Starting phenix.real_space_refine on Sun Sep 29 11:56:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1s_26304/09_2024/7u1s_26304.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1s_26304/09_2024/7u1s_26304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1s_26304/09_2024/7u1s_26304.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1s_26304/09_2024/7u1s_26304.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1s_26304/09_2024/7u1s_26304.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1s_26304/09_2024/7u1s_26304.cif" } resolution = 3.8 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 ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 1 8.98 5 P 32 5.49 5 S 113 5.16 5 C 13738 2.51 5 N 3571 2.21 5 O 3770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21225 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2641 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 16, 'TRANS': 343} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 2, 'HIS:plan': 1, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 135 Chain: "B" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2508 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 317} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2497 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 13, 'TRANS': 318} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2485 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 13, 'TRANS': 316} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 81 Chain: "E" Number of atoms: 10181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1439, 10181 Classifications: {'peptide': 1439} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 343} Link IDs: {'PTRANS': 49, 'TRANS': 1389} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1198 Unresolved non-hydrogen angles: 1498 Unresolved non-hydrogen dihedrals: 959 Unresolved non-hydrogen chiralities: 119 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 32, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 16, 'GLU:plan': 34, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 633 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 207 Unusual residues: {' K': 1, 'ATP': 2, 'POV': 1} Classifications: {'peptide': 2, 'undetermined': 4} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'POV': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 152 Unusual residues: {'ATP': 2, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'POV': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 346 Unusual residues: {'ATP': 1, 'BJX': 1, 'POV': 1, 'PTY': 6} Classifications: {'peptide': 1, 'undetermined': 9} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 124 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 12.15, per 1000 atoms: 0.57 Number of scatterers: 21225 At special positions: 0 Unit cell: (166.155, 104.5, 147.345, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 1 19.00 S 113 16.00 P 32 15.00 O 3770 8.00 N 3571 7.00 C 13738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 26 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG F 1 " - " ASN E 10 " Time building additional restraints: 5.28 Conformation dependent library (CDL) restraints added in 2.5 seconds 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5274 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 31 sheets defined 52.7% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.923A pdb=" N ASP A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 67 through 98 Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.943A pdb=" N ILE A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 345 through 357 Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 58 through 66 Processing helix chain 'B' and resid 67 through 98 Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 142 through 172 removed outlier: 4.053A pdb=" N ILE B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 179 removed outlier: 3.503A pdb=" N ALA B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 179 " --> pdb=" O HIS B 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 174 through 179' Processing helix chain 'B' and resid 265 through 270 removed outlier: 4.226A pdb=" N ASP B 269 " --> pdb=" O PRO B 266 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 270 " --> pdb=" O LEU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.645A pdb=" N LEU B 275 " --> pdb=" O PRO B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 345 through 360 removed outlier: 3.855A pdb=" N ASP B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 66 removed outlier: 3.531A pdb=" N THR C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 98 Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 142 through 172 removed outlier: 3.914A pdb=" N ILE C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.728A pdb=" N LEU C 275 " --> pdb=" O PRO C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 345 through 361 Processing helix chain 'D' and resid 53 through 58 Processing helix chain 'D' and resid 58 through 66 removed outlier: 3.685A pdb=" N THR D 62 " --> pdb=" O ASP D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 98 Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 142 through 172 removed outlier: 4.057A pdb=" N ILE D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 329 through 333 Processing helix chain 'D' and resid 345 through 359 Processing helix chain 'E' and resid 8 through 13 removed outlier: 4.417A pdb=" N ALA E 13 " --> pdb=" O GLU E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 32 removed outlier: 4.056A pdb=" N ASP E 29 " --> pdb=" O GLY E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 54 removed outlier: 3.556A pdb=" N PHE E 41 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Proline residue: E 45 - end of helix removed outlier: 3.503A pdb=" N ILE E 49 " --> pdb=" O PRO E 45 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 71 through 99 removed outlier: 3.528A pdb=" N ILE E 76 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU E 88 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY E 97 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL E 98 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR E 99 " --> pdb=" O SER E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 106 Processing helix chain 'E' and resid 107 through 130 removed outlier: 3.597A pdb=" N MET E 115 " --> pdb=" O GLY E 111 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER E 130 " --> pdb=" O ASN E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 135 removed outlier: 3.681A pdb=" N LEU E 135 " --> pdb=" O PHE E 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 132 through 135' Processing helix chain 'E' and resid 136 through 159 removed outlier: 3.856A pdb=" N THR E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 194 removed outlier: 3.550A pdb=" N ILE E 177 " --> pdb=" O GLY E 173 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 182 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE E 190 " --> pdb=" O GLU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.657A pdb=" N ASP E 212 " --> pdb=" O ASP E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 230 Processing helix chain 'E' and resid 232 through 243 removed outlier: 4.200A pdb=" N PHE E 236 " --> pdb=" O TRP E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 277 Processing helix chain 'E' and resid 283 through 314 removed outlier: 6.005A pdb=" N ARG E 297 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU E 301 " --> pdb=" O ARG E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 327 Processing helix chain 'E' and resid 347 through 352 Processing helix chain 'E' and resid 354 through 401 removed outlier: 3.955A pdb=" N GLN E 374 " --> pdb=" O ARG E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 434 removed outlier: 3.881A pdb=" N THR E 425 " --> pdb=" O VAL E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 456 removed outlier: 3.802A pdb=" N LEU E 438 " --> pdb=" O LEU E 434 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TRP E 439 " --> pdb=" O CYS E 435 " (cutoff:3.500A) Proline residue: E 442 - end of helix Processing helix chain 'E' and resid 457 through 503 removed outlier: 3.923A pdb=" N LEU E 461 " --> pdb=" O GLY E 457 " (cutoff:3.500A) Proline residue: E 472 - end of helix Processing helix chain 'E' and resid 505 through 512 removed outlier: 3.571A pdb=" N TYR E 512 " --> pdb=" O LEU E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 565 removed outlier: 3.809A pdb=" N PHE E 518 " --> pdb=" O TRP E 514 " (cutoff:3.500A) Proline residue: E 551 - end of helix Processing helix chain 'E' and resid 572 through 591 removed outlier: 3.723A pdb=" N ALA E 578 " --> pdb=" O SER E 574 " (cutoff:3.500A) Proline residue: E 589 - end of helix Processing helix chain 'E' and resid 592 through 615 Processing helix chain 'E' and resid 718 through 726 removed outlier: 3.516A pdb=" N LEU E 722 " --> pdb=" O GLY E 718 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 790 Processing helix chain 'E' and resid 795 through 807 Processing helix chain 'E' and resid 807 through 813 removed outlier: 4.392A pdb=" N