Starting phenix.real_space_refine on Sat Mar 23 17:14:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urr_26717/03_2024/7urr_26717.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urr_26717/03_2024/7urr_26717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urr_26717/03_2024/7urr_26717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urr_26717/03_2024/7urr_26717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urr_26717/03_2024/7urr_26717.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urr_26717/03_2024/7urr_26717.pdb" } resolution = 4.7 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= -0.064 sd= 1.560 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: 5 Type Number sf(0) Gaussians S 72 5.16 5 C 12130 2.51 5 N 3067 2.21 5 O 3568 1.98 5 H 19331 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 801": "OE1" <-> "OE2" Residue "A GLU 1012": "OE1" <-> "OE2" Residue "A GLU 1064": "OE1" <-> "OE2" Residue "A GLU 1066": "OE1" <-> "OE2" Residue "A GLU 1204": "OE1" <-> "OE2" Residue "A GLU 1227": "OE1" <-> "OE2" Residue "A GLU 1314": "OE1" <-> "OE2" Residue "A TYR 1367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1381": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 440": "OD1" <-> "OD2" Residue "B GLU 542": "OE1" <-> "OE2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B GLU 562": "OE1" <-> "OE2" Residue "B ASP 594": "OD1" <-> "OD2" Residue "B PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B TYR 748": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 855": "OD1" <-> "OD2" Residue "B PHE 857": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 934": "OD1" <-> "OD2" Residue "B GLU 941": "OE1" <-> "OE2" Residue "B TYR 954": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1011": "OE1" <-> "OE2" Residue "B GLU 1021": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B PHE 1096": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1158": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1193": "OE1" <-> "OE2" Residue "B GLU 1200": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 38168 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1216, 19748 Classifications: {'peptide': 1216} Link IDs: {'PTRANS': 36, 'TRANS': 1179} Chain breaks: 8 Chain: "B" Number of atoms: 18420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 18420 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 34, 'TRANS': 1094} Chain breaks: 13 Time building chain proxies: 15.98, per 1000 atoms: 0.42 Number of scatterers: 38168 At special positions: 0 Unit cell: (307.84, 166.4, 128.128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 O 3568 8.00 N 3067 7.00 C 12130 6.00 H 19331 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=0, symmetry=0 Time building additional restraints: 26.91 Conformation dependent library (CDL) restraints added in 4.0 seconds 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 1 sheets defined 74.1% alpha, 0.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'A' and resid 12 through 17 removed outlier: 4.139A pdb=" N ILE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.613A pdb=" N THR A 24 " --> pdb=" O ILE A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 83 removed outlier: 3.810A pdb=" N ILE A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 107 removed outlier: 3.802A pdb=" N ILE A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) Proline residue: A 100 - end of helix Processing helix chain 'A' and resid 111 through 129 removed outlier: 3.877A pdb=" N THR A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 151 removed outlier: 3.656A pdb=" N HIS A 151 " --> pdb=" O ASN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 179 removed outlier: 4.198A pdb=" N LEU A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 186 through 203 Processing helix chain 'A' and resid 207 through 232 removed outlier: 4.115A pdb=" N VAL A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS A 230 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 343 removed outlier: 3.685A pdb=" N ARG A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 370 removed outlier: 3.953A pdb=" N SER A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 376 removed outlier: 3.850A pdb=" N GLN A 375 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 386 removed outlier: 3.587A pdb=" N PHE A 381 " --> pdb=" O TYR A 377 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 382 " --> pdb=" O PRO A 378 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 401 through 420 Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 467 through 471 Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 493 through 505 Processing helix chain 'A' and resid 506 through 511 removed outlier: 3.518A pdb=" N LEU A 511 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 537 removed outlier: 3.881A pdb=" N ILE A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 528 " --> pdb=" O GLY A 524 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 547 removed outlier: 3.569A pdb=" N GLN A 547 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 removed outlier: 3.874A pdb=" N LYS A 555 " --> pdb=" O MET A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 567 removed outlier: 3.920A pdb=" N GLU