Starting phenix.real_space_refine on Thu Feb 15 16:21:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6e_11671/02_2024/7a6e_11671_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6e_11671/02_2024/7a6e_11671.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6e_11671/02_2024/7a6e_11671_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6e_11671/02_2024/7a6e_11671_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6e_11671/02_2024/7a6e_11671_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6e_11671/02_2024/7a6e_11671.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6e_11671/02_2024/7a6e_11671.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6e_11671/02_2024/7a6e_11671_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6e_11671/02_2024/7a6e_11671_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 8286 2.51 5 N 2094 2.21 5 O 2327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 210": "NH1" <-> "NH2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "A ARG 459": "NH1" <-> "NH2" 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 618": "OE1" <-> "OE2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A ARG 794": "NH1" <-> "NH2" Residue "A ARG 798": "NH1" <-> "NH2" Residue "A ARG 832": "NH1" <-> "NH2" Residue "A GLU 875": "OE1" <-> "OE2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 929": "NH1" <-> "NH2" Residue "A GLU 1024": "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 1211": "OE1" <-> "OE2" Residue "A GLU 1216": "OE1" <-> "OE2" Residue "A ARG 1222": "NH1" <-> "NH2" Residue "A GLU 1223": "OE1" <-> "OE2" Residue "A ARG 1233": "NH1" <-> "NH2" Residue "A GLU 1253": "OE1" <-> "OE2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12757 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: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 404 Unusual residues: {'CLR': 11, 'R1H': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Time building chain proxies: 6.45, per 1000 atoms: 0.51 Number of scatterers: 12757 At special positions: 0 Unit cell: (102.48, 206.64, 100.8, 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 2327 8.00 N 2094 7.00 C 8286 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=2.05 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=1.85 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: 4.56 Conformation dependent library (CDL) restraints added in 2.1 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: 50 helices and 15 sheets defined 48.1% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 removed outlier: 4.111A pdb=" N PHE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG A 41 " --> pdb=" O PHE A 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 41' Processing helix chain 'A' and resid 45 through 63 Processing helix chain 'A' and resid 65 through 84 removed outlier: 3.707A pdb=" N ASP A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 156 removed outlier: 3.634A pdb=" N HIS A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.694A pdb=" N VAL A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 210 removed outlier: 3.762A pdb=" N THR A 176 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLY A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 259 removed outlier: 5.302A pdb=" N THR A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASP A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 267 Processing helix chain 'A' and resid 270 through 323 Processing helix chain 'A' and resid 328 through 370 removed outlier: 4.066A pdb=" N VAL A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Proline residue: A 350 - end of helix removed outlier: 3.585A pdb=" N GLU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 440 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 468 Processing helix chain 'A' and resid 484 through 491 removed outlier: 4.456A 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 533 through 547 removed outlier: 4.666A pdb=" N ARG A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 575 Processing helix chain 'A' and resid 612 through 617 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 705 through 740 Proline residue: A 709 - end of helix removed outlier: 3.912A pdb=" N VAL A 713 " --> pdb=" O TYR A 710 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N CYS A 717 " --> pdb=" O GLY A 714 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN A 725 " --> pdb=" O GLY A 722 " (cutoff:3.500A) Proline residue: A 726 - end of helix removed outlier: 3.927A pdb=" N ILE A 731 " --> pdb=" O PHE A 728 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER A 733 " --> pdb=" O ILE A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 798 