ASP E 811 " --> pdb=" O SER E 807 " (cutoff:3.500A) Processing helix chain 'E' and resid 817 through 821 removed outlier: 3.551A pdb=" N THR E 821 " --> pdb=" O GLY E 818 " (cutoff:3.500A) Processing helix chain 'E' and resid 831 through 846 removed outlier: 3.732A pdb=" N GLN E 846 " --> pdb=" O ARG E 842 " (cutoff:3.500A) Processing helix chain 'E' and resid 862 through 881 Processing helix chain 'E' and resid 914 through 921 Processing helix chain 'E' and resid 988 through 993 removed outlier: 4.037A pdb=" N ARG E 993 " --> pdb=" O VAL E 989 " (cutoff:3.500A) Processing helix chain 'E' and resid 996 through 1009 removed outlier: 3.579A pdb=" N LYS E1003 " --> pdb=" O ARG E 999 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY E1009 " --> pdb=" O LEU E1005 " (cutoff:3.500A) Processing helix chain 'E' and resid 1010 through 1041 Processing helix chain 'E' and resid 1064 through 1107 Processing helix chain 'E' and resid 1109 through 1116 removed outlier: 3.548A pdb=" N PHE E1113 " --> pdb=" O PRO E1109 " (cutoff:3.500A) Processing helix chain 'E' and resid 1118 through 1135 removed outlier: 3.537A pdb=" N LEU E1122 " --> pdb=" O LEU E1118 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP E1128 " --> pdb=" O ARG E1124 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1135 through 1161 Processing helix chain 'E' and resid 1163 through 1210 removed outlier: 3.973A pdb=" N ALA E1167 " --> pdb=" O VAL E1163 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 3.543A pdb=" N ASP E1188 " --> pdb=" O VAL E1184 " (cutoff:3.500A) Proline residue: E1199 - end of helix Processing helix chain 'E' and resid 1210 through 1217 removed outlier: 3.541A pdb=" N PHE E1217 " --> pdb=" O THR E1213 " (cutoff:3.500A) Processing helix chain 'E' and resid 1219 through 1274 removed outlier: 3.668A pdb=" N PHE E1223 " --> pdb=" O TYR E1219 " (cutoff:3.500A) Processing helix chain 'E' and resid 1278 through 1320 removed outlier: 4.024A pdb=" N GLY E1282 " --> pdb=" O ALA E1278 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET E1290 " --> pdb=" O THR E1286 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER E1292 " --> pdb=" O ALA E1288 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASN E1293 " --> pdb=" O LEU E1289 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASN E1296 " --> pdb=" O SER E1292 " (cutoff:3.500A) Processing helix chain 'E' and resid 1383 through 1394 Processing helix chain 'E' and resid 1414 through 1421 removed outlier: 3.708A pdb=" N ARG E1421 " --> pdb=" O THR E1417 " (cutoff:3.500A) Processing helix chain 'E' and resid 1436 through 1441 removed outlier: 4.269A pdb=" N ASP E1441 " --> pdb=" O ARG E1437 " (cutoff:3.500A) Processing helix chain 'E' and resid 1450 through 1458 Processing helix chain 'E' and resid 1461 through 1467 removed outlier: 4.347A pdb=" N LYS E1465 " --> pdb=" O LYS E1461 " (cutoff:3.500A) Processing helix chain 'E' and resid 1469 through 1473 removed outlier: 4.256A pdb=" N ASP E1472 " --> pdb=" O GLY E1469 " (cutoff:3.500A) Processing helix chain 'E' and resid 1485 through 1498 Processing helix chain 'E' and resid 1512 through 1529 removed outlier: 3.857A pdb=" N THR E1516 " --> pdb=" O ILE E1512 " (cutoff:3.500A) Processing helix chain 'E' and resid 1539 through 1545 removed outlier: 3.792A pdb=" N ILE E1543 " --> pdb=" O ARG E1539 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER E1545 " --> pdb=" O HIS E1541 " (cutoff:3.500A) Processing helix chain 'E' and resid 1564 through 1570 removed outlier: 3.573A pdb=" N SER E1568 " --> pdb=" O GLU E1564 " (cutoff:3.500A) Processing helix chain 'E' and resid 1571 through 1578 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 259 through 260 Processing sheet with id=AA4, first strand: chain 'A' and resid 210 through 211 removed outlier: 3.525A pdb=" N GLU A 282 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 213 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 237 removed outlier: 4.871A pdb=" N LEU A 233 " --> pdb=" O ARG A 221 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ARG A 221 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN A 235 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL A 219 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASP A 237 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N MET A 217 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 282 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA7, first strand: chain 'A' and resid 319 through 321 removed outlier: 6.311A pdb=" N TYR A 326 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LYS D 47 " --> pdb=" O TYR A 326 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL A 328 " --> pdb=" O LYS D 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 47 removed outlier: 7.104A pdb=" N ALA B 45 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.639A pdb=" N VAL B 202 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 255 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 259 through 260 removed outlier: 6.880A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 234 through 237 removed outlier: 4.039A pdb=" N ALA B 213 " --> pdb=" O ILE B 249 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 234 through 237 removed outlier: 5.153A pdb=" N SER B 212 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL B 290 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 36 through 37 Processing sheet with id=AB5, first strand: chain 'C' and resid 182 through 183 Processing sheet with id=AB6, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.587A pdb=" N ARG C 195 " --> pdb=" O ARG C 192 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 210 through 211 Processing sheet with id=AB8, first strand: chain 'C' and resid 230 through 238 removed outlier: 5.129A pdb=" N THR C 223 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 221 " --> pdb=" O HIS C 234 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 313 through 315 Processing sheet with id=AC1, first strand: chain 'D' and resid 36 through 37 Processing sheet with id=AC2, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.586A pdb=" N VAL D 202 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.768A pdb=" N VAL D 188 " --> pdb=" O MET D 199 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 230 through 237 removed outlier: 4.934A pdb=" N THR D 223 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER D 212 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL D 290 " --> pdb=" O SER D 212 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR D 214 " --> pdb=" O GLU D 288 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 313 through 315 Processing sheet with id=AC6, first strand: chain 'E' and resid 338 through 340 removed outlier: 4.858A pdb=" N THR E 338 " --> pdb=" O PHE E 345 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE E 345 " --> pdb=" O THR E 338 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 679 through 681 Processing sheet with id=AC8, first strand: chain 'E' and resid 685 through 687 removed outlier: 6.904A pdb=" N PHE E 685 " --> pdb=" O VAL E 733 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 710 through 713 removed outlier: 5.840A pdb=" N MET E 710 " --> pdb=" O ILE E 901 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N MET E 903 " --> pdb=" O MET E 710 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL E 712 " --> pdb=" O MET E 903 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 771 through 772 Processing sheet with id=AD2, first strand: chain 'E' and resid 1348 through 1352 removed outlier: 4.824A pdb=" N ASN E1349 " --> pdb=" O ARG E1402 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ARG E1402 " --> pdb=" O ASN E1349 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 1373 through 1377 removed outlier: 7.200A pdb=" N GLN E1373 " --> pdb=" O VAL E1533 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N THR E1535 " --> pdb=" O GLN E1373 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE E1375 " --> pdb=" O THR E1535 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'E' and resid 1549 through 1553 removed outlier: 5.358A pdb=" N LYS E1553 " --> pdb=" O ILE E1557 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE E1557 " --> pdb=" O LYS E1553 " (cutoff:3.500A) 1177 hydrogen bonds defined for protein. 3420 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: 8.22 Time building geometry restraints manager: 6.