A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 573 Processing helix chain 'A' and resid 578 through 585 removed outlier: 3.567A pdb=" N ILE A 582 " --> pdb=" O ILE A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 removed outlier: 3.637A pdb=" N ILE A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 597 " --> pdb=" O LYS A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 removed outlier: 3.771A pdb=" N ILE A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU A 613 " --> pdb=" O LYS A 609 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.661A pdb=" N PHE A 631 " --> pdb=" O TYR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 649 removed outlier: 3.645A pdb=" N LYS A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 657 removed outlier: 3.694A pdb=" N GLN A 657 " --> pdb=" O GLU A 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 654 through 657' Processing helix chain 'A' and resid 658 through 672 removed outlier: 3.505A pdb=" N ILE A 662 " --> pdb=" O ILE A 658 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA A 664 " --> pdb=" O ARG A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 713 removed outlier: 4.116A pdb=" N HIS A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 728 removed outlier: 3.812A pdb=" N TYR A 726 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 727 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 728 " --> pdb=" O GLU A 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 722 through 728' Processing helix chain 'A' and resid 740 through 754 removed outlier: 3.825A pdb=" N LEU A 744 " --> pdb=" O PRO A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 775 removed outlier: 3.838A pdb=" N ASN A 775 " --> pdb=" O ASP A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 828 removed outlier: 3.975A pdb=" N ARG A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA A 808 " --> pdb=" O ASN A 804 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE A 809 " --> pdb=" O PHE A 805 " (cutoff:3.500A) Proline residue: A 815 - end of helix removed outlier: 3.942A pdb=" N ILE A 824 " --> pdb=" O THR A 820 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 826 " --> pdb=" O PHE A 822 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 827 " --> pdb=" O ASN A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 852 removed outlier: 3.948A pdb=" N THR A 835 " --> pdb=" O ASP A 831 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A 836 " --> pdb=" O HIS A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 868 Processing helix chain 'A' and resid 906 through 915 removed outlier: 3.575A pdb=" N ARG A 911 " --> pdb=" O THR A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 931 removed outlier: 3.619A pdb=" N GLN A 919 " --> pdb=" O SER A 915 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL A 923 " --> pdb=" O GLN A 919 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 929 " --> pdb=" O PHE A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 956 removed outlier: 4.033A pdb=" N ASP A 956 " --> pdb=" O THR A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 971 Processing helix chain 'A' and resid 1011 through 1025 removed outlier: 3.745A pdb=" N SER A1025 " --> pdb=" O GLU A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1033 removed outlier: 4.514A pdb=" N VAL A1032 " --> pdb=" O ILE A1028 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE A1033 " --> pdb=" O ALA A1029 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1028 through 1033' Processing helix chain 'A' and resid 1035 through 1039 removed outlier: 4.237A pdb=" N ASN A1038 " --> pdb=" O ASN A1035 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A1039 " --> pdb=" O GLU A1036 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1035 through 1039' Processing helix chain 'A' and resid 1040 through 1050 Processing helix chain 'A' and resid 1058 through 1061 removed outlier: 3.779A pdb=" N ARG A1061 " --> pdb=" O ASP A1058 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1058 through 1061' Processing helix chain 'A' and resid 1062 through 1081 removed outlier: 3.606A pdb=" N ALA A1076 " --> pdb=" O GLU A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1100 Processing helix chain 'A' and resid 1105 through 1123 removed outlier: 3.508A pdb=" N VAL A1109 " --> pdb=" O THR A1105 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A1114 " --> pdb=" O ARG A1110 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR A1115 " --> pdb=" O ARG A1111 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A1116 " --> pdb=" O MET A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1136 removed outlier: 3.733A pdb=" N LEU A1130 " --> pdb=" O GLN A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1152 removed outlier: 3.648A pdb=" N THR A1152 " --> pdb=" O LYS A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1165 removed outlier: 3.573A pdb=" N LYS A1156 " --> pdb=" O THR A1152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A1157 " --> pdb=" O ASN A1153 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A1158 " --> pdb=" O GLN A1154 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE A1163 " --> pdb=" O LEU A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1168 