Starting phenix.real_space_refine on Fri Jan 19 21:35:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6c_11670/01_2024/7a6c_11670_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6c_11670/01_2024/7a6c_11670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6c_11670/01_2024/7a6c_11670.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6c_11670/01_2024/7a6c_11670.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6c_11670/01_2024/7a6c_11670_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6c_11670/01_2024/7a6c_11670_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 8251 2.51 5 N 2092 2.21 5 O 2324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 74": "OE1" <-> "OE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A ARG 593": "NH1" <-> "NH2" Residue "A GLU 608": "OE1" <-> "OE2" Residue "A GLU 614": "OE1" <-> "OE2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A ARG 794": "NH1" <-> "NH2" Residue "A ARG 832": "NH1" <-> "NH2" Residue "A GLU 875": "OE1" <-> "OE2" Residue "A GLU 889": "OE1" <-> "OE2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A GLU 913": "OE1" <-> "OE2" Residue "A ARG 929": "NH1" <-> "NH2" Residue "A ARG 958": "NH1" <-> "NH2" Residue "A GLU 972": "OE1" <-> "OE2" Residue "A GLU 1024": "OE1" <-> "OE2" Residue "A GLU 1039": "OE1" <-> "OE2" Residue "A ARG 1047": "NH1" <-> "NH2" Residue "A GLU 1059": "OE1" <-> "OE2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "A ARG 1103": "NH1" <-> "NH2" Residue "A ARG 1138": "NH1" <-> "NH2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A GLU 1159": "OE1" <-> "OE2" Residue "A ARG 1192": "NH1" <-> "NH2" Residue "A GLU 1211": "OE1" <-> "OE2" Residue "A GLU 1216": "OE1" <-> "OE2" Residue "A ARG 1222": "NH1" <-> "NH2" Residue "A ARG 1233": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 136": "OD1" <-> "OD2" Residue "C TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 217": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12717 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9050 Classifications: {'peptide': 1164} Link IDs: {'PTRANS': 27, 'TRANS': 1136} Chain breaks: 2 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1656 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CYS%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1647 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PRO%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 364 Unusual residues: {'CLR': 10, 'R0Z': 2} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 6.86, per 1000 atoms: 0.54 Number of scatterers: 12717 At special positions: 0 Unit cell: (102.48, 206.64, 98.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2324 8.00 N 2092 7.00 C 8251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 201 " distance=2.03 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: 5.00 Conformation dependent library (CDL) restraints added in 2.2 seconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 16 sheets defined 45.2% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 45 through 64 removed outlier: 4.469A pdb=" N GLY A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 82 removed outlier: 4.052A pdb=" N GLU A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 156 removed outlier: 4.172A pdb=" N TYR A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.974A pdb=" N VAL A 165 " --> pdb=" O TRP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 210 removed outlier: 5.563A pdb=" N VAL A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASP A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ILE A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLY A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 237 removed outlier: 4.286A pdb=" N VAL A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 240 through 259 removed outlier: 5.292A pdb=" N LYS A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 271 through 323 removed outlier: 3.681A pdb=" N ASN A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR A 319 " --> pdb=" O TRP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 368 removed outlier: 4.086A pdb=" N GLY A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Proline residue: A 350 - end of helix removed outlier: 4.506A pdb=" N TYR A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 433 through 441 removed outlier: 3.733A pdb=" N GLN A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 463 through 469 Processing helix chain 'A' and resid 484 through 491 removed outlier: 4.554A pdb=" N GLY A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 506 Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 534 through 546 Processing helix chain 'A' and resid 564 through 