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3506 1.32 - 1.45: 5504 1.45 - 1.57: 12416 1.57 - 1.69: 63 1.69 - 1.81: 174 Bond restraints: 21663 Sorted by residual: bond pdb=" C16 BJX E1602 " pdb=" N1 BJX E1602 " ideal model delta sigma weight residual 1.344 1.455 -0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" N BJX E1602 " pdb=" C6 BJX E1602 " ideal model delta sigma weight residual 1.412 1.513 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C5 BJX E1602 " pdb=" C7 BJX E1602 " ideal model delta sigma weight residual 1.518 1.615 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C21 BJX E1602 " pdb=" O1 BJX E1602 " ideal model delta sigma weight residual 1.347 1.423 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C5 BJX E1602 " pdb=" C8 BJX E1602 " ideal model delta sigma weight residual 1.536 1.610 -0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 21658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 29129 1.96 - 3.93: 299 3.93 - 5.89: 70 5.89 - 7.85: 13 7.85 - 9.81: 4 Bond angle restraints: 29515 Sorted by residual: angle pdb=" C HIS E1135 " pdb=" N ILE E1136 " pdb=" CA ILE E1136 " ideal model delta sigma weight residual 120.24 122.90 -2.66 6.30e-01 2.52e+00 1.78e+01 angle pdb=" C17 BJX E1602 " pdb=" C16 BJX E1602 " pdb=" N1 BJX E1602 " ideal model delta sigma weight residual 113.90 123.71 -9.81 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C ILE E1136 " pdb=" CA ILE E1136 " pdb=" CB ILE E1136 " ideal model delta sigma weight residual 114.35 111.03 3.32 1.06e+00 8.90e-01 9.83e+00 angle pdb=" O11 PTY E1606 " pdb=" P1 PTY E1606 " pdb=" O14 PTY E1606 " ideal model delta sigma weight residual 92.90 101.55 -8.65 3.00e+00 1.11e-01 8.32e+00 angle pdb=" CA LEU E 341 " pdb=" CB LEU E 341 " pdb=" CG LEU E 341 " ideal model delta sigma weight residual 116.30 125.61 -9.31 3.50e+00 8.16e-02 7.07e+00 ... (remaining 29510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.31: 12593 34.31 - 68.61: 357 68.61 - 102.92: 66 102.92 - 137.23: 37 137.23 - 171.53: 11 Dihedral angle restraints: 13064 sinusoidal: 4953 harmonic: 8111 Sorted by residual: dihedral pdb=" N1 PTY E1606 " pdb=" C2 PTY E1606 " pdb=" C3 PTY E1606 " pdb=" O11 PTY E1606 " ideal model delta sinusoidal sigma weight residual 65.33 -106.20 171.53 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C27 P5S B 402 " pdb=" C28 P5S B 402 " pdb=" C29 P5S B 402 " pdb=" C30 P5S B 402 " ideal model delta sinusoidal sigma weight residual -61.10 109.68 -170.78 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C23 P5S A 406 " pdb=" C24 P5S A 406 " pdb=" C25 P5S A 406 " pdb=" C26 P5S A 406 " ideal model delta sinusoidal sigma weight residual 181.39 21.12 160.27 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 13061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3063 0.061 - 0.121: 445 0.121 - 0.182: 8 0.182 - 0.242: 0 0.242 - 0.303: 7 Chirality restraints: 3523 Sorted by residual: chirality pdb=" C2 P5S A 406 " pdb=" C1 P5S A 406 " pdb=" C3 P5S A 406 " pdb=" O37 P5S A 406 " both_signs ideal model delta sigma weight residual False 2.59 2.29 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C2 P5S C 403 " pdb=" C1 P5S C 403 " pdb=" C3 P5S C 403 " pdb=" O37 P5S C 403 " both_signs ideal model delta sigma weight residual False 2.59 2.31 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN E 10 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 3520 not shown) Planarity restraints: 3626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 588 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO E 589 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO E 589 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 589 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 243 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.22e+00 pdb=" N PRO E 244 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 244 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 244 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 265 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO A 266 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 266 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 266 " 0.023 5.00e-02 4.00e+02 ... (remaining 3623 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 6413 2.83 - 3.41: 23534 3.41 - 3.99: 38261 3.99 - 4.56: 52782 4.56 - 5.14: 77492 Nonbonded interactions: 198482 Sorted by model distance: nonbonded pdb=" NH1 ARG A 177 " pdb=" OG SER A 208 " model vdw 2.253 3.120 nonbonded pdb=" OD1 ASP C 329 " pdb=" OG SER C 331 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASN E 234 " pdb=" NE1 TRP E1247 " model vdw 2.264 3.120 nonbonded pdb=" NH1 ARG E 216 " pdb=" O ALA E 249 " model vdw 2.276 3.120 nonbonded pdb=" O LEU E1192 " pdb=" OG1 THR E1196 " model vdw 2.277 3.040 ... (remaining 198477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 50 or (resid 51 through 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 64 or (resid 65 and ( \ name N or name CA or name C or name O or name CB )) or resid 66 or (resid 67 and \ (name N or name CA or name C or name O or name CB )) or resid 68 through 72 or \ (resid 73 and (name N or name CA or name C or name O or name CB )) or resid 74 t \ hrough 76 or (resid 77 and (name N or name CA or name C or name O or name CB )) \ or resid 78 through 98 or (resid 99 and (name N or name CA or name C or name O o \ r name CB )) or resid 100 through 105 or (resid 106 through 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 through 112 or (resid 113 \ and (name N or name CA or name C or name O or name CB )) or resid 114 through 11 \ 7 or (resid 118 and (name N or name CA or name C or name O or name CB )) or resi \ d 119 through 139 or (resid 140 through 141 and (name N or name CA or name C or \ name O or name CB )) or resid 142 through 145 or (resid 146 and (name N or name \ CA or name C or name O or name CB )) or resid 147 through 157 or (resid 158 and \ (name N or name CA or name C or name O or name CB )) or resid 159 through 205 or \ (resid 206 through 207 and (name N or name CA or name C or name O or name CB )) \ or resid 208 through 261 or (resid 262 and (name N or name CA or name C or name \ O or name CB )) or resid 263 through 272 or (resid 273 and (name N or name CA o \ r name C or name O or name CB )) or resid 274 through 279 or (resid 280 and (nam \ e N or name CA or name C or name O or name CB )) or resid 281 through 313 or (re \ sid 314 and (name N or name CA or name C or name O or name CB )) or resid 315 th \ rough 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) \ or resid 326 through 328 or (resid 329 and (name N or name CA or name C or name \ O or name CB )) or resid 330 or (resid 331 through 332 and (name N or name CA o \ r name C or name O or name CB )) or resid 333 through 349 or (resid 350 through \ 359 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and ((resid 30 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 46 or (resid 47 and (name N or na \ me CA or name C or name O or name CB )) or resid 48 through 51 or (resid 52 and \ (name N or name CA or name C or name O or name CB )) or resid 53 or (resid 54 an \ d (name N or name CA or name C or name O or name CB )) or resid 55 through 64 or \ (resid 65 and (name N or name CA or name C or name O or name CB )) or resid 66 \ or (resid 67 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 8 through 72 or (resid 73 and (name N or name CA or name C or name O or name CB \ )) or resid 74 through 76 or (resid 77 and (name N or name CA or name C or name \ O or name CB )) or resid 78 through 98 or (resid 99 and (name N or name CA or na \ me C or name O or name CB )) or resid 100 through 105 or (resid 106 through 107 \ and (name N or name CA or name C or name O or name CB )) or resid 108 through 11 \ 2 or (resid 113 and (name N or name CA or name C or name O or name CB )) or resi \ d 114 through 117 or (resid 118 and (name N or name CA or name C or name O or na \ me CB )) or resid 119 through 125 or (resid 126 and (name N or name CA or name C \ or name O or name CB )) or resid 127 through 157 or (resid 158 and (name N or n \ ame CA or name C or name O or name CB )) or resid 159 through 174 or (resid 175 \ and (name N or name CA or name C or name O or name CB )) or resid 176 through 20 \ 5 or (resid 206 through 207 and (name N or name CA or name C or name O or name C \ B )) or resid 208 through 261 or (resid 262 and (name N or name CA or name C or \ name O or name CB )) or resid 263 through 272 or (resid 273 and (name N or name \ CA or name C or name O or name CB )) or resid 274 through 279 or (resid 280 and \ (name N or name CA or name C or name O or name CB )) or resid 281 through 287 or \ (resid 288 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 9 through 313 or (resid 314 and (name N or name CA or name C or name O or name C \ B )) or resid 315 through 320 or (resid 321 through 323 and (name N or name CA o \ r name C or name O or name CB )) or resid 324 through 328 or (resid 329 and (nam \ e N or name CA or name C or name O or name CB )) or resid 330 or (resid 331 thro \ ugh 332 and (name N or name CA or name C or name O or name CB )) or resid 333 th \ rough 338 or (resid 339 and (name N or name CA or name C or name O or name CB )) \ or resid 340 through 347 or (resid 348 through 359 and (name N or name CA or na \ me C or name O or name CB )))) selection = (chain 'C' and ((resid 30 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 46 or (resid 47 and (name N or name CA or name \ C or name O or name CB )) or resid 48 through 50 or (resid 51 through 52 and (n \ ame N or name CA or name C or name O or name CB )) or resid 53 through 64 or (re \ sid 65 and (name N or name CA or name C or name O or name CB )) or resid 66 thro \ ugh 125 or (resid 126 and (name N or name CA or name C