No H-bonds generated for 'chain 'A' and resid 1166 through 1168' Processing helix chain 'A' and resid 1171 through 1178 Processing helix chain 'A' and resid 1179 through 1190 removed outlier: 3.647A pdb=" N ALA A1190 " --> pdb=" O ARG A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1209 removed outlier: 3.711A pdb=" N GLU A1204 " --> pdb=" O GLU A1200 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A1209 " --> pdb=" O SER A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1231 removed outlier: 3.852A pdb=" N VAL A1221 " --> pdb=" O ASN A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1275 removed outlier: 4.083A pdb=" N LEU A1266 " --> pdb=" O ILE A1262 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LYS A1267 " --> pdb=" O GLU A1263 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A1268 " --> pdb=" O LEU A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1298 removed outlier: 3.941A pdb=" N ILE A1290 " --> pdb=" O GLU A1286 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS A1298 " --> pdb=" O LEU A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1320 removed outlier: 4.157A pdb=" N ASN A1319 " --> pdb=" O GLN A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1338 removed outlier: 4.020A pdb=" N LEU A1334 " --> pdb=" O SER A1330 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY A1338 " --> pdb=" O LEU A1334 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1343 removed outlier: 3.833A pdb=" N LEU A1342 " --> pdb=" O GLY A1338 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1338 through 1343' Processing helix chain 'A' and resid 1351 through 1356 Processing helix chain 'A' and resid 1360 through 1374 removed outlier: 4.144A pdb=" N SER A1364 " --> pdb=" O LEU A1360 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A1368 " --> pdb=" O SER A1364 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N HIS A1369 " --> pdb=" O ASN A1365 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR A1370 " --> pdb=" O VAL A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1388 removed outlier: 3.776A pdb=" N PHE A1381 " --> pdb=" O SER A1377 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU A1382 " --> pdb=" O ASN A1378 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A1386 " --> pdb=" O LEU A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.774A pdb=" N LYS A1399 " --> pdb=" O SER A1395 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN A1402 " --> pdb=" O GLU A1398 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A1403 " --> pdb=" O LYS A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1415 removed outlier: 3.571A pdb=" N ILE A1411 " --> pdb=" O LYS A1408 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A1412 " --> pdb=" O LYS A1409 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A1413 " --> pdb=" O SER A1410 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A1415 " --> pdb=" O GLU A1412 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 24 removed outlier: 3.949A pdb=" N LYS B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 removed outlier: 3.722A pdb=" N PHE B 76 " --> pdb=" O PHE B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 107 removed outlier: 3.723A pdb=" N LEU B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) Proline residue: B 100 - end of helix Processing helix chain 'B' and resid 111 through 129 removed outlier: 3.503A pdb=" N THR B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 128 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 129 " --> pdb=" O PHE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.895A pdb=" N THR B 150 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 179 removed outlier: 3.598A pdb=" N LEU B 167 " --> pdb=" O ASP B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 188 through 203 removed outlier: 3.645A pdb=" N ASP B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 201 " --> pdb=" O ILE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 228 removed outlier: 3.701A pdb=" N LYS B 228 " --> pdb=" O LYS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 344 Processing helix chain 'B' and resid 345 through 348 Processing helix chain 'B' and resid 352 through 370 removed outlier: 4.124A pdb=" N SER B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 376 removed outlier: 3.826A pdb=" N GLN B 375 " --> pdb=" O ASP B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 398 removed outlier: 3.826A pdb=" N PHE B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP B 386 " --> pdb=" O THR B 382 " (cutoff:3.500A) Proline residue: B 387 - end of helix removed outlier: 3.614A pdb=" N LYS B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER B 391 " --> pdb=" O PRO B 387 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 392 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE B 396 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLN B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 420 removed outlier: 3.642A pdb=" N LEU B 405 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 420 " --> pdb=" O VAL B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 439 removed outlier: 4.017A pdb=" N GLU B 428 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR B 430 " --> pdb=" O GLN B 426 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 434 " --> pdb=" O THR B 430 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 473 removed outlier: 4.273A pdb=" N GLU B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 467 " --> pdb=" O ILE B 463 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE B 468 " --> pdb=" O GLU B 464 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 Processing helix chain 'B' and resid 493 through 506 removed outlier: 3.584A pdb=" N LYS B 503 " --> pdb=" O LYS B 499 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU B 506 " --> pdb=" O THR B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 512 Processing helix chain 'B' and resid 516 through 535 removed outlier: 3.687A pdb=" N ILE B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 545 removed outlier: 3.755A pdb=" N PHE B 544 " --> pdb=" O ASP B 540 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY B 545 " --> pdb=" O ARG B 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 540 through 545' Processing helix chain 'B' and resid 556 through 571 removed outlier: 3.662A pdb=" N LYS B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU B 562 " --> pdb=" O ASP B 558 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR B 567 " --> pdb=" O PHE B 563 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 569 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 584 removed outlier: 3.959A pdb=" N MET B 580 " --> pdb=" O LYS B 576 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 583 " --> pdb=" O PRO B 579 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS B 584 " --> pdb=" O MET B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 removed outlier: 3.832A pdb=" N ASN B 602 " --> pdb=" O PHE B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 617 Processing helix chain 'B' and resid 620 through 628 removed outlier: 4.158A pdb=" N ILE B 628 " --> pdb=" O LEU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 631 No H-bonds generated for 'chain 'B' and resid 629 through 631' Processing helix chain 'B' and resid 637 through 649 removed outlier: 4.042A pdb=" N THR B 647 " --> pdb=" O ARG B 643 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 648 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 668 removed outlier: 4.359A pdb=" N ILE B 661 " --> pdb=" O GLN B 657 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER B 666 " --> pdb=" O ILE B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 removed outlier: 3.973A pdb=" N ASN B 672 " --> pdb=" O ALA B 668 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 673 " --> pdb=" O TYR B 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 668 through 673' Processing helix chain 'B' and resid 676 through 680 removed outlier: 4.068A pdb=" N ILE B 680 " --> pdb=" O PRO B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 712 removed outlier: 4.007A pdb=" N MET B 707 " --> pdb=" O TYR B 703 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 708 " --> pdb=" O SER B 704 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASN B 709 " --> pdb=" O ILE B 705 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR B 710 " --> pdb=" O ILE B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 730 removed outlier: 3.592A pdb=" N TYR B 726 " --> pdb=" O SER B 722 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 730 " --> pdb=" O TYR B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 752 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 800 through 806 Processing helix chain 'B' and resid 807 through 822 removed outlier: 4.510A pdb=" N LYS B 811 " --> pdb=" O ARG B 807 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN B 812 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Proline residue: B 815 - end of helix Processing helix chain 'B' and resid 830 through 851 removed outlier: 3.631A pdb=" N ARG B 836 " --> pdb=" O HIS B 832 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 849 " --> pdb=" O SER B 845 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 850 " --> pdb=" O TYR B 846 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE B 851 " --> pdb=" O ILE B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 868 removed outlier: 4.364A pdb=" N LEU B 861 " --> pdb=" O PHE B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 915 Processing helix chain 'B' and resid 915 through 932 removed outlier: 3.741A pdb=" N THR B 922 " --> pdb=" O GLY B 918 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL B 923 " --> pdb=" O GLN B 919 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 956 removed outlier: 3.645A pdb=" N ASN B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE B 949 " --> pdb=" O ASN B 945 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE B 950 " --> pdb=" O ILE B 946 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N THR B 952 " --> pdb=" O ASN B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 972 Processing helix chain 'B' and resid 1009 through 1026 removed outlier: 3.872A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS B1014 " --> pdb=" O GLU B1010 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER B1015 " --> pdb=" O GLU B1011 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LYS