Starting phenix.real_space_refine on Fri Dec 8 13:34:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmj_20395/12_2023/6pmj_20395_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmj_20395/12_2023/6pmj_20395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmj_20395/12_2023/6pmj_20395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmj_20395/12_2023/6pmj_20395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmj_20395/12_2023/6pmj_20395_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmj_20395/12_2023/6pmj_20395_trim_updated.pdb" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.020 sd= 0.289 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 113 5.49 5 Mg 1 5.21 5 S 110 5.16 5 C 18042 2.51 5 N 5218 2.21 5 O 5889 1.98 5 H 28609 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 268": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 1355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 57984 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3599 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3556 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 21152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 21152 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1283} Chain: "D" Number of atoms: 21010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 21010 Classifications: {'peptide': 1337} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1281} Chain breaks: 2 Chain: "E" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1261 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 3871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 3871 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "1" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1712 Classifications: {'DNA': 54} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 53} Chain: "2" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1724 Classifications: {'DNA': 54} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 53} Chain: "3" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Unusual residues: {'ATP': 1} Classifications: {'RNA': 2, 'undetermined': 1} Modifications used: {'3*END': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 1, None: 1} Not linked: pdbres="ATP 3 1 " pdbres=" A 3 2 " Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29207 SG CYS D 70 76.218 120.159 81.133 1.00 20.00 S ATOM 29466 SG CYS D 85 79.796 121.605 79.994 1.00 20.00 S ATOM 41046 SG CYS D 814 102.032 70.512 133.648 1.00 20.00 S ATOM 42183 SG CYS D 888 99.178 70.554 131.686 1.00 20.00 S ATOM 42274 SG CYS D 895 103.449 69.053 130.838 1.00 20.00 S Time building chain proxies: 18.54, per 1000 atoms: 0.32 Number of scatterers: 57984 At special positions: 0 Unit cell: (171, 149.4, 180.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 110 16.00 P 113 15.00 Mg 1 11.99 O 5889 8.00 N 5218 7.00 C 18042 6.00 H 28609 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 40.86 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6386 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 110 helices and 29 sheets defined 33.6% alpha, 9.1% beta 31 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 26.39 Creating SS restraints... Processing helix chain 'A' and resid 35 through 47 Processing helix chain 'A' and resid 78 through 87 removed outlier: 4.160A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 213 through 232 removed outlier: 3.686A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 78 through 85 Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 213 through 228 Processing helix chain 'C' and resid 5 through 8 No H-bonds generated for 'chain 'C' and resid 5 through 8' Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 49 through 55 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 271 through 279 Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'C' and resid 320 through 327 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 359 through 370 Processing helix chain 'C' and resid 378 through 390 removed outlier: 3.751A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 409 Processing helix chain 'C' and resid 422 through 437 Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 456 through 479 removed outlier: 4.280A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 492 removed outlier: 3.760A pdb=" N MET C 492 " --> pdb=" O PRO C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 489 through 492' Processing helix chain 'C' and resid 496 through 508 removed outlier: 3.560A pdb=" N GLY C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 610 through 612 No H-bonds generated for 'chain 'C' and resid 610 through 612' Processing helix chain 'C' and resid 663 through 666 No H-bonds generated for 'chain 'C' and resid 663 through 666' Processing helix chain 'C' and resid 671 through 673 No H-bonds generated for 'chain 'C' and resid 671 through 673' Processing helix chain 'C' and resid 676 through 686 Processing helix chain 'C' and resid 705 through 711 Processing helix chain 'C' and resid 821 through 825 Processing helix chain 'C' and resid 859 through 864 removed outlier: 4.509A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 