or name O or name CB )) o \ r resid 127 through 139 or (resid 140 through 141 and (name N or name CA or name \ C or name O or name CB )) or resid 142 through 145 or (resid 146 and (name N or \ name CA or name C or name O or name CB )) or resid 147 through 174 or (resid 17 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 176 through \ 205 or (resid 206 through 207 and (name N or name CA or name C or name O or name \ CB )) or resid 208 through 272 or (resid 273 and (name N or name CA or name C o \ r name O or name CB )) or resid 274 through 279 or (resid 280 and (name N or nam \ e CA or name C or name O or name CB )) or resid 281 through 287 or (resid 288 an \ d (name N or name CA or name C or name O or name CB )) or resid 289 through 313 \ or (resid 314 and (name N or name CA or name C or name O or name CB )) or resid \ 315 through 320 or (resid 321 through 323 and (name N or name CA or name C or na \ me O or name CB )) or resid 324 or (resid 325 and (name N or name CA or name C o \ r name O or name CB )) or resid 326 through 328 or (resid 329 and (name N or nam \ e CA or name C or name O or name CB )) or resid 330 or (resid 331 through 332 an \ d (name N or name CA or name C or name O or name CB )) or resid 333 through 338 \ or (resid 339 and (name N or name CA or name C or name O or name CB )) or resid \ 340 through 348 or (resid 349 through 359 and (name N or name CA or name C or na \ me O or name CB )))) selection = (chain 'D' and ((resid 30 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 46 or (resid 47 and (name N or name CA or name \ C or name O or name CB )) or resid 48 through 53 or (resid 54 and (name N or na \ me CA or name C or name O or name CB )) or resid 55 through 66 or (resid 67 and \ (name N or name CA or name C or name O or name CB )) or resid 68 through 72 or ( \ resid 73 and (name N or name CA or name C or name O or name CB )) or resid 74 th \ rough 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) o \ r resid 100 through 105 or (resid 106 through 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 through 112 or (resid 113 and (name N or \ name CA or name C or name O or name CB )) or resid 114 through 117 or (resid 11 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 119 through \ 125 or (resid 126 and (name N or name CA or name C or name O or name CB )) or re \ sid 127 through 139 or (resid 140 through 141 and (name N or name CA or name C o \ r name O or name CB )) or resid 142 through 145 or (resid 146 and (name N or nam \ e CA or name C or name O or name CB )) or resid 147 through 157 or (resid 158 an \ d (name N or name CA or name C or name O or name CB )) or resid 159 through 174 \ or (resid 175 and (name N or name CA or name C or name O or name CB )) or resid \ 176 through 206 or (resid 207 and (name N or name CA or name C or name O or name \ CB )) or resid 208 through 261 or (resid 262 and (name N or name CA or name C o \ r name O or name CB )) or resid 263 through 287 or (resid 288 and (name N or nam \ e CA or name C or name O or name CB )) or resid 289 through 320 or (resid 321 th \ rough 323 and (name N or name CA or name C or name O or name CB )) or resid 324 \ or (resid 325 and (name N or name CA or name C or name O or name CB )) or resid \ 326 through 338 or (resid 339 and (name N or name CA or name C or name O or name \ CB )) or resid 340 through 347 or (resid 348 through 359 and (name N or name CA \ or name C or name O or name CB )))) } 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: 0.180 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: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 46.340 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 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 : 0.003 0.111 21663 Z= 0.200 Angle : 0.535 9.814 29515 Z= 0.248 Chirality : 0.042 0.303 3523 Planarity : 0.004 0.054 3625 Dihedral : 18.591 171.533 7775 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.10 % Allowed : 5.33 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2774 helix: 1.43 (0.15), residues: 1315 sheet: -2.36 (0.29), residues: 287 loop : -1.95 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 899 HIS 0.003 0.000 HIS E 36 PHE 0.013 0.001 PHE C 168 TYR 0.009 0.001 TYR E1064 ARG 0.004 0.000 ARG E1145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 722 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8313 (mm-30) REVERT: A 304 TYR cc_start: 0.8536 (m-80) cc_final: 0.8299 (m-80) REVERT: A 343 LEU cc_start: 0.7061 (mt) cc_final: 0.6618 (tp) REVERT: B 47 LYS cc_start: 0.7983 (mttt) cc_final: 0.7722 (mtpp) REVERT: B 67 LYS cc_start: 0.8514 (mppt) cc_final: 0.8232 (mptt) REVERT: B 224 THR cc_start: 0.8407 (p) cc_final: 0.8199 (p) REVERT: B 264 ASN cc_start: 0.8071 (m-40) cc_final: 0.7782 (m-40) REVERT: B 286 ILE cc_start: 0.9419 (mm) cc_final: 0.9167 (mm) REVERT: C 64 VAL cc_start: 0.8729 (t) cc_final: 0.8498 (t) REVERT: C 114 ILE cc_start: 0.8422 (mm) cc_final: 0.8027 (tp) REVERT: C 119 SER cc_start: 0.8339 (p) cc_final: 0.8108 (m) REVERT: C 199 MET cc_start: 0.8627 (mtt) cc_final: 0.8305 (mtp) REVERT: D 114 ILE cc_start: 0.9258 (mm) cc_final: 0.8958 (mm) REVERT: D 212 SER cc_start: 0.9133 (m) cc_final: 0.8771 (p) REVERT: D 255 LEU cc_start: 0.8093 (mt) cc_final: 0.7887 (mt) REVERT: D 274 ASP cc_start: 0.6851 (t70) cc_final: 0.6456 (t0) REVERT: D 317 PRO cc_start: 0.8716 (Cg_exo) cc_final: 0.8461 (Cg_endo) REVERT: E 292 CYS cc_start: 0.7900 (m) cc_final: 0.7621 (t) REVERT: E 298 ARG cc_start: 0.8014 (mmm160) cc_final: 0.7642 (mmm160) REVERT: E 323 ILE cc_start: 0.8459 (mt) cc_final: 0.8135 (mt) REVERT: E 369 GLN cc_start: 0.8296 (tt0) cc_final: 0.8088 (tm-30) REVERT: E 370 ARG cc_start: 0.7984 (mtt180) cc_final: 0.7697 (mtt180) REVERT: E 381 ILE cc_start: 0.9446 (mm) cc_final: 0.9182 (mt) REVERT: E 400 MET cc_start: 0.8378 (mmp) cc_final: 0.8089 (mmt) REVERT: E 486 ARG cc_start: 0.6806 (tpp-160) cc_final: 0.6596 (mmm160) REVERT: E 493 ASN cc_start: 0.8223 (m-40) cc_final: 0.7568 (m110) REVERT: E 506 MET cc_start: 0.6847 (mmm) cc_final: 0.6610 (mmm) REVERT: E 585 ILE cc_start: 0.8234 (mt) cc_final: 0.8031 (mt) REVERT: E 787 ASN cc_start: 0.8165 (t0) cc_final: 0.7860 (t0) REVERT: E 815 LEU cc_start: 0.6476 (mt) cc_final: 0.6205 (mt) REVERT: E 995 LYS cc_start: 0.7076 (mtmm) cc_final: 0.6839 (mtmm) REVERT: E 1068 PHE cc_start: 0.8526 (t80) cc_final: 0.8311 (t80) REVERT: E 1143 LEU cc_start: 0.8646 (tp) cc_final: 0.8155 (tp) REVERT: E 1290 MET cc_start: 0.6745 (mmm) cc_final: 0.6538 (mmt) REVERT: E 1294 TYR cc_start: 0.8443 (m-10) cc_final: 0.7548 (m-10) outliers start: 2 outliers final: 0 residues processed: 723 average time/residue: 0.3208 time to fit residues: 355.5324 Evaluate side-chains 597 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 597 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 5.9990 chunk 210 optimal weight: 0.0170 chunk 116 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 142 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 217 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 252 optimal weight: 20.0000 overall best weight: 6.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN C 313 GLN C 335 ASN D 279 GLN E 71 HIS E 293 HIS E 326 HIS E1103 ASN E1521 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 21663 Z= 0.383 Angle : 0.710 11.616 29515 Z= 0.360 Chirality : 0.048 0.388 3523 Planarity : 0.005 0.060 3625 Dihedral : 20.192 162.353 3811 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.17 % Allowed : 13.37 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.60 (0.16), residues: 2774 helix: 1.26 (0.14), residues: 1326 sheet: -2.20 (0.29), residues: 274 loop : -1.94 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 232 HIS 0.012 0.002 HIS E 293 PHE 0.028 0.002 PHE C 75 TYR 0.023 0.002 TYR E1032 ARG 0.004 0.001 ARG E1096 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 624 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7324 (t0) cc_final: 0.7023 (t0) REVERT: A 93 ILE cc_start: 0.9057 (tt) cc_final: 0.8776 (mt) REVERT: A 158 MET cc_start: 0.7570 (mmm) cc_final: 0.7044 (mtm) REVERT: A 177 ARG cc_start: 0.8830 (tpt-90) cc_final: 0.8521 (tpt170) REVERT: A 258 TYR cc_start: 0.8449 (p90) cc_final: 0.8180 (p90) REVERT: A 304 TYR cc_start: 0.8913 (m-80) cc_final: 0.8401 (m-80) REVERT: B 42 CYS cc_start: 0.8208 (p) cc_final: 0.7959 (p) REVERT: B 47 LYS cc_start: 0.8092 (mttt) cc_final: 0.7849 (mtpp) REVERT: B 67 LYS cc_start: 0.8725 (mppt) cc_final: 0.8520 (mtmm) REVERT: B 72 LEU cc_start: 0.8162 (mm) cc_final: 0.6557 (mm) REVERT: B 75 PHE cc_start: 0.8364 (t80) cc_final: 0.8135 (t80) REVERT: B 264 ASN cc_start: 0.8146 (m-40) cc_final: 0.7878 (m-40) REVERT: B 313 GLN cc_start: 0.7270 (mt0) cc_final: 0.6753 (mm-40) REVERT: C 114 ILE cc_start: 0.8823 (mm) cc_final: 0.8566 (tp) REVERT: C 200 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8192 (tt) REVERT: D 113 SER cc_start: 0.8755 (m) cc_final: 0.8403 (p) REVERT: D 114 ILE cc_start: 0.9368 (mm) cc_final: 0.9124 (mm) REVERT: D 212 SER cc_start: 0.9283 (m) cc_final: 0.9029 (p) REVERT: D 274 ASP cc_start: 0.7157 (t70) cc_final: 0.6758 (t0) REVERT: D 310 