B1018 " --> pdb=" O LYS B1014 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B1019 " --> pdb=" O SER B1015 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET B1020 " --> pdb=" O SER B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1033 removed outlier: 4.002A pdb=" N VAL B1032 " --> pdb=" O ILE B1028 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE B1033 " --> pdb=" O ALA B1029 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1028 through 1033' Processing helix chain 'B' and resid 1035 through 1039 removed outlier: 3.632A pdb=" N ASN B1038 " --> pdb=" O ASN B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1051 Processing helix chain 'B' and resid 1056 through 1060 Processing helix chain 'B' and resid 1062 through 1079 removed outlier: 3.777A pdb=" N LEU B1079 " --> pdb=" O ILE B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1099 Processing helix chain 'B' and resid 1105 through 1112 Processing helix chain 'B' and resid 1115 through 1122 removed outlier: 4.212A pdb=" N LEU B1119 " --> pdb=" O TYR B1115 " (cutoff:3.500A) Processing helix chain 'B' and resid 1146 through 1152 removed outlier: 3.746A pdb=" N PHE B1150 " --> pdb=" O THR B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1168 removed outlier: 3.840A pdb=" N LEU B1165 " --> pdb=" O ARG B1161 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR B1166 " --> pdb=" O LEU B1162 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU B1167 " --> pdb=" O PHE B1163 " (cutoff:3.500A) Processing helix chain 'B' and resid 1169 through 1171 No H-bonds generated for 'chain 'B' and resid 1169 through 1171' Processing helix chain 'B' and resid 1172 through 1177 removed outlier: 4.016A pdb=" N LEU B1176 " --> pdb=" O ARG B1172 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY B1177 " --> pdb=" O GLY B1173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1172 through 1177' Processing helix chain 'B' and resid 1178 through 1191 removed outlier: 3.943A pdb=" N TRP B1182 " --> pdb=" O ASN B1178 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET B1191 " --> pdb=" O LYS B1187 " (cutoff:3.500A) Processing helix chain 'B' and resid 1194 through 1209 removed outlier: 3.979A pdb=" N THR B1208 " --> pdb=" O GLU B1204 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP B1209 " --> pdb=" O SER B1205 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1230 removed outlier: 3.631A pdb=" N VAL B1221 " --> pdb=" O ASN B1217 " (cutoff:3.500A) Processing helix chain 'B' and resid 1260 through 1279 removed outlier: 3.858A pdb=" N LEU B1264 " --> pdb=" O LYS B1260 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B1270 " --> pdb=" O LEU B1266 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B1276 " --> pdb=" O THR B1272 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU B1277 " --> pdb=" O SER B1273 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN B1279 " --> pdb=" O LEU B1275 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1297 Processing helix chain 'B' and resid 1298 through 1300 No H-bonds generated for 'chain 'B' and resid 1298 through 1300' Processing helix chain 'B' and resid 1302 through 1319 removed outlier: 3.605A pdb=" N PHE B1308 " --> pdb=" O GLN B1304 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B1318 " --> pdb=" O GLU B1314 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN B1319 " --> pdb=" O GLN B1315 " (cutoff:3.500A) Processing helix chain 'B' and resid 1332 through 1338 removed outlier: 4.241A pdb=" N GLU B1336 " --> pdb=" O GLU B1332 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B1337 " --> pdb=" O GLU B1333 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY B1338 " --> pdb=" O LEU B1334 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1332 through 1338' Processing helix chain 'B' and resid 1338 through 1344 removed outlier: 3.636A pdb=" N LEU B1342 " --> pdb=" O GLY B1338 " (cutoff:3.500A) Processing helix chain 'B' and resid 1355 through 1373 removed outlier: 4.134A pdb=" N ILE B1359 " --> pdb=" O LEU B1355 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B1363 " --> pdb=" O ILE B1359 " (cutoff:3.500A) Processing helix chain 'B' and resid 1378 through 1389 removed outlier: 3.874A pdb=" N LEU B1382 " --> pdb=" O ASN B1378 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B1383 " --> pdb=" O GLU B1379 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B1386 " --> pdb=" O LEU B1382 " (cutoff:3.500A) Processing helix chain 'B' and resid 1390 through 1392 No H-bonds generated for 'chain 'B' and resid 1390 through 1392' Processing helix chain 'B' and resid 1396 through 1412 removed outlier: 4.017A pdb=" N LEU B1401 " --> pdb=" O ILE B1397 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN B1402 " --> pdb=" O GLU B1398 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU B1412 " --> pdb=" O LYS B1408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 241 through 242 removed outlier: 3.593A pdb=" N TYR A 241 " --> pdb=" O THR A 784 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 784 " --> pdb=" O TYR A 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 943 hydrogen bonds defined for protein. 2754 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.39 Time building geometry restraints manager: 28.