576 removed outlier: 3.853A pdb=" N ALA A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 612 through 618 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 701 through 704 Processing helix chain 'A' and resid 709 through 723 Processing helix chain 'A' and resid 726 through 735 Processing helix chain 'A' and resid 737 through 740 No H-bonds generated for 'chain 'A' and resid 737 through 740' Processing helix chain 'A' and resid 745 through 797 Processing helix chain 'A' and resid 802 through 805 No H-bonds generated for 'chain 'A' and resid 802 through 805' Processing helix chain 'A' and resid 811 through 853 removed outlier: 5.064A pdb=" N ALA A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 830 " --> pdb=" O LYS A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 879 removed outlier: 3.932A pdb=" N ALA A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 864 " --> pdb=" O LEU A 860 " (cutoff:3.500A) Proline residue: A 866 - end of helix Processing helix chain 'A' and resid 896 through 902 Processing helix chain 'A' and resid 914 through 966 removed outlier: 4.148A pdb=" N MET A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) Proline residue: A 927 - end of helix removed outlier: 3.637A pdb=" N ASN A 930 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 946 " --> pdb=" O PHE A 942 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS A 966 " --> pdb=" O TYR A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 992 Processing helix chain 'A' and resid 999 through 1013 Processing helix chain 'A' and resid 1080 through 1083 No H-bonds generated for 'chain 'A' and resid 1080 through 1083' Processing helix chain 'A' and resid 1106 through 1112 removed outlier: 3.546A pdb=" N ALA A1111 " --> pdb=" O GLN A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1132 through 1134 No H-bonds generated for 'chain 'A' and resid 1132 through 1134' Processing helix chain 'A' and resid 1142 through 1151 removed outlier: 4.269A pdb=" N ARG A1147 " --> pdb=" O GLU A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1160 removed outlier: 3.538A pdb=" N SER A1160 " --> pdb=" O ALA A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1173 No H-bonds generated for 'chain 'A' and resid 1171 through 1173' Processing helix chain 'A' and resid 1178 through 1192 removed outlier: 4.175A pdb=" N ARG A1183 " --> pdb=" O GLY A1179 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A1186 " --> pdb=" O GLN A1182 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A1192 " --> pdb=" O ARG A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1221 removed outlier: 3.645A pdb=" N LYS A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA A1221 " --> pdb=" O ALA A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1260 No H-bonds generated for 'chain 'A' and resid 1257 through 1260' Processing helix chain 'A' and resid 1266 through 1270 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 191 through 194 No H-bonds generated for 'chain 'C' and resid 191 through 194' Processing sheet with id= A, first strand: chain 'A' and resid 423 through 426 removed outlier: 6.820A pdb=" N VAL A 597 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL A 426 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA A 599 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASP A 602 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ILE A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 470 through 473 removed outlier: 6.115A pdb=" N ILE A 551 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL A 473 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 553 " --> pdb=" O VAL A 473 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR A 581 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LEU A 554 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE A 583 " --> pdb=" O LEU A 554 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 1036 through 1038 Processing sheet with id= D, first strand: chain 'A' and resid 1066 through 1069 removed outlier: 6.220A pdb=" N LEU A1242 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL A1069 " --> pdb=" O LEU A1242 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL A1244 " --> pdb=" O VAL A1069 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1196 through 1200 removed outlier: 7.256A pdb=" N THR A1226 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU A1199 " --> pdb=" O THR A1226 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE A1228 " --> pdb=" O LEU A1199 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 1040 through 1042 removed outlier: 6.706A pdb=" N PHE A1042 " --> pdb=" O GLN A1054 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLN A1054 " --> pdb=" O PHE A1042 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 4 through 6 Processing sheet with id= H, first strand: chain 'B' and resid 10 through 14 removed outlier: 6.995A pdb=" N LYS B 108 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL B 13 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU B 110 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY B 89 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 119 through 123 removed outlier: 3.645A pdb=" N THR B 119 " --> pdb=" O ASN B 142 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL B 138 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N TYR B 178 " --> pdb=" O ASN B 143 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 134 through 137 Processing sheet with id= K, first strand: chain 'B' and resid 151 through 155 removed outlier: 3.548A pdb=" N TYR B 197 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 3 through 5 Processing sheet with id= M, first strand: chain 'C' and resid 17 through 20 Processing sheet with id= N, first strand: chain 'C' and resid 112 through 115 removed outlier: 3.562A pdb=" N SER C 35 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N THR C 40 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU C 45 " --> pdb=" O THR C 40 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 126 through 130 removed outlier: 3.666A pdb=" N LEU C 147 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU C 130 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY C 145 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N TYR C 181 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER C 184 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 175 through 177 573 hydrogen bonds defined for protein. 1659 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.34 Time building geometry restraints manager: 5.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2015 1.29 - 1.42: 3348 1.42 - 1.56: 7501 1.56 - 1.69: 56 1.69 - 1.82: 83 Bond restraints: 13003 Sorted by residual: bond pdb=" C28 R0Z A1301 " pdb=" N29 R0Z A1301 " ideal model delta sigma weight residual 1.451 1.266 0.185 2.00e-02 2.50e+03 8.56e+01 bond pdb=" C28 R0Z A1302 " pdb=" N29 R0Z A1302 " ideal model delta sigma weight residual 1.451 1.286 0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" C08 R0Z A1302 " pdb=" N09 R0Z A1302 " ideal model delta sigma weight residual 1.363 1.521 -0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" C10 R0Z A1302 " pdb=" N09 R0Z A1302 " ideal model delta sigma weight residual 1.356 1.510 -0.154 2.00e-02 2.50e+03 5.94e+01 bond pdb=" C08 R0Z A1301 " pdb=" N09 R0Z A1301 " ideal model delta sigma weight residual 1.363 1.502 -0.139 2.00e-02 2.50e+03 4.84e+01 ... (remaining 12998 not shown) Histogram of bond angle deviations from ideal: 94.71 - 102.62: 96 102.62 - 110.53: 3749 110.53 - 118.44: 6665 118.44 - 126.36: 7016 126.36 - 134.27: 143 Bond angle restraints: 17669 Sorted by residual: angle pdb=" C ASN A 371 " pdb=" N LYS A 372 " pdb=" CA LYS A 372 " ideal model delta sigma weight residual 121.83 133.04 -11.21 1.56e+00 4.11e-01 5.16e+01 angle pdb=" N ILE B 56 " pdb=" CA ILE B 56 " pdb=" C ILE B 56 " ideal model delta sigma weight residual 109.34 120.05 -10.71 2.08e+00 2.31e-01 2.65e+01 angle pdb=" C LEU A 175 " pdb=" N THR A 176 " pdb=" CA THR A 176 " ideal model delta sigma weight residual 122.17 114.49 7.68 1.54e+00 4.22e-01 2.49e+01 angle pdb=" C18 R0Z A1301 " pdb=" N20 R0Z A1301 " pdb=" C21 R0Z A1301 " ideal model delta sigma weight residual 128.43 114.28 14.15 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C THR C 28 " pdb=" N PHE C 29 " pdb=" CA PHE C 29 " ideal model delta sigma weight residual 120.63 127.91 -7.28 1.61e+00 3.86e-01 2.04e+01 ... (remaining 17664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.48: 7634 26.48 - 52.97: 485 52.97 - 79.45: 54 79.45 - 105.93: 12 105.93 - 132.42: 3 Dihedral angle restraints: 8188 sinusoidal: 3602 harmonic: 4586 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual 93.00 140.45 -47.45 1 1.00e+01 1.00e-02 3.11e+01 dihedral pdb=" CA VAL A 472 " pdb=" C VAL A 472 " pdb=" N VAL A 473 " pdb=" CA VAL A 473 " ideal model delta harmonic sigma weight residual 180.00 152.38 27.62 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA HIS B 98 " pdb=" C HIS B 98 " pdb=" N ALA B 99 " pdb=" CA ALA B 99 " ideal model delta harmonic sigma weight residual -180.00 -154.10 -25.90 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 8185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1764 0.101 - 0.201: 238 0.201 - 0.301: 27 0.301 - 0.402: 4 0.402 - 0.502: 5 Chirality restraints: 2038 Sorted