Processing helix chain 'C' and resid 943 through 980 removed outlier: 4.147A pdb=" N ARG C 974 " --> pdb=" O GLY C 970 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEU C 979 " --> pdb=" O ILE C 975 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 1008 through 1037 Processing helix chain 'C' and resid 1100 through 1102 No H-bonds generated for 'chain 'C' and resid 1100 through 1102' Processing helix chain 'C' and resid 1110 through 1134 removed outlier: 3.524A pdb=" N ALA C1121 " --> pdb=" O LEU C1117 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS C1122 " --> pdb=" O GLY C1118 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY C1123 " --> pdb=" O MET C1119 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1149 Processing helix chain 'C' and resid 1166 through 1178 removed outlier: 5.425A pdb=" N LYS C1178 " --> pdb=" O GLU C1174 " (cutoff:3.500A) Processing helix chain 'C' and resid 1192 through 1201 Processing helix chain 'C' and resid 1262 through 1264 No H-bonds generated for 'chain 'C' and resid 1262 through 1264' Processing helix chain 'C' and resid 1272 through 1281 Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1298 through 1309 Processing helix chain 'C' and resid 1321 through 1333 removed outlier: 3.679A pdb=" N LEU C1326 " --> pdb=" O SER C1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 59 through 62 No H-bonds generated for 'chain 'D' and resid 59 through 62' Processing helix chain 'D' and resid 125 through 128 No H-bonds generated for 'chain 'D' and resid 125 through 128' Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 164 through 172 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.964A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 229 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 264 through 285 Processing helix chain 'D' and resid 290 through 307 Processing helix chain 'D' and resid 328 through 330 No H-bonds generated for 'chain 'D' and resid 328 through 330' Processing helix chain 'D' and resid 337 through 340 No H-bonds generated for 'chain 'D' and resid 337 through 340' Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 378 through 388 Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 406 through 416 Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 451 through 454 Processing helix chain 'D' and resid 475 through 482 Processing helix chain 'D' and resid 506 through 513 Processing helix chain 'D' and resid 530 through 537 Processing helix chain 'D' and resid 574 through 582 removed outlier: 3.661A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 592 No H-bonds generated for 'chain 'D' and resid 590 through 592' Processing helix chain 'D' and resid 598 through 612 Processing helix chain 'D' and resid 615 through 634 Processing helix chain 'D' and resid 651 through 670 Processing helix chain 'D' and resid 676 through 701 Processing helix chain 'D' and resid 721 through 728 Processing helix chain 'D' and resid 734 through 741 Processing helix chain 'D' and resid 769 through 787 removed outlier: 4.472A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 806 removed outlier: 5.712A pdb=" N ASP D 806 " --> pdb=" O ASP D 802 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 839 Processing helix chain 'D' and resid 866 through 873 Processing helix chain 'D' and resid 916 through 929 Proline residue: D 926 - end of helix removed outlier: 4.587A pdb=" N GLN D 929 " --> pdb=" O GLU D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 1139 through 1145 Processing helix chain 'D' and resid 1217 through 1223 Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 4.049A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1260 removed outlier: 3.789A pdb=" N VAL D1255 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE D1256 " --> pdb=" O ILE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1287 Processing helix chain 'D' and resid 1309 through 1314 removed outlier: 3.666A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1322 through 1324 No H-bonds generated for 'chain 'D' and resid 1322 through 1324' Processing helix chain 'D' and resid 1328 through 1338 removed outlier: 4.152A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1353 removed outlier: 3.713A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1363 through 1374 Processing helix chain 'E' and resid 8 through 13 removed outlier: 3.582A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 31 Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 61 through 79 Processing helix chain 'F' and resid 8 through 19 removed outlier: 4.016A pdb=" N LYS F 13 " --> pdb=" O GLY F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 30 removed outlier: 4.600A pdb=" N ARG F 30 " --> pdb=" O HIS F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 40 No H-bonds generated for 'chain 'F' and resid 37 through 40' Processing helix chain 'F' and resid 42 through 58 removed outlier: 3.505A pdb=" N ARG F 58 " --> pdb=" O ASN F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 86 removed outlier: 4.285A pdb=" N GLN F 73 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG F 74 " --> pdb=" O TYR F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 111 Processing helix chain 'F' and resid 117 through 123 removed outlier: 3.741A pdb=" N ARG F 123 " --> pdb=" O VAL F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 138 removed outlier: 4.242A pdb=" N LEU F 136 " --> pdb=" O ARG F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 188 removed outlier: 3.536A pdb=" N LEU F 173 " --> pdb=" O PRO F 169 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 201 Processing helix chain 'F' and resid 208 through 214 Processing helix chain 'F' and resid 220 through 232 Processing sheet with id= A, first strand: chain 'A' and resid 24 through 28 Processing sheet with id= B, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'A' and resid 97 through 105 removed outlier: 5.669A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 108 through 110 Processing sheet with id= E, first strand: chain 'B' and resid 23 through 26 removed outlier: 4.124A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 170 through 172 removed outlier: 6.538A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 93 through 95 Processing sheet with id= H, first strand: chain 'C' and resid 116 through 123 removed outlier: 4.066A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 148 through 151 Processing sheet with id= J, first strand: chain 'C' and resid 154 through 161 Processing sheet with id= K, first strand: chain 'C' and resid 332 through 336 removed outlier: 5.119A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS C 236 " --> pdb=" O ARG C 233 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 579 through 581 Processing sheet with id= M, first strand: chain 'C' and resid 634 through 638 Processing sheet with id= N, first strand: chain 'C' and resid 750 through 752 removed outlier: 6.044A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 798 through 803 Processing sheet with id= P, first strand: chain 'C' and resid 830 through 832 Processing sheet with id= Q, first strand: chain 'C' and resid 876 through 878 Processing sheet with id= R, first strand: chain 'C' and resid 887 through 889 Processing sheet with id= S, first strand: chain 'C' and resid 931 through 935 removed outlier: 6.692A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 816 through 818 removed outlier: 8.313A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 103 through 106 Processing sheet with id= V, first strand: chain 'D' and resid 351 through 354 Processing sheet with id= W, first strand: chain 'D' and resid 548 through 552 Processing sheet with id= X, first strand: chain 'D' and resid 820 through 822 Processing sheet with id= Y, first strand: chain 'D' and resid 957 through 959 removed outlier: 3.784A pdb=" N LYS D 959 " --> pdb=" O LYS D 983 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 965 through 967 Processing sheet with id= AA, first strand: chain 'D' and resid 1034 through 1036 removed outlier: 4.012A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 1162 through 1165 Processing sheet with id= AC, first strand: chain 'D' and resid 949 through 952 removed outlier: 6.695A pdb=" N VAL D 952 " --> pdb=" O THR D1016 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N THR D1016 " --> pdb=" O VAL D 952 " (cutoff:3.500A) 881 hydrogen bonds defined for protein. 2481 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 20.79 Time building geometry restraints manager: 42.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 28585 1.01 - 1.21: 27 1.21 - 1.41: 12044 1.41 - 1.61: 17793 1.61 - 1.81: 205 Bond restraints: 58654 Sorted by residual: bond pdb=" CA VAL D 997 " pdb=" C VAL D 997 " ideal model delta sigma weight residual 1.522 1.589 -0.067 7.10e-03 1.98e+04 8.97e+01 bond pdb=" CA PRO D 584 " pdb=" CB PRO D 584 " ideal model delta sigma weight residual 1.531 1.628 -0.097 1.22e-02 6.72e+03 6.27e+01 bond pdb=" C4 ATP 3 1 " pdb=" C5 ATP 3 1 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.06e+01 bond pdb=" C5 ATP 3 1 " pdb=" C6 ATP 3 1 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.63e+01 bond pdb=" C5 ATP 3 1 " pdb=" N7 ATP 3 1 " ideal model delta sigma weight residual 1.387 1.333 0.054 1.00e-02 1.00e+04 2.94e+01 ... (remaining 58649 not shown) Histogram of bond angle deviations from ideal: 96.74 - 104.73: 1026 104.73 - 112.72: 68678 112.72 - 120.71: 21296 120.71 - 128.70: 15062 128.70 - 136.69: 306 Bond angle restraints: 106368 Sorted by residual: angle pdb=" PB ATP 3 1 " pdb=" O3B ATP 3 1 " pdb=" PG ATP 3 1 " ideal model delta sigma weight residual 139.87 117.42 22.45 1.00e+00 1.00e+00 5.04e+02 angle pdb=" PA ATP 3 1 " pdb=" O3A ATP 3 1 " pdb=" PB ATP 3 1 " ideal model delta sigma weight residual 136.83 118.77 18.06 1.00e+00 1.00e+00 3.26e+02 angle pdb=" C5 ATP 3 1 " pdb=" C4 ATP 3 1 " pdb=" N3 ATP 3 1 " ideal model delta sigma weight residual 126.80 116.96 9.84 1.00e+00 1.00e+00 9.68e+01 angle pdb=" N3 ATP 3 1 " pdb=" C4 ATP 3 1 " pdb=" N9 ATP 3 1 " ideal model delta sigma weight residual 127.04 136.69 -9.65 1.15e+00 7.59e-01 7.07e+01 angle pdb=" C LEU F 31 " pdb=" N GLN F 32 " pdb=" CA GLN F 32 " ideal model delta sigma weight