LEU cc_start: 0.9320 (mt) cc_final: 0.9104 (mt) REVERT: E 222 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8343 (m) REVERT: E 234 ASN cc_start: 0.8187 (m-40) cc_final: 0.7741 (m-40) REVERT: E 282 GLN cc_start: 0.5025 (mt0) cc_final: 0.4295 (pp30) REVERT: E 369 GLN cc_start: 0.8326 (tt0) cc_final: 0.7851 (tm-30) REVERT: E 381 ILE cc_start: 0.9554 (mm) cc_final: 0.9331 (mt) REVERT: E 409 MET cc_start: 0.8511 (tpt) cc_final: 0.8041 (tpt) REVERT: E 441 MET cc_start: 0.8146 (mmm) cc_final: 0.7934 (mtt) REVERT: E 486 ARG cc_start: 0.6969 (tpp-160) cc_final: 0.6734 (mmm160) REVERT: E 591 PHE cc_start: 0.6273 (t80) cc_final: 0.5281 (t80) REVERT: E 785 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6583 (mt-10) REVERT: E 1034 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8793 (tp) REVERT: E 1064 TYR cc_start: 0.7953 (m-80) cc_final: 0.7605 (m-80) REVERT: E 1068 PHE cc_start: 0.8471 (t80) cc_final: 0.8235 (t80) REVERT: E 1099 ARG cc_start: 0.7711 (ttp80) cc_final: 0.7342 (tpt170) REVERT: E 1224 GLN cc_start: 0.7752 (mt0) cc_final: 0.7539 (tt0) REVERT: E 1290 MET cc_start: 0.6860 (mmm) cc_final: 0.6377 (mmt) REVERT: E 1294 TYR cc_start: 0.8420 (m-10) cc_final: 0.7486 (m-10) REVERT: E 1308 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7792 (mp10) outliers start: 101 outliers final: 67 residues processed: 660 average time/residue: 0.3200 time to fit residues: 330.3356 Evaluate side-chains 659 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 587 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 257 MET Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 701 ILE Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 865 SER Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1074 LEU Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1276 LEU Chi-restraints excluded: chain E residue 1308 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 40.0000 chunk 78 optimal weight: 0.8980 chunk 210 optimal weight: 20.0000 chunk 171 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 252 optimal weight: 9.9990 chunk 273 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 86 optimal weight: 0.3980 chunk 202 optimal weight: 6.9990 overall best weight: 5.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN B 175 HIS C 335 ASN D 235 GLN ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 GLN E 293 HIS E 326 HIS E 787 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 21663 Z= 0.325 Angle : 0.649 10.403 29515 Z= 0.330 Chirality : 0.047 0.347 3523 Planarity : 0.005 0.069 3625 Dihedral : 18.913 162.493 3811 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 7.22 % Allowed : 15.27 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.16), residues: 2774 helix: 1.43 (0.14), residues: 1329 sheet: -2.03 (0.30), residues: 262 loop : -1.91 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 739 HIS 0.007 0.001 HIS E 125 PHE 0.024 0.002 PHE D 75 TYR 0.023 0.002 TYR E1032 ARG 0.009 0.001 ARG D 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 601 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7210 (t0) cc_final: 0.6803 (t0) REVERT: A 93 ILE cc_start: 0.9065 (tt) cc_final: 0.8726 (mt) REVERT: A 158 MET cc_start: 0.7415 (mmm) cc_final: 0.7034 (mtm) REVERT: A 177 ARG cc_start: 0.8910 (tpt-90) cc_final: 0.8403 (tpt170) REVERT: A 258 TYR cc_start: 0.8368 (p90) cc_final: 0.8151 (p90) REVERT: A 304 TYR cc_start: 0.8820 (m-80) cc_final: 0.8408 (m-80) REVERT: A 343 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7038 (tp) REVERT: B 47 LYS cc_start: 0.8181 (mttt) cc_final: 0.7910 (mttm) REVERT: B 56 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6485 (mt) REVERT: B 67 LYS cc_start: 0.8716 (mppt) cc_final: 0.8397 (mptt) REVERT: B 72 LEU cc_start: 0.8079 (mm) cc_final: 0.6643 (mm) REVERT: B 75 PHE cc_start: 0.8376 (t80) cc_final: 0.8154 (t80) REVERT: B 77 MET cc_start: 0.6900 (mmm) cc_final: 0.6497 (mmt) REVERT: B 264 ASN cc_start: 0.8149 (m-40) cc_final: 0.7869 (m-40) REVERT: B 313 GLN cc_start: 0.7425 (mt0) cc_final: 0.6783 (mm-40) REVERT: C 114 ILE cc_start: 0.8868 (mm) cc_final: 0.8638 (tp) REVERT: C 200 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8279 (tt) REVERT: D 113 SER cc_start: 0.8738 (m) cc_final: 0.8373 (p) REVERT: D 114 ILE cc_start: 0.9377 (mm) cc_final: 0.9176 (mm) REVERT: D 158 MET cc_start: 0.7937 (mmm) cc_final: 0.7454 (tmm) REVERT: D 212 SER cc_start: 0.9318 (m) cc_final: 0.9000 (p) REVERT: D 235 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7684 (mt0) REVERT: D 274 ASP cc_start: 0.7127 (t70) cc_final: 0.6630 (t0) REVERT: E 282 GLN cc_start: 0.5015 (mt0) cc_final: 0.4454 (pp30) REVERT: E 381 ILE cc_start: 0.9546 (mm) cc_final: 0.9333 (mt) REVERT: E 409 MET cc_start: 0.8700 (tpt) cc_final: 0.8128 (tpt) REVERT: E 486 ARG cc_start: 0.6960 (tpp-160) cc_final: 0.6697 (mmm160) REVERT: E 559 PHE cc_start: 0.7966 (m-80) cc_final: 0.7148 (m-80) REVERT: E 598 ARG cc_start: 0.8754 (ttm-80) cc_final: 0.8380 (ttm110) REVERT: E 785 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6554 (mt-10) REVERT: E 1034 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8659 (tp) REVERT: E 1068 PHE cc_start: 0.8405 (t80) cc_final: 0.8127 (t80) REVERT: E 1115 THR cc_start: 0.7180 (p) cc_final: 0.6948 (t) REVERT: E 1224 GLN cc_start: 0.7761 (mt0) cc_final: 0.7519 (tt0) REVERT: E 1290 MET cc_start: 0.6608 (mmm) cc_final: 0.6336 (mmt) REVERT: E 1308 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7728 (mp10) REVERT: E 1320 LYS cc_start: 0.8385 (mttt) cc_final: 0.8030 (mttt) outliers start: 141 outliers final: 90 residues processed: 654 average time/residue: 0.3121 time to fit residues: 319.5928 Evaluate side-chains 671 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 574 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 170 CYS Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 257 MET Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 701 ILE Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 865 SER Chi-restraints excluded: chain E residue 893 TYR Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1089 THR Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1308 GLN Chi-restraints excluded: chain E residue 1309 LEU Chi-restraints excluded: chain E residue 1312 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 253 optimal weight: 30.0000 chunk 268 optimal weight: 40.0000 chunk 132 optimal weight: 1.9990 chunk 240 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN B 173 GLN B 175 HIS ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN D 235 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 HIS E 326 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21663 Z= 0.237 Angle : 0.605 9.643 29515 Z= 0.304 Chirality : 0.045 0.343 3523 Planarity : 0.004 0.053 3625 Dihedral : 17.843 163.423 3811 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 5.38 % Allowed : 18.44 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2774 helix: 1.63 (0.14), residues: 1331 sheet: -1.96 (0.29), residues: 273 loop : -1.79 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 91 HIS 0.005 0.001 HIS E 125 PHE 0.024 0.002 PHE B 198 TYR 0.021 0.002 TYR E 124 ARG 0.007 0.001 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 572 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7215 (t0) cc_final: 0.6745 (t0) REVERT: A 93 ILE cc_start: 0.9041 (tt) cc_final: 0.8711 (mt) REVERT: A 140 GLU cc_start: 0.8128 (mp0) cc_final: 0.7896 (mp0) REVERT: A 158 MET cc_start: 0.7218 (mmm) cc_final: 0.6895 (mtm) REVERT: A 170 LYS cc_start: 0.8473 (ttpp) cc_final: 0.8208 (tttp) REVERT: A 177 ARG cc_start: 0.8907 (tpt-90) cc_final: 0.8439 (tpt170) REVERT: A 258 TYR cc_start: 0.8352 (p90) cc_final: 0.8098 (p90) REVERT: A 304 TYR cc_start: 0.8731 (m-80) cc_final: 0.8316 (m-80) REVERT: A 343 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7238 (tp) REVERT: B 47 LYS cc_start: 0.8226 (mttt) cc_final: 0.7982 (mttm) REVERT: B 56 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6501 (mt) REVERT: B 67 LYS cc_start: 0.8734 (mppt) cc_final: 0.8402 (mptt) REVERT: B 72 LEU cc_start: 0.8033 (mm) cc_final: 0.6596 (mm) REVERT: B 75 PHE cc_start: 0.8371 (t80) cc_final: 0.8135 (t80) REVERT: B 264 ASN cc_start: 0.8127 (m-40) cc_final: 0.7851 (m-40) REVERT: B 275 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7914 (tp) REVERT: B 313 GLN cc_start: 0.7336 (mt0) cc_final: 0.6709 (mm-40) REVERT: C 114 ILE cc_start: 0.8834 (mm) cc_final: 0.8561 (tp) REVERT: C 164 LEU cc_start: 0.9392 (tp) cc_final: 0.9190 (tt) REVERT: C 200 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8279 (tt) REVERT: D 38 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8397 (mmmt) REVERT: D 113 SER cc_start: 0.8667 (m) cc_final: 0.8297 (p) REVERT: D 158 MET cc_start: 0.7890 (mmm) cc_final: 0.7405 (tmm) REVERT: D 212 SER cc_start: 0.9325 (m) cc_final: 0.8955 (p) REVERT: D 235 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7723 (mt0) REVERT: D 274 ASP cc_start: 0.7176 (t70) cc_final: 0.6677 (t0) REVERT: D 338 LYS cc_start: 0.7022 (tmmt) cc_final: 0.6686 (mppt) REVERT: E 282 GLN cc_start: 0.4884 (mt0) cc_final: 0.4518 (pp30) REVERT: E 381 ILE cc_start: 