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19297 1.03 - 1.23: 167 1.23 - 1.43: 7528 1.43 - 1.63: 11365 1.63 - 1.82: 110 Bond restraints: 38467 Sorted by residual: bond pdb=" CB ASN A 84 " pdb=" CG ASN A 84 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.50e-02 1.60e+03 5.30e+00 bond pdb=" CB GLU B1193 " pdb=" CG GLU B1193 " ideal model delta sigma weight residual 1.520 1.587 -0.067 3.00e-02 1.11e+03 5.05e+00 bond pdb=" CB ILE A 357 " pdb=" CG2 ILE A 357 " ideal model delta sigma weight residual 1.521 1.590 -0.069 3.30e-02 9.18e+02 4.36e+00 bond pdb=" CG1 ILE A 392 " pdb=" CD1 ILE A 392 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.35e+00 bond pdb=" C ILE A 578 " pdb=" N PRO A 579 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.19e-02 7.06e+03 4.21e+00 ... (remaining 38462 not shown) Histogram of bond angle deviations from ideal: 99.38 - 106.37: 993 106.37 - 113.37: 46085 113.37 - 120.36: 13099 120.36 - 127.36: 9565 127.36 - 134.35: 127 Bond angle restraints: 69869 Sorted by residual: angle pdb=" CA GLU B1012 " pdb=" CB GLU B1012 " pdb=" CG GLU B1012 " ideal model delta sigma weight residual 114.10 123.61 -9.51 2.00e+00 2.50e-01 2.26e+01 angle pdb=" CA GLN B 410 " pdb=" CB GLN B 410 " pdb=" CG GLN B 410 " ideal model delta sigma weight residual 114.10 123.60 -9.50 2.00e+00 2.50e-01 2.26e+01 angle pdb=" CA GLU B 565 " pdb=" CB GLU B 565 " pdb=" CG GLU B 565 " ideal model delta sigma weight residual 114.10 122.92 -8.82 2.00e+00 2.50e-01 1.94e+01 angle pdb=" C SER B1026 " pdb=" N ASN B1027 " pdb=" CA ASN B1027 " ideal model delta sigma weight residual 121.54 129.86 -8.32 1.91e+00 2.74e-01 1.90e+01 angle pdb=" CA ASN A 84 " pdb=" CB ASN A 84 " pdb=" CG ASN A 84 " ideal model delta sigma weight residual 112.60 116.52 -3.92 1.00e+00 1.00e+00 1.54e+01 ... (remaining 69864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 15136 17.95 - 35.90: 2069 35.90 - 53.85: 537 53.85 - 71.79: 129 71.79 - 89.74: 38 Dihedral angle restraints: 17909 sinusoidal: 9901 harmonic: 8008 Sorted by residual: dihedral pdb=" CA TYR B1062 " pdb=" C TYR B1062 " pdb=" N PHE B1063 " pdb=" CA PHE B1063 " ideal model delta harmonic sigma weight residual 180.00 -151.93 -28.07 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA ASP A 676 " pdb=" C ASP A 676 " pdb=" N PRO A 677 " pdb=" CA PRO A 677 " ideal model delta harmonic sigma weight residual -180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA THR A1009 " pdb=" C THR A1009 " pdb=" N GLU A1010 " pdb=" CA GLU A1010 " ideal model delta harmonic sigma weight residual 180.00 -155.37 -24.63 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 17906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2644 0.061 - 0.121: 397 0.121 - 0.182: 34 0.182 - 0.242: 4 0.242 - 0.303: 3 Chirality restraints: 3082 Sorted by residual: chirality pdb=" CB ILE A 860 " pdb=" CA ILE A 860 " pdb=" CG1 ILE A 860 " pdb=" CG2 ILE A 860 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB THR A 222 " pdb=" CA THR A 222 " pdb=" OG1 THR A 222 " pdb=" CG2 THR A 222 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CB ILE B 418 " pdb=" CA ILE B 418 " pdb=" CG1 ILE B 418 " pdb=" CG2 ILE B 418 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 3079 not shown) Planarity restraints: 5489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 506 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO A 507 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 507 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 507 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1340 " -0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO A1341 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A1341 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A1341 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 739 " 0.021 2.00e-02 2.50e+03 1.80e-02 9.76e+00 pdb=" CG PHE A 739 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 739 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 739 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 739 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 739 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 739 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 739 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE A 739 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE A 739 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 739 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 739 " -0.001 2.00e-02 2.50e+03 ... (remaining 5486 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 6706 2.28 - 2.86: 84904 2.86 - 3.44: 97573 3.44 - 4.02: 120356 4.02 - 4.60: 183939 Nonbonded interactions: 493478 Sorted by model distance: nonbonded pdb=" OE1 GLU B 562 " pdb=" H GLU B 562 " model vdw 1.700 1.850 nonbonded pdb=" OE1 GLU A 543 " pdb=" H GLU A 543 " model vdw 1.706 1.850 nonbonded pdb=" OE1 GLU B 801 " pdb=" H GLU B 801 " model vdw 1.707 1.850 nonbonded pdb=" H CYS B 734 " pdb=" O LYS B 737 " model vdw 1.734 1.850 nonbonded pdb=" O ASN B 858 " pdb="HD21 ASN B 862 " model vdw 1.739 1.850 ... (remaining 493473 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 11 through 154 or (resid 162 