by residual: chirality pdb=" C17 CLR A1308 " pdb=" C13 CLR A1308 " pdb=" C16 CLR A1308 " pdb=" C20 CLR A1308 " both_signs ideal model delta sigma weight residual False 2.55 3.06 -0.50 2.00e-01 2.50e+01 6.31e+00 chirality pdb=" CB VAL A 981 " pdb=" CA VAL A 981 " pdb=" CG1 VAL A 981 " pdb=" CG2 VAL A 981 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" C17 CLR A1311 " pdb=" C13 CLR A1311 " pdb=" C16 CLR A1311 " pdb=" C20 CLR A1311 " both_signs ideal model delta sigma weight residual False 2.55 2.99 -0.44 2.00e-01 2.50e+01 4.75e+00 ... (remaining 2035 not shown) Planarity restraints: 2164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 744 " 0.054 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO A 745 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 745 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 745 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 277 " 0.031 2.00e-02 2.50e+03 2.20e-02 9.69e+00 pdb=" CG TYR A 277 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 277 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 277 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 277 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 277 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 277 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 277 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 852 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.90e+00 pdb=" C ILE A 852 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE A 852 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR A 853 " -0.017 2.00e-02 2.50e+03 ... (remaining 2161 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 939 2.69 - 3.25: 12984 3.25 - 3.80: 19436 3.80 - 4.35: 25262 4.35 - 4.90: 41783 Nonbonded interactions: 100404 Sorted by model distance: nonbonded pdb=" O SER B 176 " pdb=" OG SER B 176 " model vdw 2.143 2.440 nonbonded pdb=" O SER C 85 " pdb=" OG SER C 85 " model vdw 2.199 2.440 nonbonded pdb=" NH1 ARG A 442 " pdb=" O ILE A 461 " model vdw 2.199 2.520 nonbonded pdb=" N ASP B 156 " pdb=" O SER B 196 " model vdw 2.204 2.520 nonbonded pdb=" OH TYR B 41 " pdb=" N PHE C 106 " model vdw 2.213 2.520 ... (remaining 100399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.360 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: 0.010 Extract box with map and model: 12.140 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 36.240 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 : 0.017 0.185 13003 Z= 1.053 Angle : 1.366 14.146 17669 Z= 0.721 Chirality : 0.075 0.502 2038 Planarity : 0.006 0.081 2164 Dihedral : 16.988 132.418 5233 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 25.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.05 % Favored : 88.70 % Rotamer: Outliers : 3.00 % Allowed : 7.94 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -4.28 (0.17), residues: 1584 helix: -2.66 (0.15), residues: 744 sheet: -1.83 (0.29), residues: 257 loop : -3.34 (0.21), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP A 698 HIS 0.009 0.002 HIS A 166 PHE 0.033 0.004 PHE A 72 TYR 0.052 0.003 TYR A 277 ARG 0.009 0.001 ARG C 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 LYS cc_start: 0.5430 (OUTLIER) cc_final: 0.4862 (ptpt) REVERT: A 450 MET cc_start: 0.5983 (tmm) cc_final: 0.5149 (tmm) REVERT: A 1015 THR cc_start: 0.5297 (OUTLIER) cc_final: 0.4934 (t) REVERT: B 115 ASP cc_start: 0.5328 (OUTLIER) cc_final: 0.5005 (t0) outliers start: 40 outliers final: 20 residues processed: 164 average time/residue: 0.3029 time to fit residues: 69.5446 Evaluate side-chains 107 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 885 LYS Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1014 LYS Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 136 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 92 optimal weight: 8.9990 chunk 143 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 GLN A 508 ASN A 611 ASN A 725 GLN A 809 ASN A 839 ASN A 912 GLN A 966 HIS A1054 GLN ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN B 143 ASN B 218 ASN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13003 Z= 0.197 Angle : 0.690 8.676 17669 Z= 0.347 Chirality : 0.041 0.154 2038 Planarity : 0.004 0.050 2164 Dihedral : 10.651 134.503 2453 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.11 % Favored : 94.82 % Rotamer: Outliers : 1.42 % Allowed : 13.71 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.26 (0.19), residues: 1584 helix: -0.65 (0.18), residues: 747 sheet: -1.21 (0.30), residues: 255 loop : -2.67 (0.22), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 105 HIS 0.006 0.001 HIS A1254 PHE 0.038 0.002 PHE A 904 TYR 0.013 0.002 