0.9513 (mm) cc_final: 0.9294 (mt) REVERT: E 486 ARG cc_start: 0.6987 (tpp-160) cc_final: 0.6682 (mmm160) REVERT: E 502 MET cc_start: 0.8061 (ttt) cc_final: 0.7779 (ttt) REVERT: E 559 PHE cc_start: 0.7933 (m-80) cc_final: 0.7095 (m-80) REVERT: E 598 ARG cc_start: 0.8741 (ttm-80) cc_final: 0.8137 (ttm110) REVERT: E 785 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6574 (mt-10) REVERT: E 1034 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8553 (tp) REVERT: E 1068 PHE cc_start: 0.8366 (t80) cc_final: 0.8107 (t80) REVERT: E 1115 THR cc_start: 0.7167 (p) cc_final: 0.6901 (t) REVERT: E 1224 GLN cc_start: 0.7729 (mt0) cc_final: 0.7505 (tt0) REVERT: E 1290 MET cc_start: 0.6447 (mmm) cc_final: 0.6014 (mmt) REVERT: E 1294 TYR cc_start: 0.8292 (m-10) cc_final: 0.7458 (m-10) REVERT: E 1308 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7614 (mp10) outliers start: 105 outliers final: 72 residues processed: 616 average time/residue: 0.3065 time to fit residues: 295.4538 Evaluate side-chains 635 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 555 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 170 CYS Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 257 MET Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 701 ILE Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 893 TYR Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1308 GLN Chi-restraints excluded: chain E residue 1309 LEU Chi-restraints excluded: chain E residue 1312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 20.0000 chunk 152 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 229 optimal weight: 20.0000 chunk 185 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 137 optimal weight: 10.0000 chunk 241 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN B 175 HIS ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN D 128 GLN D 235 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 HIS E1224 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 21663 Z= 0.447 Angle : 0.736 10.894 29515 Z= 0.373 Chirality : 0.049 0.320 3523 Planarity : 0.005 0.058 3625 Dihedral : 17.519 163.136 3811 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 8.04 % Allowed : 17.57 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.16), residues: 2774 helix: 1.36 (0.14), residues: 1322 sheet: -1.88 (0.30), residues: 264 loop : -2.00 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 311 HIS 0.010 0.001 HIS E 125 PHE 0.031 0.002 PHE B 198 TYR 0.026 0.002 TYR E1032 ARG 0.007 0.001 ARG E 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 578 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7382 (t0) cc_final: 0.6927 (t0) REVERT: A 59 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8565 (t) REVERT: A 83 TRP cc_start: 0.9036 (m-10) cc_final: 0.8657 (m-10) REVERT: A 93 ILE cc_start: 0.9098 (tt) cc_final: 0.8748 (mt) REVERT: A 140 GLU cc_start: 0.8242 (mp0) cc_final: 0.8013 (mp0) REVERT: A 177 ARG cc_start: 0.9104 (tpt-90) cc_final: 0.8510 (tpt170) REVERT: A 304 TYR cc_start: 0.8860 (m-80) cc_final: 0.8461 (m-80) REVERT: B 47 LYS cc_start: 0.8403 (mttt) cc_final: 0.8112 (mttm) REVERT: B 67 LYS cc_start: 0.8801 (mppt) cc_final: 0.8492 (mptt) REVERT: B 75 PHE cc_start: 0.8402 (t80) cc_final: 0.7944 (t80) REVERT: B 264 ASN cc_start: 0.8145 (m-40) cc_final: 0.7904 (m110) REVERT: B 313 GLN cc_start: 0.7671 (mt0) cc_final: 0.6967 (mm-40) REVERT: C 200 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8278 (tt) REVERT: D 38 LYS cc_start: 0.8657 (mmmt) cc_final: 0.8450 (mmmt) REVERT: D 113 SER cc_start: 0.8701 (m) cc_final: 0.8376 (p) REVERT: D 158 MET cc_start: 0.8080 (mmm) cc_final: 0.7591 (tmm) REVERT: D 212 SER cc_start: 0.9415 (m) cc_final: 0.9132 (p) REVERT: D 235 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7727 (mt0) REVERT: D 274 ASP cc_start: 0.7269 (t70) cc_final: 0.6737 (t0) REVERT: E 39 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8171 (tt) REVERT: E 348 SER cc_start: 0.8095 (p) cc_final: 0.7734 (m) REVERT: E 381 ILE cc_start: 0.9546 (mm) cc_final: 0.9320 (mt) REVERT: E 486 ARG cc_start: 0.6923 (tpp-160) cc_final: 0.6699 (mmm160) REVERT: E 559 PHE cc_start: 0.8108 (m-80) cc_final: 0.7374 (m-80) REVERT: E 598 ARG cc_start: 0.8864 (ttm-80) cc_final: 0.8433 (ttm110) REVERT: E 785 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6571 (mt-10) REVERT: E 1224 GLN cc_start: 0.7806 (mt0) cc_final: 0.7537 (tt0) REVERT: E 1305 MET cc_start: 0.8055 (tpp) cc_final: 0.7819 (tpp) REVERT: E 1308 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7704 (mp10) REVERT: E 1320 LYS cc_start: 0.8527 (mttt) cc_final: 0.8151 (mttt) outliers start: 157 outliers final: 119 residues processed: 647 average time/residue: 0.3027 time to fit residues: 311.3107 Evaluate side-chains 687 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 562 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 170 CYS Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 257 MET Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 462 ILE Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 701 ILE Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 722 LEU Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 865 SER Chi-restraints excluded: chain E residue 893 TYR Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1074 LEU Chi-restraints excluded: chain E residue 1089 THR Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1276 LEU Chi-restraints excluded: chain E residue 1308 GLN Chi-restraints excluded: chain E residue 1312 VAL Chi-restraints excluded: chain E residue 1557 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 9.9990 chunk 241 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 268 optimal weight: 40.0000 chunk 223 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 141 optimal weight: 0.3980 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN B 48 ASN B 175 HIS ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 HIS E 326 HIS E 584 HIS E1224 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21663 Z= 0.277 Angle : 0.641 11.331 29515 Z= 0.322 Chirality : 0.046 0.312 3523 Planarity : 0.004 0.057 3625 Dihedral : 16.866 163.423 3811 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 6.71 % Allowed : 20.13 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2774 helix: 1.60 (0.14), residues: 1323 sheet: -1.87 (0.30), residues: 269 loop : -1.85 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 311 HIS 0.009 0.001 HIS B 175 PHE 0.027 0.002 PHE B 198 TYR 0.020 0.002 TYR E1032 ARG 0.008 0.001 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 567 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7329 (t0) cc_final: 0.6850 (t0) REVERT: A 59 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8517 (t) REVERT: A 83 TRP cc_start: 0.8912 (m-10) cc_final: 0.8560 (m-10) REVERT: A 93 ILE cc_start: 0.9074 (tt) cc_final: 0.8815 (mt) REVERT: A 140 GLU cc_start: 0.8200 (mp0) cc_final: 0.7994 (mp0) REVERT: A 177 ARG cc_start: 0.9049 (tpt-90) cc_final: 0.8578 (tpt170) REVERT: A 304 TYR cc_start: 0.8834 (m-80) cc_final: 0.8446 (m-80) REVERT: A 343 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.6999 (tp) REVERT: B 47 LYS cc_start: 0.8418 (mttt) cc_final: 0.8127 (mttm) REVERT: B 75 PHE cc_start: 0.8368 (t80) cc_final: 0.7861 (t80) REVERT: B 313 GLN cc_start: 0.7462 (mm-40) cc_final: 0.6829 (mm-40) REVERT: C 200 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8096 (tt) REVERT: C 274 ASP cc_start: 0.5987 (t70) cc_final: 0.5475 (t0) REVERT: D 38 LYS cc_start: 0.8675 (mmmt) cc_final: 0.8451 (mmmt) REVERT: D 73 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8209 (tt) REVERT: D 113 SER cc_start: 0.8591 (m) cc_final: 0.8281 (p) REVERT: D 158 MET cc_start: 0.7937 (mmm) cc_final: 0.7542 (tmm) REVERT: D 212 SER cc_start: 0.9528 (m) cc_final: 0.9066 (p) REVERT: D 274 ASP cc_start: 0.7215 (t70) cc_final: 0.6694 (t0) REVERT: D 338 LYS cc_start: 0.7094 (tmmt) cc_final: 0.6878 (mppt) REVERT: E 91 GLU cc_start: 0.8254 (tt0) cc_final: 0.8044 (tt0) REVERT: E 181 MET cc_start: 0.7981 (ttp) cc_final: 0.7677 (ttm) REVERT: E 348 SER cc_start: 0.8422 (p) cc_final: 0.8090 (m) REVERT: E 381 ILE cc_start: 0.9520 (mm) cc_final: 0.9308 (mt) REVERT: E 486 ARG cc_start: 0.6940 (tpp-160) cc_final: 0.6687 (mmm160) REVERT: E 559 PHE cc_start: 0.8033 (m-80) cc_final: 0.7214 (m-80) REVERT: E 598 ARG cc_start: 0.8823 (ttm-80) cc_final: 0.8164 (ttm110) REVERT: E 785 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6596 (mt-10) REVERT: E 1034 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8637 (tp) REVERT: E 1224 GLN cc_start: 0.7676 (mt0) cc_final: 0.7398 (tt0) REVERT: E 1294 TYR cc_start: 0.8349 (m-10) cc_final: 0.7575 (m-10) REVERT: E 1308 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7672 (mp10) REVERT: E 1320 LYS cc_start: 0.8506 (mttt) cc_final: 0.8132 (mttt) outliers start: 131 outliers final: 99 residues processed: 624 average time/residue: 0.3072 time to fit residues: 301.9520 Evaluate side-chains 663 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 557 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 170 CYS Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 257 MET Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 893 TYR Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1074 LEU Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1308 GLN Chi-restraints excluded: chain E residue 1309 LEU Chi-restraints excluded: chain E residue 1312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 259 optimal weight: 30.0000 chunk 30 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 196 optimal weight: 0.1980 chunk 152 optimal weight: 10.0000 chunk 226 optimal weight: 30.0000 chunk 150 optimal weight: 4.9990 chunk 267 optimal weight: 40.0000 chunk 167 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 overall best weight: 6.