residual 123.04 131.24 -8.20 1.08e+00 8.57e-01 5.76e+01 ... (remaining 106363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 25096 35.91 - 71.82: 883 71.82 - 107.73: 18 107.73 - 143.64: 1 143.64 - 179.56: 9 Dihedral angle restraints: 26007 sinusoidal: 15011 harmonic: 10996 Sorted by residual: dihedral pdb=" CA ASP D 67 " pdb=" C ASP D 67 " pdb=" N TYR D 68 " pdb=" CA TYR D 68 " ideal model delta harmonic sigma weight residual -180.00 -114.16 -65.84 0 5.00e+00 4.00e-02 1.73e+02 dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual -180.00 -128.50 -51.50 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA GLU F 151 " pdb=" C GLU F 151 " pdb=" N GLU F 152 " pdb=" CA GLU F 152 " ideal model delta harmonic sigma weight residual -180.00 -130.72 -49.28 0 5.00e+00 4.00e-02 9.71e+01 ... (remaining 26004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3736 0.076 - 0.151: 851 0.151 - 0.227: 84 0.227 - 0.303: 3 0.303 - 0.378: 1 Chirality restraints: 4675 Sorted by residual: chirality pdb=" CB VAL D 65 " pdb=" CA VAL D 65 " pdb=" CG1 VAL D 65 " pdb=" CG2 VAL D 65 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CG LEU C 971 " pdb=" CB LEU C 971 " pdb=" CD1 LEU C 971 " pdb=" CD2 LEU C 971 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CG LEU F 80 " pdb=" CB LEU F 80 " pdb=" CD1 LEU F 80 " pdb=" CD2 LEU F 80 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 4672 not shown) Planarity restraints: 8383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 68 " -0.018 2.00e-02 2.50e+03 3.71e-02 4.14e+01 pdb=" CG TYR D 68 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR D 68 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR D 68 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR D 68 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR D 68 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR D 68 " -0.080 2.00e-02 2.50e+03 pdb=" OH TYR D 68 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 TYR D 68 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR D 68 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR D 68 " 0.025 2.00e-02 2.50e+03 pdb=" HE2 TYR D 68 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT 1 47 " 0.034 2.00e-02 2.50e+03 1.92e-02 1.10e+01 pdb=" N1 DT 1 47 " -0.038 2.00e-02 2.50e+03 pdb=" C2 DT 1 47 " -0.007 2.00e-02 2.50e+03 pdb=" O2 DT 1 47 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT 1 47 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DT 1 47 " 0.023 2.00e-02 2.50e+03 pdb=" O4 DT 1 47 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DT 1 47 " 0.025 2.00e-02 2.50e+03 pdb=" C7 DT 1 47 " -0.023 2.00e-02 2.50e+03 pdb=" C6 DT 1 47 " -0.002 2.00e-02 2.50e+03 pdb=" H3 DT 1 47 " -0.001 2.00e-02 2.50e+03 pdb=" H6 DT 1 47 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 795 " -0.001 2.00e-02 2.50e+03 1.89e-02 1.07e+01 pdb=" CG TYR D 795 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR D 795 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR D 795 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR D 795 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 795 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR D 795 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 795 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TYR D 795 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR D 795 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 TYR D 795 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR D 795 " 0.001 2.00e-02 2.50e+03 ... (remaining 8380 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 2538 2.14 - 2.76: 114005 2.76 - 3.37: 162681 3.37 - 3.99: 205581 3.99 - 4.60: 315120 Nonbonded interactions: 799925 Sorted by model distance: nonbonded pdb=" HB3 LYS D 87 " pdb=" HZ3 LYS D 87 " model vdw 1.528 2.270 nonbonded pdb=" O GLU C 985 " pdb=" H LEU C 989 " model vdw 1.592 1.850 nonbonded pdb=" O ALA C 399 " pdb=" H MET C 403 " model vdw 1.600 1.850 nonbonded pdb=" O SER F 219 " pdb=" HG SER F 222 " model vdw 1.615 1.850 nonbonded pdb=" OE2 GLU A 214 " pdb=" HE ARG A 218 " model vdw 1.619 1.850 ... (remaining 799920 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 233) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.620 Extract box with map and model: 9.260 Check model and map are aligned: 0.680 Set scattering table: 0.420 Process input model: 174.670 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 191.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4379 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 : 0.011 0.097 30045 Z= 0.701 Angle : 1.211 22.446 41067 Z= 0.709 Chirality : 0.061 0.378 4675 Planarity : 0.007 0.080 4992 Dihedral : 16.103 179.555 11826 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.36 % Favored : 89.29 % Rotamer: Outliers : 0.31 % Allowed : 4.93 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.11), residues: 3437 helix: -2.49 (0.11), residues: 1202 sheet: -3.35 (0.21), residues: 344 loop : -3.23 (0.12), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP F 149 HIS 0.023 0.004 HIS F 14 PHE 0.042 0.004 PHE C 505 TYR 0.065 0.005 TYR D 68 ARG 0.029 0.002 ARG D 799 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 557 time to evaluate : 3.