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: 3.786A pdb=" N THR A 815 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LYS A 826 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY A 846 " --> pdb=" O ASN A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 880 removed outlier: 3.586A pdb=" N LEU A 860 " --> pdb=" O GLN A 856 " (cutoff:3.500A) removed outlier: 4.024A 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 885 through 902 removed outlier: 5.167A pdb=" N GLY A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ALA A 893 " --> pdb=" O GLU A 889 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY A 894 " --> pdb=" O LEU A 890 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS A 895 " --> pdb=" O GLU A 891 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE A 896 " --> pdb=" O GLY A 892 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 901 " --> pdb=" O ALA A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 909 No H-bonds generated for 'chain 'A' and resid 906 through 909' Processing helix chain 'A' and resid 913 through 965 removed outlier: 4.084A pdb=" N VAL A 926 " --> pdb=" O GLN A 922 " (cutoff:3.500A) Proline residue: A 927 - end of helix removed outlier: 3.589A pdb=" N ASN A 930 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 932 " --> pdb=" O TYR A 928 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG A 933 " --> pdb=" O ARG A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 994 removed outlier: 3.861A pdb=" N GLY A 984 " --> pdb=" O ALA A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1012 Processing helix chain 'A' and resid 1078 through 1083 Processing helix chain 'A' and resid 1101 through 1103 No H-bonds generated for 'chain 'A' and resid 1101 through 1103' Processing helix chain 'A' and resid 1106 through 1112 removed outlier: 3.651A pdb=" N ARG A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1142 through 1151 Processing helix chain 'A' and resid 1155 through 1159 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: 3.607A pdb=" N VAL A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG A1192 " --> pdb=" O ARG A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1221 removed outlier: 3.867A pdb=" N LYS A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A1218 " --> pdb=" O VAL A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1238 No H-bonds generated for 'chain 'A' and resid 1235 through 1238' Processing helix chain 'A' and resid 1257 through 1262 Processing helix chain 'A' and resid 1266 through 1271 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 191 through 194 No H-bonds generated for 'chain 'C' and resid 191 through 194' Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing sheet with id= A, first strand: chain 'A' and resid 415 through 417 removed outlier: 3.844A pdb=" N ARG A 395 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET A 450 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 605 through 608 removed outlier: 6.489A pdb=" N GLY A 600 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR A 582 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N LEU A 425 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL A 584 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1093 through 1096 removed outlier: 5.104A pdb=" N LEU A1056 " --> pdb=" O GLU A1039 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1066 through 1069 removed outlier: 6.711A pdb=" N LEU A1242 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL A1069 " --> pdb=" O LEU A1242 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL A1244 " --> pdb=" O VAL A1069 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU A1253 " --> pdb=" O VAL A1245 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLN A1247 " --> pdb=" O VAL A1251 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL A1251 " --> pdb=" O GLN A1247 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1114 through 1116 removed outlier: 3.766A pdb=" N LEU A1198 " --> pdb=" O GLY A1114 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A1116 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP A1200 " --> pdb=" O VAL A1116 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR A1226 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU A1199 " --> pdb=" O THR A1226 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A1228 " --> pdb=" O LEU A1199 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 4 through 6 Processing sheet with id= G, first strand: chain 'B' and resid 10 through 14 removed outlier: 6.843A pdb=" N LYS B 108 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL B 13 