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name H \ B2 or name HB3)) or resid 163 through 230 or (resid 329 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD1 or name CD2 or name HA or n \ ame HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD \ 21 or name HD22 or name HD23)) or resid 330 through 545 or (resid 554 and (name \ N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 o \ r name HA or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name H \ D13 or name HD21 or name HD22 or name HD23)) or resid 555 through 758 or (resid \ 765 and (name N or name CA or name C or name O or name CB or name CG or name OD1 \ or name ND2 or name HA or name HB2 or name HB3 or name HD21 or name HD22)) or r \ esid 766 through 779 or resid 799 through 871 or resid 889 through 986 or (resid \ 1007 and (name N or name CA or name C or name O or name CB or name CG or name C \ D or name OE1 or name OE2 or name HA or name HB2 or name HB3 or name HG2 or name \ HG3)) or resid 1008 through 1344 or (resid 1352 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or r \ esid 1353 through 1392 or (resid 1395 and (name N or name CA or name C or name O \ or name CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid \ 1396 through 1415)) 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.530 Extract box with map and model: 7.890 Check model and map are aligned: 0.520 Set scattering table: 0.320 Process input model: 109.290 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.110 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 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 : 0.006 0.081 19136 Z= 0.356 Angle : 0.962 9.611 25829 Z= 0.496 Chirality : 0.044 0.303 3082 Planarity : 0.006 0.104 3232 Dihedral : 18.749 89.742 7202 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.87 % Favored : 94.00 % Rotamer: Outliers : 0.23 % Allowed : 32.89 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.17), residues: 2299 helix: -0.31 (0.13), residues: 1421 sheet: None (None), residues: 0 loop : -1.19 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 943 HIS 0.017 0.001 HIS A1369 PHE 0.054 0.002 PHE A 739 TYR 0.030 0.001 TYR A1367 ARG 0.021 0.001 ARG B1186 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 644 time to evaluate : 2.978 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: A 81 LEU cc_start: 0.8721 (mm) cc_final: 0.8480 (mm) REVERT: A 84 ASN cc_start: 0.8473 (t0) cc_final: 0.8208 (m110) REVERT: A 372 ASP cc_start: 0.7692 (p0) cc_final: 0.7445 (p0) REVERT: A 376 LEU cc_start: 0.9185 (mp) cc_final: 0.8951 (mp) REVERT: A 560 LYS cc_start: 0.9350 (mmmm) cc_final: 0.9023 (mmmm) REVERT: A 562 GLU cc_start: 0.7689 (mt-10) cc_final: 0.6953 (mm-30) REVERT: A 567 THR cc_start: 0.8121 (m) cc_final: 0.7709 (p) REVERT: A 663 GLU cc_start: 0.6249 (tm-30) cc_final: 0.5635 (mt-10) REVERT: A 723 PHE cc_start: 0.8034 (t80) cc_final: 0.7628 (t80) REVERT: A 758 MET cc_start: 0.6494 (ptm) cc_final: 0.5732 (ptm) REVERT: A 832 HIS cc_start: 0.8795 (m-70) cc_final: 0.8569 (m170) REVERT: A 837 MET cc_start: 0.9270 (mmm) cc_final: 0.8739 (mmm) REVERT: A 911 ARG cc_start: 0.7155 (mmt180) cc_final: 0.6744 (mpt180) REVERT: A 973 LEU cc_start: 0.9100 (tp) cc_final: 0.8872 (tp) REVERT: A 1036 GLU cc_start: 0.7546 (mp0) cc_final: 0.7255 (mp0) REVERT: A 1157 GLU cc_start: 0.8532 (tp30) cc_final: 0.8167 (tp30) REVERT: B 361 GLU cc_start: 0.8022 (mp0) cc_final: 0.7713 (mp0) REVERT: B 379 ARG cc_start: 0.7649 (tpt90) cc_final: 0.7339 (tpt90) REVERT: B 616 CYS cc_start: 0.8665 (m) cc_final: 0.8393 (m) REVERT: B 729 ASN cc_start: 0.6720 (t0) cc_final: 0.6424 (m110) REVERT: B 812 GLN cc_start: 0.8124 (tp-100) cc_final: 0.7527 (mp10) REVERT: B 1062 TYR cc_start: 0.6896 (m-10) cc_final: 0.6490 (m-10) outliers start: 5 outliers final: 3 residues processed: 646 average time/residue: 0.6184 time to fit residues: 638.8789 Evaluate side-chains 596 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 593 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 196 optimal weight: 0.8980 chunk 176 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN A 617 HIS A 672 ASN A 729 ASN A 762 HIS A 945 ASN A1365 ASN B 215 GLN B 398 ASN B 410 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 ASN B 921 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 19136 Z= 0.267 Angle : 0.597 6.841 25829 Z= 0.326 Chirality : 0.036 0.143 3082 Planarity : 0.005 0.069 3232 Dihedral : 5.262 33.386 2457 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.96 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.17), residues: 2299 helix: 0.25 (0.13), residues: 1447 sheet: None (None), residues: 0 loop : -1.24 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 470 HIS 0.004 0.001 HIS B 351 PHE 0.030 0.002 PHE A 171 TYR 0.019 0.002 TYR B1115 ARG 0.003 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 691 time to evaluate : 2.778 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: A 20 ILE cc_start: 0.8728 (mm) cc_final: 0.8484 (mm) REVERT: A 84 ASN cc_start: 0.8536 (t0) cc_final: 0.8096 (m110) REVERT: A 481 PHE cc_start: 0.9318 (t80) cc_final: 0.9080 (t80) REVERT: A 487 ASN cc_start: 0.8378 (m-40) cc_final: 0.7753 (m-40) REVERT: A 495 ILE cc_start: 0.8215 (mm) cc_final: 0.7986 (mm) REVERT: A 531 