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 564 average time/residue: 1.0329 time to fit residues: 848.9096 Evaluate side-chains 374 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 370 time to evaluate : 3.350 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 1.0225 time to fit residues: 10.1477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 5.9990 chunk 266 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 275 optimal weight: 20.0000 chunk 106 optimal weight: 0.8980 chunk 167 optimal weight: 8.9990 chunk 205 optimal weight: 0.8980 chunk 319 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 137 ASN A 186 ASN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 560 ASN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4417 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30045 Z= 0.209 Angle : 0.715 9.226 41067 Z= 0.392 Chirality : 0.044 0.166 4675 Planarity : 0.005 0.065 4992 Dihedral : 18.641 175.865 5044 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.77 % Favored : 92.06 % Rotamer: Outliers : 1.29 % Allowed : 10.60 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.18 % 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: -3.39 (0.12), residues: 3437 helix: -1.32 (0.13), residues: 1223 sheet: -2.99 (0.22), residues: 344 loop : -2.83 (0.12), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 17 HIS 0.006 0.001 HIS C 273 PHE 0.023 0.002 PHE C1265 TYR 0.030 0.002 TYR D 68 ARG 0.012 0.001 ARG C 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 409 time to evaluate : 3.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 27 residues processed: 429 average time/residue: 1.0351 time to fit residues: 633.6541 Evaluate side-chains 386 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 359 time to evaluate : 3.792 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.5913 time to fit residues: 31.8865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 6.9990 chunk 99 optimal weight: 30.0000 chunk 266 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 320 optimal weight: 9.9990 chunk 345 optimal weight: 10.0000 chunk 285 optimal weight: 20.0000 chunk 317 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 256 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN ** C 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 665 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4770 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 30045 Z= 0.369 Angle : 0.801 9.492 41067 Z= 0.442 Chirality : 0.045 0.169 4675 Planarity : 0.006 0.061 4992 Dihedral : 18.406 178.267 5044 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 29.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.79 % Favored : 89.00 % Rotamer: Outliers : 2.00 % Allowed : 11.85 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.21 % 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: -3.35 (0.12), residues: 3437 helix: -1.29 (0.13), residues: 1230 sheet: -2.52 (0.23), residues: 380 loop : -2.90 (0.12), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 868 HIS 0.012 0.002 HIS C1237 PHE 0.028 0.002 PHE C 804 TYR 0.025 0.003 TYR D 68 ARG 0.016 0.001 ARG D1290 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 341 time to evaluate : 3.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 50 residues processed: 380 average time/residue: 1.0782 time to fit residues: 588.1440 Evaluate side-chains 359 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 309 time to evaluate : 3.356 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 50 outliers final: 1 residues processed: 50 average time/residue: 0.5829 time to fit residues: 56.1844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 40.0000 chunk 240 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 152 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 321 optimal weight: 0.8980 chunk 340 optimal weight: 30.0000 chunk 167 optimal weight: 6.9990 chunk 304 optimal weight: 0.3980 chunk 91 optimal weight: 8.9990 overall best weight: 5.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 GLN ** C 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN D 424 ASN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4760 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30045 Z= 0.241 Angle : 0.676 8.975 41067 Z= 0.373 Chirality : 0.043 0.164 4675 Planarity : 0.005 0.104 4992 Dihedral : 18.341 174.281 5044 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.00 % Favored : 91.85 % Rotamer: Outliers : 0.99 % Allowed : 13.86 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.13), residues: 3437 helix: -0.88 (0.14), residues: 1235 sheet: -2.33 (0.24), residues: 376 loop : -2.75 (0.13), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 868 HIS 0.005 0.001 HIS C 273 PHE 0.017 0.002 PHE C1265 TYR 0.021 0.002 TYR D 795 ARG 0.007 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 324 time to evaluate : 3.