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N GLU B 110 " --> pdb=" O VAL B 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 90 through 95 removed outlier: 3.837A pdb=" N ILE B 53 " --> pdb=" O TRP B 40 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU B 42 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU B 51 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 119 through 123 removed outlier: 3.532A pdb=" N ASN B 142 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 150 through 155 removed outlier: 3.709A pdb=" N LYS B 154 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR B 197 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 3 through 7 Processing sheet with id= L, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.516A pdb=" N SER C 35 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 126 through 130 removed outlier: 4.269A pdb=" N SER C 184 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 157 through 160 removed outlier: 4.312A pdb=" N ILE C 199 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 175 through 177 647 hydrogen bonds defined for protein. 1791 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: 4.75 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2015 1.30 - 1.44: 3463 1.44 - 1.57: 7484 1.57 - 1.71: 1 1.71 - 1.84: 83 Bond restraints: 13046 Sorted by residual: bond pdb=" C13 R1H A1302 " pdb=" N08 R1H A1302 " ideal model delta sigma weight residual 1.455 1.292 0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" C13 R1H A1301 " pdb=" N08 R1H A1301 " ideal model delta sigma weight residual 1.455 1.296 0.159 2.00e-02 2.50e+03 6.32e+01 bond pdb=" C06 R1H A1301 " pdb=" C11 R1H A1301 " ideal model delta sigma weight residual 1.388 1.296 0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C07 R1H A1301 " pdb=" N08 R1H A1301 " ideal model delta sigma weight residual 1.449 1.358 0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C09 R1H A1301 " pdb=" N08 R1H A1301 " ideal model delta sigma weight residual 1.471 1.385 0.086 2.00e-02 2.50e+03 1.86e+01 ... (remaining 13041 not shown) Histogram of bond angle deviations from ideal: 97.71 - 105.01: 228 105.01 - 112.30: 6886 112.30 - 119.60: 4271 119.60 - 126.89: 6226 126.89 - 134.19: 120 Bond angle restraints: 17731 Sorted by residual: angle pdb=" C SER A1126 " pdb=" N ILE A1127 " pdb=" CA ILE A1127 " ideal model delta sigma weight residual 120.46 125.94 -5.48 1.37e+00 5.33e-01 1.60e+01 angle pdb=" N LYS A 808 " pdb=" CA LYS A 808 " pdb=" C LYS A 808 " ideal model delta sigma weight residual 111.36 107.10 4.26 1.09e+00 8.42e-01 1.53e+01 angle pdb=" N ALA C 92 " pdb=" CA ALA C 92 " pdb=" C ALA C 92 " ideal model delta sigma weight residual 107.73 113.97 -6.24 1.61e+00 3.86e-01 1.50e+01 angle pdb=" C07 R1H A1301 " pdb=" N08 R1H A1301 " pdb=" C13 R1H A1301 " ideal model delta sigma weight residual 109.49 120.48 -10.99 3.00e+00 1.11e-01 1.34e+01 angle pdb=" N LYS A 380 " pdb=" CA LYS A 380 " pdb=" C LYS A 380 " ideal model delta sigma weight residual 113.23 108.88 4.35 1.24e+00 6.50e-01 1.23e+01 ... (remaining 17726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.19: 7787 22.19 - 44.38: 382 44.38 - 66.57: 66 66.57 - 88.76: 7 88.76 - 110.95: 3 Dihedral angle restraints: 8245 sinusoidal: 3659 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 93.00 159.28 -66.28 1 1.00e+01 1.00e-02 5.74e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 93 " pdb=" CB CYS B 93 " ideal model delta sinusoidal sigma weight residual 93.00 46.99 46.01 1 1.00e+01 1.00e-02 2.93e+01 dihedral pdb=" CA ALA C 104 " pdb=" C ALA C 104 " pdb=" N TRP C 105 " pdb=" CA TRP C 105 " ideal model delta harmonic sigma weight residual -180.00 -153.95 -26.05 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 8242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1649 0.064 - 0.127: 324 0.127 - 0.191: 42 0.191 - 0.255: 24 0.255 - 0.318: 7 Chirality restraints: 2046 Sorted by residual: chirality pdb=" CB VAL A 224 " pdb=" CA VAL A 224 " pdb=" CG1 VAL A 224 " pdb=" CG2 VAL A 224 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" C10 CLR A1304 " pdb=" C1 CLR A1304 " pdb=" C5 CLR A1304 " pdb=" C9 CLR A1304 " both_signs ideal model delta sigma weight residual False -2.85 -2.54 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C13 CLR A1311 " pdb=" C12 CLR A1311 " pdb=" C14 CLR A1311 " pdb=" C17 CLR A1311 " both_signs ideal model delta sigma weight residual False -2.93 -2.62 -0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 2043 not shown) Planarity restraints: 2168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 807 " 0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C PRO A 807 " -0.064 2.00e-02 