326 Fit side-chains REVERT: D 30 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8214 (pt0) REVERT: D 90 LYS cc_start: 0.8534 (ttpt) cc_final: 0.8182 (tttm) REVERT: E 27 TYR cc_start: 0.8964 (m-80) cc_final: 0.8702 (m-10) REVERT: F 315 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8595 (m-80) REVERT: F 316 HIS cc_start: 0.8522 (OUTLIER) cc_final: 0.8242 (m-70) REVERT: F 399 MET cc_start: 0.8785 (mmt) cc_final: 0.8061 (mtt) REVERT: G 65 ILE cc_start: 0.9236 (mm) cc_final: 0.8918 (mt) REVERT: B 238 GLU cc_start: 0.8011 (tp30) cc_final: 0.7602 (tm-30) outliers start: 54 outliers final: 39 residues processed: 247 average time/residue: 0.2599 time to fit residues: 105.9759 Evaluate side-chains 230 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 188 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1303 GLU Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1489 ASN Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain F residue 53 TYR Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 245 ASN Chi-restraints excluded: chain F residue 315 PHE Chi-restraints excluded: chain F residue 316 HIS Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 81 optimal weight: 4.9990 chunk 218 optimal weight: 0.0270 chunk 47 optimal weight: 8.9990 chunk 142 optimal weight: 20.0000 chunk 59 optimal weight: 0.4980 chunk 242 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 GLN E 2 ASN G 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.246 19665 Z= 0.349 Angle : 1.212 50.490 26854 Z= 0.784 Chirality : 0.229 6.326 3141 Planarity : 0.003 0.048 3258 Dihedral : 10.001 74.066 2974 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.16 % Allowed : 25.51 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.17), residues: 2468 helix: 1.97 (0.17), residues: 951 sheet: -0.90 (0.28), residues: 330 loop : -1.07 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 103 HIS 0.003 0.001 HIS D 51 PHE 0.014 0.001 PHE E 215 TYR 0.019 0.001 TYR A 353 ARG 0.004 0.000 ARG B 936 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 209 time to evaluate : 2.105 Fit side-chains REVERT: A 1050 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8615 (mm) REVERT: A 1082 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8714 (tm-30) REVERT: D 30 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8178 (pt0) REVERT: E 27 TYR cc_start: 0.8972 (m-80) cc_final: 0.8692 (m-80) REVERT: F 103 TRP cc_start: 0.8802 (p-90) cc_final: 0.8534 (p-90) REVERT: F 316 HIS cc_start: 0.8469 (OUTLIER) cc_final: 0.8192 (m-70) REVERT: F 399 MET cc_start: 0.8701 (mmt) cc_final: 0.8047 (mtt) REVERT: G 65 ILE cc_start: 0.9237 (mm) cc_final: 0.8927 (mt) outliers start: 50 outliers final: 34 residues processed: 252 average time/residue: 0.2744 time to fit residues: 114.1718 Evaluate side-chains 232 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 194 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1082 GLN Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1260 ILE Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 245 ASN Chi-restraints excluded: chain F residue 316 HIS Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 234 optimal weight: 0.0570 chunk 27 optimal weight: 7.9990 chunk 138 optimal weight: 0.9980 chunk 177 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 241 optimal weight: 0.0770 chunk 151 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.245 19665 Z= 0.337 Angle : 1.208 50.465 26854 Z= 0.783 Chirality : 0.229 6.328 3141 Planarity : 0.003 0.049 3258 Dihedral : 9.922 73.069 2974 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.16 % Allowed : 25.25 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.17), residues: 2468 helix: 2.08 (0.17), residues: 949 sheet: -0.90 (0.28), residues: 332 loop : -1.02 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 103 HIS 0.004 0.000 HIS D 51 PHE 0.021 0.001 PHE A 741 TYR 0.018 0.001 TYR D 34 ARG 0.005 0.000 ARG B 936 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 199 time to evaluate : 2.185 Fit side-chains REVERT: A 1050 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8598 (mm) REVERT: D 30 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8136 (pt0) REVERT: E 27 TYR cc_start: 0.8938 (m-80) cc_final: 0.8689 (m-10) REVERT: F 103 TRP cc_start: 0.8773 (p-90) cc_final: 0.8481 (p-90) REVERT: F 298 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8670 (mm) REVERT: F 316 HIS cc_start: 0.8432 (OUTLIER) cc_final: 0.7825 (m90) REVERT: F 399 MET cc_start: 0.8697 (mmt) cc_final: 0.7830 (mtt) REVERT: F 403 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7231 (mpp) REVERT: G 65 ILE cc_start: 0.9236 (mm) cc_final: 0.8917 (mt) outliers start: 50 outliers final: 38 residues processed: 242 average time/residue: 0.2604 time to fit residues: 104.6210 Evaluate side-chains 237 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 194 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 53 TYR Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 245 ASN Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 316 HIS Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 149 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 119 optimal weight: 0.4980 chunk 22 optimal weight: 0.2980 chunk 190 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.245 19665 Z= 0.355 Angle : 1.210 50.497 26854 Z= 0.784 Chirality : 0.229 6.323 3141 Planarity : 0.003 0.049 3258 Dihedral : 9.905 72.518 2974 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.48 % Allowed : 25.57 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.17), residues: 2468 helix: 2.11 (0.17), residues: 949 sheet: -0.90 (0.29), residues: 332 loop : -1.02 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 103 HIS 0.004 0.001 HIS D 51 PHE 0.018 0.001 PHE A 741 TYR 0.018 0.001 TYR A 353 ARG 0.005 0.000 ARG B 936 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 195 time to evaluate : 2.505 Fit side-chains REVERT: A 984 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8308 (mmm) REVERT: A 1050 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8624 (mm) REVERT: D 30 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8168 (pt0) REVERT: E 27 TYR cc_start: 0.8928 (m-80) cc_final: 0.8688 (m-80) REVERT: F 298 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8691 (mm) REVERT: F 316 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.7893 (m90) REVERT: F 399 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.7868 (mtt) REVERT: F 403 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7365 (mpp) REVERT: G 65 ILE cc_start: 0.9243 (mm) cc_final: 0.8929 (mt) outliers start: 55 outliers final: 41 residues processed: 241 average time/residue: 0.2675 time to fit residues: 106.6610 Evaluate side-chains 241 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 193 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1260 ILE Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 53 TYR Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 245 ASN Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 316 HIS Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 399 MET Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 220 optimal weight: 0.7980 chunk 231 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 98 optimal weight: 0.2980 chunk 177 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 203 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 822 HIS ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.244 19665 Z= 0.338 Angle : 1.205 50.480 26854 Z= 0.781 Chirality : 0.229 6.327 3141 Planarity : 0.003 0.047 3258 Dihedral : 9.809 72.542 2974 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.29 % Allowed : 25.57 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.17), residues: 2468 helix: 2.20 (0.17), residues: 949 sheet: -0.85 (0.29), residues: 332 loop : -0.99 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 103 HIS 0.004 0.000 HIS D 51 PHE 0.016 0.001 PHE A 741 TYR 0.020 0.001 TYR A 353 ARG 0.006 0.000 ARG B 936 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 200 time to evaluate : 2.386 Fit side-chains REVERT: A 984 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8292 (mmm) REVERT: A 1050 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8588 (mm) REVERT: D 30 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8141 (pt0) REVERT: E 27 TYR cc_start: 0.8954 (m-80) cc_final: 0.8705 (m-10) REVERT: F 316 HIS cc_start: 0.8379 (OUTLIER) cc_final: 0.8158 (m90) REVERT: F 399 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.7778 (mtt) REVERT: F 403 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7323 (mpp) REVERT: G 65 ILE cc_start: 0.9239 (mm) cc_final: 0.8912 (mt) outliers start: 52 outliers final: 40 residues processed: 242 average time/residue: 0.2585 time to fit residues: 104.8240 Evaluate side-chains 240 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 194 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 53 TYR Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 245 ASN Chi-restraints excluded: chain F residue 316 HIS Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 399 MET Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 148 optimal weight: 0.7980 chunk 238 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 250 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 199 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 19665 Z= 0.419 Angle : 1.230 50.548 26854 Z= 0.792 Chirality : 0.229 6.330 3141 Planarity : 0.004 0.053 3258 Dihedral : 10.025 73.610 2974 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.42 % Allowed : 25.76 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.17), residues: 2468 helix: 2.03 (0.17), residues: 949 sheet: -0.90 (0.29), residues: 319 loop : -1.03 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 103 HIS 0.005 0.001 HIS D 51 PHE 0.018 0.001 PHE A 741 TYR 0.019 0.001 TYR A 353 ARG 0.005 0.000 ARG B 936 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 193 time to evaluate : 2.593 Fit side-chains REVERT: A 760 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7782 (m-30) REVERT: A 984 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.7357 (mmm) REVERT: A 1050 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8676 (mm) REVERT: D 30 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8322 (pt0) REVERT: E 27 TYR cc_start: 0.9001 (m-80) cc_final: 0.8769 (m-80) REVERT: F 54 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.7171 (t80) REVERT: F 316 HIS cc_start: 0.8507 (OUTLIER) cc_final: 0.8237 (m-70) REVERT: F 399 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.7719 (mtt) REVERT: G 65 ILE cc_start: 0.9239 (mm) cc_final: 0.8932 (mt) outliers start: 54 outliers final: 39 residues processed: 238 average time/residue: 0.2893 time to fit residues: 115.4035 Evaluate side-chains 235 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 189 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1059 MET Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1260 ILE Chi-restraints excluded: chain A residue 1347 ILE Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain F residue 53 TYR Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 245 ASN Chi-restraints excluded: chain F residue 316 HIS Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 399 MET Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain F residue 432 TRP Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 976 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 158 optimal weight: 0.9990 chunk 212 optimal weight: 0.0670 chunk 61 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 199 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 204 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.106257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.089752 restraints weight = 34277.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.092064 restraints weight = 20971.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.093596 restraints weight = 15132.343| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.245 19665 Z= 0.355 Angle : 1.215 50.511 26854 Z= 0.785 Chirality : 0.229 6.329 3141 Planarity : 0.003 0.048 3258 Dihedral : 9.930 74.084 2974 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.97 % Allowed : 25.89 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.17), residues: 2468 helix: 2.13 (0.17), residues: 949 sheet: -0.88 (0.29), residues: 319 loop : -1.02 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 103 HIS 0.004 0.001 HIS D 51 PHE 0.017 0.001 PHE A 741 TYR 0.023 0.001 TYR A 353 ARG 0.005 0.000 ARG B 936 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3340.91 seconds wall clock time: 64 minutes 53.52 seconds (3893.52 seconds total)