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN B 175 HIS ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 HIS E 326 HIS E 787 ASN E1224 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 21663 Z= 0.377 Angle : 0.689 11.530 29515 Z= 0.348 Chirality : 0.048 0.311 3523 Planarity : 0.005 0.060 3625 Dihedral : 16.490 162.963 3811 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 6.86 % Allowed : 20.65 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.16), residues: 2774 helix: 1.53 (0.14), residues: 1322 sheet: -1.85 (0.30), residues: 264 loop : -1.91 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 65 HIS 0.016 0.001 HIS B 175 PHE 0.029 0.002 PHE B 198 TYR 0.035 0.002 TYR A 258 ARG 0.012 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 561 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7480 (t0) cc_final: 0.6976 (t0) REVERT: A 83 TRP cc_start: 0.8977 (m-10) cc_final: 0.8568 (m-10) REVERT: A 93 ILE cc_start: 0.9052 (tt) cc_final: 0.8814 (mt) REVERT: A 158 MET cc_start: 0.7393 (mmm) cc_final: 0.6918 (mtm) REVERT: A 177 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8707 (tpt170) REVERT: A 304 TYR cc_start: 0.8884 (m-80) cc_final: 0.8480 (m-80) REVERT: A 343 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7058 (tp) REVERT: B 47 LYS cc_start: 0.8434 (mttt) cc_final: 0.8121 (mttm) REVERT: B 313 GLN cc_start: 0.7566 (mm-40) cc_final: 0.6899 (mm-40) REVERT: C 200 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8208 (tt) REVERT: C 274 ASP cc_start: 0.6024 (t70) cc_final: 0.5529 (t0) REVERT: D 38 LYS cc_start: 0.8677 (mmmt) cc_final: 0.8461 (mmmt) REVERT: D 73 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8231 (tt) REVERT: D 113 SER cc_start: 0.8663 (m) cc_final: 0.8306 (p) REVERT: D 158 MET cc_start: 0.7966 (mmm) cc_final: 0.7568 (tmm) REVERT: D 212 SER cc_start: 0.9522 (m) cc_final: 0.9107 (p) REVERT: D 274 ASP cc_start: 0.7267 (t70) cc_final: 0.6744 (t0) REVERT: E 91 GLU cc_start: 0.8273 (tt0) cc_final: 0.8068 (tt0) REVERT: E 181 MET cc_start: 0.8075 (ttp) cc_final: 0.7713 (ttm) REVERT: E 486 ARG cc_start: 0.6946 (tpp-160) cc_final: 0.6683 (mmm160) REVERT: E 502 MET cc_start: 0.8057 (ttt) cc_final: 0.7851 (ttt) REVERT: E 559 PHE cc_start: 0.8094 (m-80) cc_final: 0.7359 (m-80) REVERT: E 598 ARG cc_start: 0.8864 (ttm-80) cc_final: 0.8210 (ttm110) REVERT: E 785 GLU cc_start: 0.7343 (pt0) cc_final: 0.6794 (mt-10) REVERT: E 1034 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8698 (tp) REVERT: E 1224 GLN cc_start: 0.7817 (mt0) cc_final: 0.7517 (tt0) REVERT: E 1294 TYR cc_start: 0.8404 (m-10) cc_final: 0.7591 (m-10) REVERT: E 1308 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7689 (mp10) REVERT: E 1320 LYS cc_start: 0.8534 (mttt) cc_final: 0.8162 (mttt) outliers start: 134 outliers final: 114 residues processed: 624 average time/residue: 0.3079 time to fit residues: 302.8171 Evaluate side-chains 669 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 549 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 170 CYS Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 257 MET Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 514 TRP Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 709 THR Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 893 TYR Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1074 LEU Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1308 GLN Chi-restraints excluded: chain E residue 1309 LEU Chi-restraints excluded: chain E residue 1312 VAL Chi-restraints excluded: chain E residue 1557 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 165 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 170 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 24 optimal weight: 0.0270 chunk 210 optimal weight: 20.0000 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 52 GLN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN A 335 ASN B 175 HIS B 264 ASN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN E 293 HIS E 326 HIS E1224 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21663 Z= 0.234 Angle : 0.622 11.040 29515 Z= 0.313 Chirality : 0.045 0.313 3523 Planarity : 0.004 0.059 3625 Dihedral : 15.963 163.209 3811 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.58 % Allowed : 22.34 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2774 helix: 1.72 (0.14), residues: 1323 sheet: -1.82 (0.30), residues: 268 loop : -1.78 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 65 HIS 0.013 0.001 HIS B 175 PHE 0.031 0.002 PHE E 198 TYR 0.029 0.001 TYR A 258 ARG 0.009 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 547 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7425 (t0) cc_final: 0.6911 (t0) REVERT: A 59 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8514 (t) REVERT: A 83 TRP cc_start: 0.8911 (m-10) cc_final: 0.8545 (m-10) REVERT: A 177 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8644 (tpt170) REVERT: A 304 TYR cc_start: 0.8803 (m-80) cc_final: 0.8395 (m-80) REVERT: A 305 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7068 (mt) REVERT: A 343 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7049 (tp) REVERT: B 313 GLN cc_start: 0.7365 (mm-40) cc_final: 0.6755 (mm-40) REVERT: B 339 VAL cc_start: 0.7000 (OUTLIER) cc_final: 0.6796 (p) REVERT: C 200 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8058 (tt) REVERT: C 274 ASP cc_start: 0.5969 (t70) cc_final: 0.5473 (t0) REVERT: D 38 LYS cc_start: 0.8690 (mmmt) cc_final: 0.8460 (mmmt) REVERT: D 73 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8160 (tt) REVERT: D 113 SER cc_start: 0.8524 (m) cc_final: 0.8187 (p) REVERT: D 158 MET cc_start: 0.7890 (mmm) cc_final: 0.7560 (tmm) REVERT: D 212 SER cc_start: 0.9507 (m) cc_final: 0.8984 (p) REVERT: D 274 ASP cc_start: 0.7214 (t70) cc_final: 0.6761 (t0) REVERT: D 278 HIS cc_start: 0.7250 (m90) cc_final: 0.6866 (m-70) REVERT: D 338 LYS cc_start: 0.7270 (tmmt) cc_final: 0.6973 (mppt) REVERT: E 181 MET cc_start: 0.7886 (ttp) cc_final: 0.7532 (ttm) REVERT: E 210 LEU cc_start: 0.8901 (tp) cc_final: 0.8522 (tt) REVERT: E 238 LYS cc_start: 0.7858 (mttt) cc_final: 0.7600 (mptt) REVERT: E 348 SER cc_start: 0.8590 (p) cc_final: 0.8133 (m) REVERT: E 486 ARG cc_start: 0.6922 (tpp-160) cc_final: 0.6644 (mmm160) REVERT: E 502 MET cc_start: 0.8023 (ttt) cc_final: 0.7796 (ttt) REVERT: E 559 PHE cc_start: 0.7946 (m-80) cc_final: 0.7179 (m-80) REVERT: E 598 ARG cc_start: 0.8780 (ttm-80) cc_final: 0.8184 (ttm110) REVERT: E 785 GLU cc_start: 0.7266 (pt0) cc_final: 0.6775 (mt-10) REVERT: E 1034 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8520 (tp) REVERT: E 1224 GLN cc_start: 0.7668 (mt0) cc_final: 0.7380 (tt0) REVERT: E 1294 TYR cc_start: 0.8318 (m-10) cc_final: 0.7580 (m-10) REVERT: E 1305 MET cc_start: 0.7919 (tpp) cc_final: 0.7654 (tpp) REVERT: E 1308 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7714 (mp10) REVERT: E 1320 LYS cc_start: 0.8509 (mttt) cc_final: 0.8115 (mttt) REVERT: E 1525 MET cc_start: 0.2700 (mtm) cc_final: 0.2043 (ptp) outliers start: 109 outliers final: 89 residues processed: 597 average time/residue: 0.3091 time to fit residues: 288.0818 Evaluate side-chains 633 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 535 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 170 CYS Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 257 MET Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 893 TYR Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1074 LEU Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1308 GLN Chi-restraints excluded: chain E residue 1309 LEU Chi-restraints excluded: chain E residue 1312 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 243 optimal weight: 10.0000 chunk 256 optimal weight: 30.0000 chunk 234 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 225 optimal weight: 0.7980 chunk 236 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN B 175 HIS ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 HIS E 326 HIS E 444 GLN E1224 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21663 Z= 0.335 Angle : 0.668 11.356 29515 Z= 0.337 Chirality : 0.047 0.313 3523 Planarity : 0.004 0.061 3625 Dihedral : 15.874 162.903 3811 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 6.25 % Allowed : 22.28 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2774 helix: 1.58 (0.14), residues: 1331 sheet: -1.89 (0.29), residues: 266 loop : -1.85 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 