2.50e+03 pdb=" O PRO A 807 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS A 808 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 380 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C LYS A 380 " -0.060 2.00e-02 2.50e+03 pdb=" O LYS A 380 " 0.023 2.00e-02 2.50e+03 pdb=" N SER A 381 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 224 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C VAL A 224 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL A 224 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 225 " 0.013 2.00e-02 2.50e+03 ... (remaining 2165 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 2 2.07 - 2.77: 2637 2.77 - 3.48: 17862 3.48 - 4.19: 28706 4.19 - 4.90: 50910 Nonbonded interactions: 100117 Sorted by model distance: nonbonded pdb=" O TRP A 803 " pdb=" ND2 ASN A 809 " model vdw 1.357 2.520 nonbonded pdb=" OG SER A 238 " pdb=" NZ LYS A 242 " model vdw 2.033 2.520 nonbonded pdb=" N GLN A 347 " pdb=" OE1 GLN A 347 " model vdw 2.079 2.520 nonbonded pdb=" N ASP B 156 " pdb=" O SER B 196 " model vdw 2.127 2.520 nonbonded pdb=" ND2 ASN A 721 " pdb=" OE1 GLN A 773 " model vdw 2.128 2.520 ... (remaining 100112 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: 2.150 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: 12.500 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 34.710 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 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 : 0.009 0.163 13046 Z= 0.597 Angle : 0.929 10.988 17731 Z= 0.518 Chirality : 0.057 0.318 2046 Planarity : 0.005 0.047 2168 Dihedral : 13.086 110.950 5290 Min Nonbonded Distance : 1.357 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.72 % Allowed : 5.09 % Favored : 93.18 % 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: -2.92 (0.18), residues: 1584 helix: -1.62 (0.16), residues: 770 sheet: -1.00 (0.30), residues: 271 loop : -2.67 (0.22), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 232 HIS 0.006 0.001 HIS A1112 PHE 0.020 0.002 PHE B 94 TYR 0.022 0.002 TYR C 95 ARG 0.005 0.001 ARG A 749 *********************** 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: 23 poor density : 151 time to evaluate : 1.410 Fit side-chains REVERT: A 156 MET cc_start: 0.7959 (mmm) cc_final: 0.7735 (mmp) REVERT: A 616 MET cc_start: 0.1551 (mmp) cc_final: -0.2230 (ptp) REVERT: A 953 TYR cc_start: 0.7943 (t80) cc_final: 0.7320 (t80) REVERT: A 1027 MET cc_start: -0.0786 (tpp) cc_final: -0.2536 (mpp) REVERT: B 86 GLU cc_start: 0.7607 (tp30) cc_final: 0.7331 (tt0) REVERT: C 87 ARG cc_start: 0.7837 (ttm170) cc_final: 0.7610 (mtt180) REVERT: C 103 GLU cc_start: 0.7468 (mp0) cc_final: 0.7248 (mt-10) outliers start: 23 outliers final: 13 residues processed: 172 average time/residue: 0.3049 time to fit residues: 72.7780 Evaluate side-chains 106 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 121 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 3.9990 chunk 119 optimal weight: 0.0270 chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 92 optimal weight: 0.0020 chunk 143 optimal weight: 1.9990 overall best weight: 0.5448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 HIS A 438 GLN A 475 GLN A 537 GLN A 612 HIS A 725 GLN A 824 GLN A 839 ASN A 912 GLN A1054 GLN A1105 ASN ** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1182 GLN A1239 ASN A1248 ASN B 27 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 ASN B 218 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13046 Z= 0.182 Angle : 0.590 8.876 17731 Z= 0.297 Chirality : 0.041 0.196 2046 Planarity : 0.004 0.036 2168 Dihedral : 9.064 89.349 2483 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.87 % Allowed : 8.76 % Favored : 89.36 % 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: -0.98 (0.20), residues: 1584 helix: 0.31 (0.18), residues: 771 sheet: -0.42 (0.31), residues: 268 loop : -2.11 (0.23), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 708 HIS 0.003 0.001 HIS A1112 PHE 0.016 0.002 PHE B 76 TYR 0.015 0.001 TYR A 953 ARG 0.009 0.000 ARG B 113 *********************** 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 143 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 1.474 Fit side-chains revert: symmetry clash REVERT: A 78 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7991 (mt) REVERT: A 378 TYR cc_start: 0.6060 (OUTLIER) cc_final: 0.4065 (m-80) REVERT: A 953 TYR cc_start: 0.7530 (t80) cc_final: 0.6803 (t80) REVERT: A 1027 MET cc_start: -0.0896 (tpp) cc_final: -0.2499 (mpp) REVERT: B 86 GLU cc_start: 0.7757 (tp30) cc_final: 0.7495 (tt0) REVERT: B 110 GLU cc_start: 0.6275 (OUTLIER) cc_final: 0.5825 (mp0) REVERT: C 103 GLU cc_start: 