TYR A 622 ARG 0.006 0.001 ARG A 794 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.7374 (tpp) cc_final: 0.6662 (tpp) REVERT: A 380 LYS cc_start: 0.5343 (OUTLIER) cc_final: 0.5083 (ptpt) REVERT: A 450 MET cc_start: 0.6264 (tmm) cc_final: 0.5372 (tmm) REVERT: A 479 LEU cc_start: 0.7646 (mt) cc_final: 0.7399 (mt) outliers start: 19 outliers final: 10 residues processed: 129 average time/residue: 0.2472 time to fit residues: 47.5455 Evaluate side-chains 106 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain C residue 136 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 143 optimal weight: 0.0870 chunk 155 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 115 optimal weight: 0.0000 overall best weight: 1.6168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 145 HIS ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN A1136 ASN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13003 Z= 0.288 Angle : 0.658 8.240 17669 Z= 0.335 Chirality : 0.042 0.168 2038 Planarity : 0.004 0.073 2164 Dihedral : 9.239 134.124 2409 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.88 % Favored : 93.06 % Rotamer: Outliers : 2.25 % Allowed : 16.48 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.64 (0.20), residues: 1584 helix: -0.08 (0.18), residues: 752 sheet: -1.00 (0.30), residues: 256 loop : -2.44 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 105 HIS 0.005 0.001 HIS A1254 PHE 0.020 0.002 PHE A 904 TYR 0.017 0.002 TYR B 145 ARG 0.005 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 103 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8005 (mmm) cc_final: 0.7694 (mmm) REVERT: A 450 MET cc_start: 0.6251 (tmm) cc_final: 0.5306 (tmm) REVERT: A 479 LEU cc_start: 0.7678 (mt) cc_final: 0.7411 (mt) REVERT: A 770 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.7223 (t80) outliers start: 30 outliers final: 20 residues processed: 130 average time/residue: 0.2505 time to fit residues: 48.1314 Evaluate side-chains 115 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1081 GLN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain C residue 148 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 144 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 136 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13003 Z= 0.204 Angle : 0.587 7.698 17669 Z= 0.299 Chirality : 0.040 0.153 2038 Planarity : 0.004 0.070 2164 Dihedral : 8.576 134.284 2403 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.56 % Favored : 94.38 % Rotamer: Outliers : 2.47 % Allowed : 18.50 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.04 (0.21), residues: 1584 helix: 0.50 (0.19), residues: 745 sheet: -0.83 (0.31), residues: 249 loop : -2.16 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 105 HIS 0.005 0.001 HIS A1254 PHE 0.023 0.001 PHE B 215 TYR 0.016 0.001 TYR B 145 ARG 0.006 0.000 ARG A 794 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 97 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.7839 (mmm) cc_final: 0.7617 (mmm) REVERT: A 450 MET cc_start: 0.6224 (tmm) cc_final: 0.5263 (tmm) REVERT: A 770 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.7253 (t80) REVERT: A 912 GLN cc_start: 0.7253 (mm110) cc_final: 0.7024 (mm-40) REVERT: A 1159 GLU cc_start: 0.5353 (OUTLIER) cc_final: 0.5034 (mp0) outliers start: 33 outliers final: 24 residues processed: 123 average time/residue: 0.2232 time to fit residues: 42.3017 Evaluate side-chains 118 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1125 CYS Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain C residue 50 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 0.0010 chunk 86 optimal weight: 0.0570 chunk 2 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 overall best weight: 0.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 HIS ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13003 Z= 0.152 Angle : 0.555 8.265 17669 Z= 0.282 Chirality : 0.039 0.153 2038 Planarity : 0.004 0.065 2164 Dihedral : 8.241 132.924 2401 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.43 % Favored : 94.51 % Rotamer: Outliers : 2.55 % Allowed : 20.07 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.58 (0.21), residues: 1584 helix: 0.91 (0.19), residues: 747 sheet: -0.58 (0.32), residues: 239 loop : -1.98 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 105 HIS 0.005 0.001 HIS A 61 PHE 0.034 0.001 PHE A 904 TYR 0.015 0.001 TYR C 151 ARG 0.006 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 100 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.6285 (tmm) cc_final: 0.5391 (tmm) REVERT: A 479 LEU cc_start: 0.7679 (mt) cc_final: 0.7459 (mt) REVERT: A 1119 GLU cc_start: 0.6618 (tm-30) cc_final: 0.6138 (pm20) REVERT: A 1159 GLU cc_start: 0.5287 (OUTLIER) cc_final: 0.4984 (mp0) outliers start: 34 outliers final: 22 residues processed: 128 average time/residue: 0.2573 time to fit residues: 50.5684 Evaluate side-chains 118 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1125 CYS Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain C residue 148 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 30 optimal weight: 0.0470 chunk 89 optimal weight: 0.9980 chunk 37 optimal weight: 30.0000 chunk 152 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.7878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13003 Z= 0.176 Angle : 0.552 8.207 17669 Z= 0.282 Chirality : 0.039 0.154 2038 Planarity : 0.003 0.055 2164 Dihedral : 8.077 133.249 2399 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.37 % Favored : 94.57 % Rotamer: Outliers : 2.47 % Allowed : 20.30 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.37 (0.21), residues: 1584 helix: 1.06 (0.19), residues: 747 sheet: -0.45 (0.32), residues: 239 loop : -1.86 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 105 HIS 0.005 0.001 HIS A1254 PHE 0.024 0.001 PHE A 904 TYR 0.015 0.001 TYR C 151 ARG 0.007 0.000 ARG A 794 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 96 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.6333 (tmm) cc_final: 0.5474 (tmm) REVERT: A 948 MET cc_start: 0.7571 (tpp) cc_final: 0.7365 (tpp) REVERT: A 1119 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6544 (mm-30) REVERT: A 1159 GLU cc_start: 0.5266 (OUTLIER) cc_final: 0.4986 (mp0) outliers start: 33 outliers final: 25 residues processed: 121 average time/residue: 0.2232 time to fit residues: 41.8736 Evaluate side-chains 121 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1125 CYS Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain A residue 1191 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain C residue 148 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 128 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13003 Z= 0.182 Angle : 0.550 8.717 17669 Z= 0.281 Chirality : 0.039 0.152 2038 Planarity : 0.003 0.051 2164 Dihedral : 7.940 133.252 2399 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 3.15 % Allowed : 20.07 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.24 (0.21), residues: 1584 helix: 1.14 (0.19), residues: 749 sheet: -0.31 (0.33), residues: 239 loop : -1.79 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 194 HIS 0.004 0.001 HIS A1254 PHE 0.021 0.001 PHE A 904 TYR 0.015 0.001 TYR C 151 ARG 0.005 0.000 ARG A 794 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 98 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.6322 (tmm) cc_final: 0.5468 (tmm) REVERT: A 479 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7009 (mt) REVERT: A 1087 TYR cc_start: 0.7098 (m-80) cc_final: 0.6874 (m-80) REVERT: A 1119 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6811 (mm-30) REVERT: A 1159 GLU cc_start: 0.5324 (OUTLIER) cc_final: 0.4999 (mp0) outliers start: 42 outliers final: 35 residues processed: 128 average time/residue: 0.2285 time to fit residues: 45.9713 Evaluate side-chains 131 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 94 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1125 CYS Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain A residue 1191 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 138 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13003 Z= 0.175 Angle : 0.548 7.926 17669 Z= 0.279 Chirality : 0.039 0.150 2038 Planarity : 0.003 0.051 2164 Dihedral : 7.842 132.902 2399 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 2.85 % Allowed : 21.05 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.21), residues: 1584 helix: 1.23 (0.19), residues: 748 sheet: -0.21 (0.32), residues: 239 loop : -1.74 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 194 HIS 0.004 0.001 HIS A1254 PHE 0.013 0.001 PHE B 76 TYR 0.015 0.001 TYR C 151 ARG 0.005 0.000 ARG A 794 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 97 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.6316 (tmm) cc_final: 0.5493 (tmm) REVERT: A 479 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7036 (mt) REVERT: A 1087 TYR cc_start: 0.7169 (m-80) cc_final: 0.6898 (m-80) REVERT: A 1119 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6859 (mm-30) REVERT: A 1159 GLU cc_start: 0.5293 (OUTLIER) cc_final: 0.5005 (mp0) outliers start: 38 outliers final: 34 residues processed: 124 average time/residue: 0.2219 time to fit residues: 43.0956 Evaluate side-chains 129 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 93 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1125 