65 HIS 0.013 0.001 HIS B 175 PHE 0.029 0.002 PHE B 198 TYR 0.026 0.002 TYR A 258 ARG 0.008 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 550 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7390 (t0) cc_final: 0.6893 (t0) REVERT: A 83 TRP cc_start: 0.8943 (m-10) cc_final: 0.8552 (m-10) REVERT: A 177 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8570 (tpt170) REVERT: A 304 TYR cc_start: 0.8843 (m-80) cc_final: 0.8430 (m-80) REVERT: A 305 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6965 (mt) REVERT: A 343 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7110 (tp) REVERT: B 75 PHE cc_start: 0.8052 (t80) cc_final: 0.7780 (t80) REVERT: B 313 GLN cc_start: 0.7404 (mm-40) cc_final: 0.6820 (mm-40) REVERT: C 170 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8855 (ttmm) REVERT: C 200 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8148 (tt) REVERT: C 274 ASP cc_start: 0.5955 (t70) cc_final: 0.5491 (t0) REVERT: D 73 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8215 (tt) REVERT: D 113 SER cc_start: 0.8588 (m) cc_final: 0.8233 (p) REVERT: D 158 MET cc_start: 0.8038 (mmm) cc_final: 0.7586 (tmm) REVERT: D 212 SER cc_start: 0.9530 (m) cc_final: 0.9076 (p) REVERT: D 254 PRO cc_start: 0.9138 (Cg_exo) cc_final: 0.8927 (Cg_endo) REVERT: D 274 ASP cc_start: 0.7160 (t70) cc_final: 0.6700 (t0) REVERT: E 181 MET cc_start: 0.7968 (ttp) cc_final: 0.7581 (ttm) REVERT: E 210 LEU cc_start: 0.8989 (tp) cc_final: 0.8576 (tt) REVERT: E 444 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7481 (tt0) REVERT: E 486 ARG cc_start: 0.6934 (tpp-160) cc_final: 0.6662 (mmm160) REVERT: E 502 MET cc_start: 0.8049 (ttt) cc_final: 0.7806 (ttt) REVERT: E 529 GLU cc_start: 0.6080 (tm-30) cc_final: 0.5569 (tm-30) REVERT: E 559 PHE cc_start: 0.7989 (m-80) cc_final: 0.7225 (m-80) REVERT: E 598 ARG cc_start: 0.8832 (ttm-80) cc_final: 0.8220 (ttm110) REVERT: E 785 GLU cc_start: 0.7275 (pt0) cc_final: 0.6780 (mt-10) REVERT: E 1034 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8752 (tp) REVERT: E 1068 PHE cc_start: 0.8519 (t80) cc_final: 0.7990 (t80) REVERT: E 1099 ARG cc_start: 0.8256 (mmm-85) cc_final: 0.7609 (tpm170) REVERT: E 1224 GLN cc_start: 0.7790 (mt0) cc_final: 0.7479 (tt0) REVERT: E 1294 TYR cc_start: 0.8371 (m-10) cc_final: 0.7605 (m-10) REVERT: E 1308 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7715 (mp10) REVERT: E 1320 LYS cc_start: 0.8535 (mttt) cc_final: 0.8144 (mttt) outliers start: 122 outliers final: 108 residues processed: 613 average time/residue: 0.3098 time to fit residues: 296.3314 Evaluate side-chains 655 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 538 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 170 CYS Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 257 MET Chi-restraints excluded: chain E residue 305 PHE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 444 GLN Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 462 ILE Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 709 THR Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 865 SER Chi-restraints excluded: chain E residue 893 TYR Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1074 LEU Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1308 GLN Chi-restraints excluded: chain E residue 1309 LEU Chi-restraints excluded: chain E residue 1312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 163 optimal weight: 3.9990 chunk 264 optimal weight: 30.0000 chunk 161 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 276 optimal weight: 50.0000 chunk 254 optimal weight: 0.0010 chunk 220 optimal weight: 0.0020 chunk 22 optimal weight: 20.0000 chunk 170 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN B 173 GLN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 HIS E 326 HIS E 444 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.373 21663 Z= 0.413 Angle : 0.872 59.199 29515 Z= 0.483 Chirality : 0.046 0.305 3523 Planarity : 0.005 0.159 3625 Dihedral : 15.871 162.831 3811 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 6.10 % Allowed : 22.49 % Favored : 71.41 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2774 helix: 1.60 (0.14), residues: 1329 sheet: -1.89 (0.29), residues: 266 loop : -1.87 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 65 HIS 0.134 0.002 HIS B 175 PHE 0.031 0.002 PHE E1164 TYR 0.023 0.002 TYR A 258 ARG 0.018 0.001 ARG E 526 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5548 Ramachandran restraints generated. 2774 Oldfield, 0 Emsley, 2774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 539 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.7456 (t0) cc_final: 0.6910 (t0) REVERT: A 83 TRP cc_start: 0.8935 (m-10) cc_final: 0.8540 (m-10) REVERT: A 177 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8637 (tpt170) REVERT: A 304 TYR cc_start: 0.8847 (m-80) cc_final: 0.8426 (m-80) REVERT: A 305 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6965 (mt) REVERT: A 343 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7103 (tp) REVERT: B 313 GLN cc_start: 0.7429 (mm-40) cc_final: 0.6804 (mm-40) REVERT: C 170 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8851 (ttmm) REVERT: C 200 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8133 (tt) REVERT: C 274 ASP cc_start: 0.5940 (t70) cc_final: 0.5477 (t0) REVERT: D 73 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8212 (tt) REVERT: D 113 SER cc_start: 0.8578 (m) cc_final: 0.8217 (p) REVERT: D 158 MET cc_start: 0.8032 (mmm) cc_final: 0.7599 (tmm) REVERT: D 212 SER cc_start: 0.9531 (m) cc_final: 0.9079 (p) REVERT: D 274 ASP cc_start: 0.7132 (t70) cc_final: 0.6690 (t0) REVERT: E 181 MET cc_start: 0.7961 (ttp) cc_final: 0.7570 (ttm) REVERT: E 210 LEU cc_start: 0.8889 (tp) cc_final: 0.8417 (tt) REVERT: E 486 ARG cc_start: 0.6929 (tpp-160) cc_final: 0.6652 (mmm160) REVERT: E 502 MET cc_start: 0.8042 (ttt) cc_final: 0.7787 (ttt) REVERT: E 529 GLU cc_start: 0.5980 (tm-30) cc_final: 0.5668 (tm-30) REVERT: E 559 PHE cc_start: 0.7989 (m-80) cc_final: 0.7220 (m-80) REVERT: E 598 ARG cc_start: 0.8820 (ttm-80) cc_final: 0.8191 (ttm110) REVERT: E 785 GLU cc_start: 0.7275 (pt0) cc_final: 0.6775 (mt-10) REVERT: E 1034 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8746 (tp) REVERT: E 1068 PHE cc_start: 0.8499 (t80) cc_final: 0.7990 (t80) REVERT: E 1224 GLN cc_start: 0.7778 (mt0) cc_final: 0.7475 (tt0) REVERT: E 1294 TYR cc_start: 0.8368 (m-10) cc_final: 0.7598 (m-10) REVERT: E 1308 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7703 (mp10) REVERT: E 1320 LYS cc_start: 0.8531 (mttt) cc_final: 0.8143 (mttt) outliers start: 119 outliers final: 106 residues processed: 601 average time/residue: 0.3156 time to fit residues: 296.3295 Evaluate side-chains 651 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 537 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 170 CYS Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 257 MET Chi-restraints excluded: chain E residue 305 PHE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 462 ILE Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 514 TRP Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 709 THR Chi-restraints excluded: chain E residue 717 CYS Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 893 TYR Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1034 LEU Chi-restraints excluded: chain E residue 1074 LEU Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1168 LEU Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1219 TYR Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1308 GLN Chi-restraints excluded: chain E residue 1309 LEU Chi-restraints excluded: chain E residue 1312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 175 optimal weight: 30.0000 chunk 234 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 203 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 220 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 226 optimal weight: 40.0000 chunk 27 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 HIS E 326 HIS ** E 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.175060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.152068 restraints weight = 27004.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.153269 restraints weight = 16936.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.155651 restraints weight = 12844.783| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.373 21663 Z= 0.413 Angle : 0.872 59.199 29515 Z= 0.483 Chirality : 0.046 0.305 3523 Planarity : 0.005 0.159 3625 Dihedral : 15.871 162.831 3811 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 5.84 % Allowed : 22.80 % Favored : 71.36 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2774 helix: 1.60 (0.14), residues: 1329 sheet: -1.89 (0.29), residues: 266 loop : -1.87 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 65 HIS 0.134 0.002 HIS B 175 PHE 0.031 0.002 PHE E1164 TYR 0.023 0.002 TYR A 258 ARG 0.018 0.001 ARG E 526 =============================================================================== Job complete usr+sys time: 5234.45 seconds wall clock time: 93 minutes 6.94 seconds (5586.94 seconds total)