0.7503 (mp0) cc_final: 0.7149 (mt-10) REVERT: C 111 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7132 (pt0) outliers start: 25 outliers final: 15 residues processed: 137 average time/residue: 0.2329 time to fit residues: 49.0478 Evaluate side-chains 109 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 119 optimal weight: 0.0980 chunk 97 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 143 optimal weight: 0.4980 chunk 155 optimal weight: 20.0000 chunk 128 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 HIS ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN C 170 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13046 Z= 0.253 Angle : 0.617 9.300 17731 Z= 0.310 Chirality : 0.043 0.154 2046 Planarity : 0.004 0.040 2168 Dihedral : 8.546 78.248 2467 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.47 % Allowed : 13.11 % Favored : 84.42 % 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: -0.51 (0.20), residues: 1584 helix: 0.67 (0.18), residues: 775 sheet: -0.17 (0.31), residues: 274 loop : -1.88 (0.23), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 708 HIS 0.006 0.001 HIS B 98 PHE 0.017 0.002 PHE B 94 TYR 0.021 0.002 TYR C 95 ARG 0.005 0.000 ARG B 113 *********************** 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 130 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 97 time to evaluate : 1.344 Fit side-chains revert: symmetry clash REVERT: A 78 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7859 (mt) REVERT: A 105 MET cc_start: 0.6288 (mpp) cc_final: 0.5910 (mpp) REVERT: A 876 MET cc_start: 0.7696 (tpp) cc_final: 0.7346 (tpt) REVERT: A 953 TYR cc_start: 0.7698 (t80) cc_final: 0.7107 (t80) REVERT: A 1027 MET cc_start: -0.1078 (tpp) cc_final: -0.2733 (mpp) REVERT: B 86 GLU cc_start: 0.7860 (tp30) cc_final: 0.7541 (tt0) REVERT: B 110 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.5753 (mp0) REVERT: C 103 GLU cc_start: 0.7554 (mp0) cc_final: 0.7215 (mt-10) outliers start: 33 outliers final: 21 residues processed: 117 average time/residue: 0.2143 time to fit residues: 39.9264 Evaluate side-chains 113 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 96 optimal weight: 0.4980 chunk 144 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 136 optimal weight: 30.0000 chunk 41 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1182 GLN A1232 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13046 Z= 0.155 Angle : 0.527 8.255 17731 Z= 0.265 Chirality : 0.039 0.146 2046 Planarity : 0.003 0.041 2168 Dihedral : 8.193 74.965 2466 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.55 % Allowed : 13.86 % Favored : 83.60 % 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: 0.16 (0.21), residues: 1584 helix: 1.26 (0.19), residues: 771 sheet: 0.21 (0.32), residues: 272 loop : -1.65 (0.24), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 708 HIS 0.003 0.001 HIS B 194 PHE 0.014 0.001 PHE A 465 TYR 0.014 0.001 TYR A 953 ARG 0.003 0.000 ARG B 113 *********************** 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 132 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 98 time to evaluate : 1.358 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.6273 (mpp) cc_final: 0.5976 (mpp) REVERT: A 440 MET cc_start: 0.3515 (ppp) cc_final: 0.2674 (pmm) REVERT: A 450 MET cc_start: 0.2846 (mmt) cc_final: 0.2584 (mmm) REVERT: A 744 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7798 (p0) REVERT: A 876 MET cc_start: 0.7700 (tpp) cc_final: 0.7355 (tpt) REVERT: A 953 TYR cc_start: 0.7565 (t80) cc_final: 0.6927 (t80) REVERT: A 1027 MET cc_start: -0.1272 (tpp) cc_final: -0.2824 (mpp) REVERT: B 17 ASP cc_start: 0.7127 (m-30) cc_final: 0.5911 (t70) REVERT: B 81 SER cc_start: 0.6765 (OUTLIER) cc_final: 0.6420 (m) REVERT: B 86 GLU cc_start: 0.7821 (tp30) cc_final: 0.7584 (tt0) REVERT: B 215 PHE cc_start: 0.2572 (OUTLIER) cc_final: 0.1001 (m-80) REVERT: C 103 GLU cc_start: 0.7494 (mp0) cc_final: 0.7157 (mt-10) REVERT: C 105 TRP cc_start: 0.7376 (m100) cc_final: 0.6919 (m100) REVERT: C 111 GLN cc_start: 0.7876 (tp40) cc_final: 0.7041 (pt0) outliers start: 34 outliers final: 19 residues processed: 121 average time/residue: 0.2164 time to fit residues: 41.4988 Evaluate side-chains 112 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 0.3980 chunk 86 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1182 GLN A1215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13046 Z= 0.149 Angle : 0.509 7.938 17731 Z= 0.255 Chirality : 0.039 0.132 2046 Planarity : 0.003 0.040 2168 Dihedral : 7.735 70.890 2463 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.77 % Allowed : 14.98 % Favored : 82.25 % 