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 342 average time/residue: 1.0538 time to fit residues: 511.8202 Evaluate side-chains 312 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 295 time to evaluate : 3.345 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.6565 time to fit residues: 22.6564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 7.9990 chunk 193 optimal weight: 0.0870 chunk 4 optimal weight: 5.9990 chunk 253 optimal weight: 0.5980 chunk 140 optimal weight: 0.8980 chunk 290 optimal weight: 8.9990 chunk 235 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 305 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 overall best weight: 3.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN C 519 ASN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 GLN F 106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4744 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30045 Z= 0.195 Angle : 0.634 8.545 41067 Z= 0.346 Chirality : 0.042 0.149 4675 Planarity : 0.004 0.051 4992 Dihedral : 18.216 175.505 5044 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.26 % Favored : 91.59 % Rotamer: Outliers : 1.05 % Allowed : 14.64 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.13), residues: 3437 helix: -0.47 (0.14), residues: 1231 sheet: -2.17 (0.24), residues: 386 loop : -2.57 (0.13), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 409 HIS 0.006 0.001 HIS C1023 PHE 0.014 0.001 PHE C1265 TYR 0.018 0.001 TYR F 131 ARG 0.007 0.000 ARG D 798 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 315 time to evaluate : 3.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 337 average time/residue: 1.0384 time to fit residues: 505.4819 Evaluate side-chains 314 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 296 time to evaluate : 3.345 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.5478 time to fit residues: 21.9147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 1.9990 chunk 306 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 199 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 340 optimal weight: 9.9990 chunk 282 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 ASN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4980 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 30045 Z= 0.356 Angle : 0.748 8.863 41067 Z= 0.415 Chirality : 0.044 0.167 4675 Planarity : 0.006 0.074 4992 Dihedral : 18.316 177.611 5044 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 32.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.55 % Favored : 88.30 % Rotamer: Outliers : 2.07 % Allowed : 15.05 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.12 % 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: -3.00 (0.13), residues: 3437 helix: -1.02 (0.14), residues: 1243 sheet: -2.22 (0.25), residues: 378 loop : -2.71 (0.13), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D1193 HIS 0.009 0.002 HIS D 430 PHE 0.015 0.002 PHE D 49 TYR 0.020 0.002 TYR F 59 ARG 0.018 0.001 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 302 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 51 residues processed: 332 average time/residue: 1.0504 time to fit residues: 508.2336 Evaluate side-chains 337 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 286 time to evaluate : 3.370 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 3 residues processed: 51 average time/residue: 0.5869 time to fit residues: 57.2955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 192 optimal weight: 1.9990 chunk 286 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 339 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 chunk 206 optimal weight: 0.3980 chunk 156 optimal weight: 9.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4880 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30045 Z= 0.206 Angle : 0.647 8.499 41067 Z= 0.353 Chirality : 0.042 0.144 4675 Planarity : 0.005 0.060 4992 Dihedral : 18.193 175.888 5044 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 21.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.20 % Favored : 91.65 % Rotamer: Outliers : 0.75 % Allowed : 15.76 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.13), residues: 3437 helix: -0.60 (0.14), residues: 1245 sheet: -1.96 (0.25), residues: 384 loop : -2.52 (0.13), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 580 HIS 0.010 0.001 HIS F 225 PHE 0.012 0.002 PHE D 763 TYR 0.026 0.002 TYR D 68 ARG 0.005 0.000 ARG C 470 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 291 time to evaluate : 3.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 305 average time/residue: 1.0297 time to fit residues: 454.4054 Evaluate side-chains 292 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 279 time to evaluate : 3.433 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 13 average time/residue: 0.6912 time to fit residues: 19.0017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 chunk 202 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 231 optimal weight: 10.0000 chunk 167 optimal weight: 0.7980 chunk 31 optimal weight: 30.0000 chunk 266 optimal weight: 20.