CYS Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain A residue 1191 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 0.6980 chunk 133 optimal weight: 0.0870 chunk 141 optimal weight: 0.2980 chunk 85 optimal weight: 0.0870 chunk 61 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 134 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 150 optimal weight: 0.0070 overall best weight: 0.2354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13003 Z= 0.134 Angle : 0.523 7.606 17669 Z= 0.266 Chirality : 0.038 0.199 2038 Planarity : 0.003 0.048 2164 Dihedral : 7.645 133.210 2399 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.55 % Favored : 95.39 % Rotamer: Outliers : 2.10 % Allowed : 22.02 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.17 (0.22), residues: 1584 helix: 1.47 (0.19), residues: 752 sheet: -0.05 (0.33), residues: 239 loop : -1.62 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 105 HIS 0.004 0.001 HIS A 61 PHE 0.012 0.001 PHE A 983 TYR 0.015 0.001 TYR C 151 ARG 0.005 0.000 ARG A 794 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 96 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.6306 (tmm) cc_final: 0.5526 (tmm) REVERT: A 479 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7059 (mt) REVERT: A 912 GLN cc_start: 0.7085 (mm-40) cc_final: 0.6476 (tm-30) REVERT: A 1087 TYR cc_start: 0.7139 (m-80) cc_final: 0.6827 (m-80) REVERT: A 1119 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6818 (mm-30) REVERT: A 1159 GLU cc_start: 0.5291 (OUTLIER) cc_final: 0.5034 (mp0) outliers start: 28 outliers final: 24 residues processed: 117 average time/residue: 0.2208 time to fit residues: 40.9437 Evaluate side-chains 120 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain A residue 1191 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain C residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 20.0000 chunk 71 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 157 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 99 optimal weight: 0.0870 chunk 133 optimal weight: 1.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13003 Z= 0.196 Angle : 0.554 9.060 17669 Z= 0.280 Chirality : 0.039 0.155 2038 Planarity : 0.003 0.049 2164 Dihedral : 7.711 132.952 2399 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.37 % Favored : 94.57 % Rotamer: Outliers : 2.32 % Allowed : 21.95 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.18 (0.21), residues: 1584 helix: 1.45 (0.19), residues: 739 sheet: -0.03 (0.32), residues: 244 loop : -1.53 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 194 HIS 0.005 0.001 HIS A1254 PHE 0.015 0.001 PHE B 76 TYR 0.015 0.001 TYR C 151 ARG 0.005 0.000 ARG A 794 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 96 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.6315 (tmm) cc_final: 0.5468 (tmm) REVERT: A 479 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7060 (mt) REVERT: A 1087 TYR cc_start: 0.7187 (m-80) cc_final: 0.6864 (m-80) REVERT: A 1159 GLU cc_start: 0.5317 (OUTLIER) cc_final: 0.5071 (mp0) outliers start: 31 outliers final: 24 residues processed: 120 average time/residue: 0.2189 time to fit residues: 40.9725 Evaluate side-chains 120 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1125 CYS Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain A residue 1191 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain C residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 1.9990 chunk 115 optimal weight: 0.0050 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 110 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.193810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.149428 restraints weight = 18075.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.140760 restraints weight = 34346.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.133249 restraints weight = 32320.567| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13003 Z= 0.272 Angle : 0.611 9.911 17669 Z= 0.308 Chirality : 0.041 0.154 2038 Planarity : 0.003 0.051 2164 Dihedral : 7.940 133.299 2399 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.74 % Favored : 94.19 % Rotamer: Outliers : 2.32 % Allowed : 21.80 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.10 (0.21), residues: 1584 helix: 1.09 (0.19), residues: 750 sheet: -0.04 (0.32), residues: 244 loop : -1.60 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 105 HIS 0.005 0.001 HIS A1254 PHE 0.018 0.002 PHE B 76 TYR 0.015 0.002 TYR C 151 ARG 0.007 0.000 ARG B 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2367.55 seconds wall clock time: 44 minutes 19.27 seconds (2659.27 seconds total)