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: 0.46 (0.21), residues: 1584 helix: 1.49 (0.19), residues: 776 sheet: 0.40 (0.32), residues: 268 loop : -1.51 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 708 HIS 0.005 0.001 HIS A1155 PHE 0.011 0.001 PHE A 942 TYR 0.014 0.001 TYR C 95 ARG 0.003 0.000 ARG B 113 *********************** 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 140 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 103 time to evaluate : 1.383 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8159 (tp) REVERT: A 105 MET cc_start: 0.6334 (mpp) cc_final: 0.4959 (tpp) REVERT: A 174 ARG cc_start: 0.6012 (OUTLIER) cc_final: 0.5217 (ptt90) REVERT: A 440 MET cc_start: 0.3769 (ppp) cc_final: 0.3013 (pmm) REVERT: A 450 MET cc_start: 0.2861 (mmt) cc_final: 0.2541 (mmm) REVERT: A 469 ILE cc_start: 0.6037 (OUTLIER) cc_final: 0.5791 (mp) REVERT: A 779 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7912 (ttmm) REVERT: A 876 MET cc_start: 0.7763 (tpp) cc_final: 0.7478 (tpt) REVERT: A 953 TYR cc_start: 0.7473 (t80) cc_final: 0.6833 (t80) REVERT: A 1027 MET cc_start: -0.1245 (tpp) cc_final: -0.2796 (mpp) REVERT: B 17 ASP cc_start: 0.6962 (m-30) cc_final: 0.5867 (t70) REVERT: B 81 SER cc_start: 0.6695 (OUTLIER) cc_final: 0.6371 (m) REVERT: B 86 GLU cc_start: 0.7866 (tp30) cc_final: 0.7541 (tt0) REVERT: B 215 PHE cc_start: 0.2558 (OUTLIER) cc_final: 0.0955 (m-80) REVERT: C 103 GLU cc_start: 0.7537 (mp0) cc_final: 0.7222 (mt-10) REVERT: C 105 TRP cc_start: 0.7358 (m100) cc_final: 0.6960 (m100) REVERT: C 111 GLN cc_start: 0.7897 (tp40) cc_final: 0.7093 (pt0) outliers start: 37 outliers final: 25 residues processed: 129 average time/residue: 0.2419 time to fit residues: 47.3146 Evaluate side-chains 128 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 97 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1133 TYR Chi-restraints excluded: chain A residue 1191 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 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 172 ASN ** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 ASN A1182 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13046 Z= 0.194 Angle : 0.537 8.184 17731 Z= 0.272 Chirality : 0.040 0.133 2046 Planarity : 0.003 0.039 2168 Dihedral : 7.777 69.404 2462 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.32 % Allowed : 15.88 % Favored : 81.80 % 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: 0.50 (0.21), residues: 1584 helix: 1.46 (0.19), residues: 776 sheet: 0.55 (0.32), residues: 269 loop : -1.48 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 168 HIS 0.003 0.001 HIS B 98 PHE 0.015 0.001 PHE A 152 TYR 0.018 0.001 TYR C 95 ARG 0.004 0.000 ARG A 262 *********************** 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 128 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 97 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.6341 (mpp) cc_final: 0.4849 (tpp) REVERT: A 440 MET cc_start: 0.4016 (ppp) cc_final: 0.2602 (ptp) REVERT: A 450 MET cc_start: 0.2683 (mmt) cc_final: 0.2424 (mmm) REVERT: A 744 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7909 (p0) REVERT: A 876 MET cc_start: 0.7869 (tpp) cc_final: 0.7529 (tpt) REVERT: A 953 TYR cc_start: 0.7686 (t80) cc_final: 0.7109 (t80) REVERT: A 1027 MET cc_start: -0.1221 (tpp) cc_final: -0.2924 (mpp) REVERT: A 1090 LEU cc_start: 0.2161 (OUTLIER) cc_final: 0.1913 (pp) REVERT: B 86 GLU cc_start: 0.7852 (tp30) cc_final: 0.7544 (tt0) REVERT: B 180 MET cc_start: 0.5931 (tpt) cc_final: 0.5351 (tpt) REVERT: B 215 PHE cc_start: 0.2573 (OUTLIER) cc_final: 0.0889 (m-80) REVERT: C 103 GLU cc_start: 0.7541 (mp0) cc_final: 0.7219 (mt-10) REVERT: C 105 TRP cc_start: 0.7519 (m100) cc_final: 0.7023 (m100) REVERT: C 121 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7503 (mttm) outliers start: 31 outliers final: 20 residues processed: 118 average time/residue: 0.2485 time to fit residues: 46.4971 Evaluate side-chains 116 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 0.8980 chunk 17 optimal weight: 0.0980 chunk 87 optimal weight: 4.9990 chunk 111 optimal weight: 30.0000 chunk 86 optimal weight: 0.9990 chunk 128 optimal weight: 20.0000 chunk 85 optimal weight: 0.0040 chunk 152 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 92 optimal weight: 0.0020 chunk 70 optimal weight: 2.9990 overall best weight: 0.