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4919 moved from start: 0.6093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30045 Z= 0.226 Angle : 0.649 8.791 41067 Z= 0.355 Chirality : 0.042 0.160 4675 Planarity : 0.005 0.053 4992 Dihedral : 18.119 176.717 5044 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.10 % Favored : 89.76 % Rotamer: Outliers : 0.78 % Allowed : 16.81 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.13), residues: 3437 helix: -0.49 (0.14), residues: 1245 sheet: -1.94 (0.24), residues: 399 loop : -2.44 (0.13), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1193 HIS 0.007 0.001 HIS F 225 PHE 0.012 0.001 PHE C 514 TYR 0.021 0.002 TYR D 68 ARG 0.006 0.001 ARG D1140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 279 time to evaluate : 3.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 294 average time/residue: 1.0009 time to fit residues: 428.4064 Evaluate side-chains 286 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 272 time to evaluate : 3.408 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 14 average time/residue: 0.6172 time to fit residues: 18.9360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 9.9990 chunk 325 optimal weight: 20.0000 chunk 296 optimal weight: 0.9990 chunk 316 optimal weight: 7.9990 chunk 324 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 285 optimal weight: 20.0000 chunk 299 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4919 moved from start: 0.6377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30045 Z= 0.214 Angle : 0.639 9.001 41067 Z= 0.348 Chirality : 0.042 0.159 4675 Planarity : 0.005 0.068 4992 Dihedral : 18.071 176.240 5044 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.61 % Favored : 91.27 % Rotamer: Outliers : 0.61 % Allowed : 17.19 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.14), residues: 3437 helix: -0.37 (0.15), residues: 1241 sheet: -1.88 (0.25), residues: 386 loop : -2.36 (0.13), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 580 HIS 0.007 0.001 HIS D 865 PHE 0.017 0.001 PHE D 141 TYR 0.025 0.002 TYR D 68 ARG 0.004 0.001 ARG D 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 277 time to evaluate : 3.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 286 average time/residue: 1.0177 time to fit residues: 423.3479 Evaluate side-chains 284 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 270 time to evaluate : 3.387 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 14 average time/residue: 0.6265 time to fit residues: 19.1519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 334 optimal weight: 20.0000 chunk 204 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 232 optimal weight: 10.0000 chunk 350 optimal weight: 8.9990 chunk 322 optimal weight: 4.9990 chunk 279 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4873 moved from start: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30045 Z= 0.182 Angle : 0.617 9.505 41067 Z= 0.333 Chirality : 0.042 0.144 4675 Planarity : 0.004 0.069 4992 Dihedral : 17.972 175.934 5044 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.18 % Favored : 91.71 % Rotamer: Outliers : 0.44 % Allowed : 17.15 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.14), residues: 3437 helix: -0.18 (0.15), residues: 1267 sheet: -1.72 (0.26), residues: 378 loop : -2.27 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 580 HIS 0.006 0.001 HIS D 865 PHE 0.012 0.001 PHE C 514 TYR 0.030 0.001 TYR D 68 ARG 0.007 0.000 ARG D 388 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 282 time to evaluate : 3.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 291 average time/residue: 0.9875 time to fit residues: 419.2339 Evaluate side-chains 279 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 269 time to evaluate : 3.379 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 10 average time/residue: 0.6485 time to fit residues: 15.0981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 9.9990 chunk 221 optimal weight: 0.9980 chunk 297 optimal weight: 0.0000 chunk 85 optimal weight: 9.9990 chunk 257 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 287 optimal weight: 10.0000 chunk 35 optimal weight: 0.3980 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.070416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.053659 restraints weight = 769031.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.055854 restraints weight = 456845.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.057376 restraints weight = 316831.325| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.6676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30045 Z= 0.178 Angle : 0.613 10.057 41067 Z= 0.329 Chirality : 0.041 0.151 4675 Planarity : 0.004 0.055 4992 Dihedral : 17.929 175.979 5044 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.54 % Favored : 92.35 % Rotamer: Outliers : 0.24 % Allowed : 17.73 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.14), residues: 3437 helix: -0.07 (0.15), residues: 1263 sheet: -1.69 (0.25), residues: 381 loop : -2.18 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 580 HIS 0.006 0.001 HIS D 865 PHE 0.013 0.001 PHE D 141 TYR 0.025 0.001 TYR D 68 ARG 0.008 0.000 ARG D 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11033.90 seconds wall clock time: 192 minutes 23.02 seconds (11543.02 seconds total)