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A1130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13046 Z= 0.125 Angle : 0.483 8.954 17731 Z= 0.243 Chirality : 0.038 0.131 2046 Planarity : 0.003 0.039 2168 Dihedral : 7.352 65.961 2460 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.87 % Allowed : 16.63 % Favored : 81.50 % 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: 0.88 (0.22), residues: 1584 helix: 1.79 (0.19), residues: 771 sheet: 0.61 (0.33), residues: 268 loop : -1.22 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 708 HIS 0.001 0.000 HIS A1007 PHE 0.012 0.001 PHE A 152 TYR 0.012 0.001 TYR C 100 ARG 0.002 0.000 ARG A 749 *********************** 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 125 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 1.995 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.6220 (mpp) cc_final: 0.4916 (tpp) REVERT: A 174 ARG cc_start: 0.5792 (OUTLIER) cc_final: 0.5044 (ptt90) REVERT: A 242 LYS cc_start: 0.6936 (mmtm) cc_final: 0.6078 (mmmm) REVERT: A 440 MET cc_start: 0.4110 (ppp) cc_final: 0.2698 (ptt) REVERT: A 744 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7862 (p0) REVERT: A 779 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7906 (ttmt) REVERT: A 876 MET cc_start: 0.7877 (tpp) cc_final: 0.7551 (tpt) REVERT: A 953 TYR cc_start: 0.7387 (t80) cc_final: 0.6761 (t80) REVERT: A 1027 MET cc_start: -0.1116 (tpp) cc_final: -0.2992 (mpp) REVERT: B 17 ASP cc_start: 0.6993 (m-30) cc_final: 0.5990 (t70) REVERT: B 86 GLU cc_start: 0.7867 (tp30) cc_final: 0.7607 (tt0) REVERT: B 170 ASP cc_start: 0.6892 (p0) cc_final: 0.6168 (t70) REVERT: B 215 PHE cc_start: 0.2768 (OUTLIER) cc_final: 0.0987 (m-80) REVERT: C 103 GLU cc_start: 0.7428 (mp0) cc_final: 0.6831 (mp0) REVERT: C 105 TRP cc_start: 0.7329 (m100) cc_final: 0.6814 (m100) REVERT: C 121 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7443 (mttm) outliers start: 25 outliers final: 16 residues processed: 117 average time/residue: 0.2484 time to fit residues: 44.4857 Evaluate side-chains 113 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 994 PHE Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 121 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13046 Z= 0.202 Angle : 0.544 8.245 17731 Z= 0.273 Chirality : 0.040 0.130 2046 Planarity : 0.003 0.038 2168 Dihedral : 7.549 64.928 2458 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.80 % Allowed : 17.68 % Favored : 80.52 % 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: 0.75 (0.22), residues: 1584 helix: 1.59 (0.19), residues: 776 sheet: 0.70 (0.33), residues: 272 loop : -1.26 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 708 HIS 0.004 0.001 HIS B 98 PHE 0.015 0.001 PHE A 152 TYR 0.019 0.002 TYR C 100 ARG 0.002 0.000 ARG A 749 *********************** 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 115 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 1.169 Fit side-chains REVERT: A 105 MET cc_start: 0.6203 (mpp) cc_final: 0.4845 (tpp) REVERT: A 242 LYS cc_start: 0.6970 (mmtm) cc_final: 0.6166 (mmmm) REVERT: A 440 MET cc_start: 0.4315 (ppp) cc_final: 0.2976 (ptp) REVERT: A 744 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7963 (p0) REVERT: A 779 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7980 (ttmm) REVERT: A 876 MET cc_start: 0.7903 (tpp) cc_final: 0.7550 (tpt) REVERT: A 953 TYR cc_start: 0.7683 (t80) cc_final: 0.7178 (t80) REVERT: A 1027 MET cc_start: -0.1043 (tpp) cc_final: -0.1633 (mmm) REVERT: B 17 ASP cc_start: 0.7025 (m-30) cc_final: 0.6030 (t70) REVERT: B 81 SER cc_start: 0.6622 (OUTLIER) cc_final: 0.6350 (m) REVERT: B 86 GLU cc_start: 0.7861 (tp30) cc_final: 0.7603 (tt0) REVERT: B 170 ASP cc_start: 0.6908 (p0) cc_final: 0.6296 (t70) REVERT: B 180 MET cc_start: 0.5906 (tpt) cc_final: 0.5253 (tpt) REVERT: B 215 PHE cc_start: 0.2600 (OUTLIER) cc_final: 0.0920 (m-80) REVERT: C 103 GLU cc_start: 0.7472 (mp0) cc_final: 0.7161 (mt-10) REVERT: C 105 TRP cc_start: 0.7505 (m100) cc_final: 0.6906 (m100) REVERT: C 121 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7433 (mttm) outliers start: 24 outliers final: 17 residues processed: 109 average time/residue: 0.2501 time to fit residues: 41.5100 Evaluate side-chains 111 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 121 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 0.0770 chunk 111 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 128 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 93 optimal weight: 0.0020 chunk 150 optimal weight: 4.9990 overall best weight: 1.7950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13046 Z= 0.270 Angle : 0.610 9.541 17731 Z= 0.311 Chirality : 0.042 0.142 2046 Planarity : 0.004 0.038 2168 Dihedral : 8.234 69.812 2458 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.17 % Allowed : 17.75 % Favored : 80.07 % 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: 0.42 (0.21), residues: 1584 helix: 1.37 (0.19), residues: 766 sheet: 0.55 (0.33), residues: 270 loop : -1.45 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 708 HIS 0.005 0.001 HIS B 98 PHE 0.019 0.002 PHE A 314 TYR 0.026 0.002 TYR C 100 ARG 0.003 0.000 ARG A 749 *********************** 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 117 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 88 time to evaluate : 1.422 Fit side-chains REVERT: A 105 MET cc_start: 0.6286 (mpp) cc_final: 0.5978 (mpp) REVERT: A 235 ILE cc_start: 0.7779 (mm) cc_final: 0.7565 (mm) REVERT: A 242 LYS cc_start: 0.6940 (mmtm) cc_final: 0.6176 (mmmm) REVERT: A 779 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8012 (ttmm) REVERT: A 876 MET cc_start: 0.7947 (tpp) cc_final: 0.7626 (tpt) REVERT: A 1027 MET cc_start: -0.0831 (tpp) cc_final: -0.1609 (mmm) REVERT: B 86 GLU cc_start: 0.7813 (tp30) cc_final: 0.7566 (tt0) REVERT: B 170 ASP cc_start: 0.6924 (p0) cc_final: 0.6606 (t70) REVERT: B 174 LYS cc_start: 0.6152 (mmtm) cc_final: 0.5913 (mmtm) REVERT: B 215 PHE cc_start: 0.2704 (OUTLIER) cc_final: 0.1016 (m-80) REVERT: C 103 GLU cc_start: 0.7503 (mp0) cc_final: 0.7280 (mt-10) REVERT: C 105 TRP cc_start: 0.7602 (m100) cc_final: 0.6999 (m100) REVERT: C 121 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7395 (mttm) outliers start: 29 outliers final: 25 residues processed: 113 average time/residue: 0.2450 time to fit residues: 42.2943 Evaluate side-chains 113 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 85 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 121 LYS 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: 0.9980 chunk 104 optimal weight: 0.0670 chunk 157 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13046 Z= 0.162 Angle : 0.537 8.924 17731 Z= 0.271 Chirality : 0.039 0.132 2046 Planarity : 0.003 0.038 2168 Dihedral : 7.830 66.977 2458 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.65 % Allowed : 18.50 % Favored : 79.85 % 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: 0.70 (0.22), residues: 1584 helix: 1.61 (0.19), residues: 766 sheet: 0.67 (0.33), residues: 270 loop : -1.33 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 708 HIS 0.003 0.000 HIS B 98 PHE 0.055 0.001 PHE A 904 TYR 0.021 0.001 TYR C 100 ARG 0.002 0.000 ARG A1192 ********************** 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 113 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 1.347 Fit side-chains REVERT: A 105 MET cc_start: 0.6260 (mpp) cc_final: 0.6001 (mpp) REVERT: A 174 ARG cc_start: 0.5989 (OUTLIER) cc_final: 0.5127 (ptt90) REVERT: A 242 LYS cc_start: 0.6959 (mmtm) cc_final: 0.6133 (mmmm) REVERT: A 744 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.7943 (p0) REVERT: A 779 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7977 (ttmm) REVERT: A 876 MET cc_start: 0.7908 (tpp) cc_final: 0.7576 (tpt) REVERT: A 953 TYR cc_start: 0.7670 (t80) cc_final: 0.7109 (t80) REVERT: A 1027 MET cc_start: -0.0736 (tpp) cc_final: -0.1547 (mmm) REVERT: B 86 GLU cc_start: 0.7834 (tp30) cc_final: 0.7576 (tt0) REVERT: B 170 ASP cc_start: 0.6869 (p0) cc_final: 0.6618 (t70) REVERT: B 215 PHE cc_start: 0.2690 (OUTLIER) cc_final: 0.0967 (m-80) REVERT: C 103 GLU cc_start: 0.7444 (mp0) cc_final: 0.7193 (mt-10) REVERT: C 105 TRP cc_start: 0.7460 (m100) cc_final: 0.6832 (m100) REVERT: C 121 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7381 (mttm) outliers start: 22 outliers final: 17 residues processed: 109 average time/residue: 0.2413 time to fit residues: 39.9258 Evaluate side-chains 111 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 779 LYS Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 121 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.207444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.153230 restraints weight = 16778.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.149553 restraints weight = 29397.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.152060 restraints weight = 21857.249| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13046 Z= 0.218 Angle : 0.567 8.635 17731 Z= 0.287 Chirality : 0.040 0.133 2046 Planarity : 0.004 0.038 2168 Dihedral : 7.899 67.157 2458 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.10 % Allowed : 18.50 % Favored : 79.40 % 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: 1.49 (0.19), residues: 768 sheet: 0.64 (0.33), residues: 270 loop : -1.38 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 708 HIS 0.003 0.001 HIS B 98 PHE 0.049 0.002 PHE A 904 TYR 0.023 0.002 TYR C 100 ARG 0.002 0.000 ARG A 749 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2397.40 seconds wall clock time: 45 minutes 16.60 seconds (2716.60 seconds total)