ASP cc_start: 0.8283 (m-30) cc_final: 0.8001 (m-30) REVERT: A 562 GLU cc_start: 0.7391 (tt0) cc_final: 0.7151 (mm-30) REVERT: A 723 PHE cc_start: 0.7924 (t80) cc_final: 0.7699 (t80) REVERT: A 785 GLU cc_start: 0.7182 (pm20) cc_final: 0.6248 (tm-30) REVERT: A 795 ASP cc_start: 0.7249 (m-30) cc_final: 0.6959 (m-30) REVERT: A 889 MET cc_start: 0.7092 (pmm) cc_final: 0.6846 (pmm) REVERT: A 936 LYS cc_start: 0.8782 (mtpp) cc_final: 0.8429 (mtmm) REVERT: A 973 LEU cc_start: 0.9000 (tp) cc_final: 0.8795 (tp) REVERT: A 1012 GLU cc_start: 0.8170 (mp0) cc_final: 0.7753 (mp0) REVERT: A 1036 GLU cc_start: 0.7633 (mp0) cc_final: 0.7259 (mp0) REVERT: A 1157 GLU cc_start: 0.8337 (tp30) cc_final: 0.7925 (tp30) REVERT: A 1191 MET cc_start: 0.7842 (mtt) cc_final: 0.7624 (tpp) REVERT: A 1287 ILE cc_start: 0.8568 (tt) cc_final: 0.8365 (tt) REVERT: B 13 THR cc_start: 0.7797 (m) cc_final: 0.7020 (m) REVERT: B 14 ILE cc_start: 0.8255 (mm) cc_final: 0.8048 (mm) REVERT: B 163 ASP cc_start: 0.9098 (m-30) cc_final: 0.8801 (m-30) REVERT: B 208 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7859 (mt-10) REVERT: B 222 THR cc_start: 0.7901 (m) cc_final: 0.7629 (m) REVERT: B 225 ILE cc_start: 0.8011 (tp) cc_final: 0.7791 (tp) REVERT: B 346 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8611 (mp0) REVERT: B 361 GLU cc_start: 0.7787 (mp0) cc_final: 0.7364 (mp0) REVERT: B 464 GLU cc_start: 0.8723 (tp30) cc_final: 0.8486 (tp30) REVERT: B 465 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8428 (mm-40) REVERT: B 523 GLU cc_start: 0.8834 (tp30) cc_final: 0.8500 (mm-30) REVERT: B 542 GLU cc_start: 0.8971 (mp0) cc_final: 0.8736 (mm-30) REVERT: B 580 MET cc_start: 0.6468 (mtp) cc_final: 0.5893 (mtt) REVERT: B 729 ASN cc_start: 0.6763 (t0) cc_final: 0.6408 (m110) REVERT: B 758 MET cc_start: 0.0264 (ptt) cc_final: -0.0042 (ppp) REVERT: B 812 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7486 (mp10) REVERT: B 933 LYS cc_start: 0.8224 (mmmt) cc_final: 0.7951 (mmmt) REVERT: B 938 PHE cc_start: 0.8273 (m-10) cc_final: 0.7893 (m-10) REVERT: B 966 ASP cc_start: 0.7695 (t70) cc_final: 0.7450 (t70) REVERT: B 1021 GLU cc_start: 0.8084 (tp30) cc_final: 0.7701 (tp30) REVERT: B 1036 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8013 (mm-30) REVERT: B 1038 ASN cc_start: 0.8896 (m110) cc_final: 0.8693 (m110) REVERT: B 1056 ASN cc_start: 0.8200 (t0) cc_final: 0.7960 (t0) REVERT: B 1058 ASP cc_start: 0.9047 (p0) cc_final: 0.8736 (p0) REVERT: B 1123 CYS cc_start: 0.8377 (t) cc_final: 0.8126 (t) REVERT: B 1169 GLU cc_start: 0.8397 (tt0) cc_final: 0.8196 (tt0) REVERT: B 1180 ASN cc_start: 0.9158 (m-40) cc_final: 0.8932 (m-40) REVERT: B 1191 MET cc_start: 0.8376 (mmt) cc_final: 0.8090 (mmt) REVERT: B 1193 GLU cc_start: 0.7705 (mp0) cc_final: 0.7422 (mp0) outliers start: 0 outliers final: 0 residues processed: 691 average time/residue: 0.6240 time to fit residues: 676.0667 Evaluate side-chains 604 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 604 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 176 optimal weight: 0.5980 chunk 144 optimal weight: 0.9990 chunk 58 optimal weight: 0.0570 chunk 211 optimal weight: 0.8980 chunk 228 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 210 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 chunk 170 optimal weight: 0.0060 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS A1038 ASN B 212 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1211 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 19136 Z= 0.156 Angle : 0.513 7.004 25829 Z= 0.275 Chirality : 0.034 0.127 3082 Planarity : 0.004 0.064 3232 Dihedral : 4.927 30.623 2457 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.52 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2299 helix: 0.56 (0.13), residues: 1458 sheet: None (None), residues: 0 loop : -1.21 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 470 HIS 0.003 0.001 HIS B 351 PHE 0.018 0.001 PHE B 101 TYR 0.014 0.001 TYR B1115 ARG 0.005 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 683 time to evaluate : 3.026 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: A 20 ILE cc_start: 0.8717 (mm) cc_final: 0.8313 (mm) REVERT: A 21 ASN cc_start: 0.8913 (t0) cc_final: 0.8583 (m-40) REVERT: A 84 ASN cc_start: 0.8576 (t0) cc_final: 0.8095 (m110) REVERT: A 358 PHE cc_start: 0.7820 (t80) cc_final: 0.7507 (t80) REVERT: A 393 LEU cc_start: 0.8934 (tp) cc_final: 0.8685 (tp) REVERT: A 397 GLN cc_start: 0.8595 (tp40) cc_final: 0.8316 (tp40) REVERT: A 481 PHE cc_start: 0.9305 (t80) cc_final: 0.9096 (t80) REVERT: A 487 ASN cc_start: 0.8136 (m-40) cc_final: 0.7500 (m-40) REVERT: A 495 ILE cc_start: 0.8541 (mm) cc_final: 0.8282 (mm) REVERT: A 562 GLU cc_start: 0.7466 (tt0) cc_final: 0.7165 (mm-30) REVERT: A 597 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8681 (tm-30) REVERT: A 785 GLU cc_start: 0.7196 (pm20) cc_final: 0.6399 (tm-30) REVERT: A 795 ASP cc_start: 0.7769 (m-30) cc_final: 0.7401 (m-30) REVERT: A 806 ASP cc_start: 0.9204 (m-30) cc_final: 0.8750 (m-30) REVERT: A 832 HIS cc_start: 0.8953 (m-70) cc_final: 0.8690 (m170) REVERT: A 837 MET cc_start: 0.9416 (mmm) cc_final: 0.8807 (mmm) REVERT: A 889 MET cc_start: 0.7118 (pmm) cc_final: 0.6883 (pmm) REVERT: A 936 LYS cc_start: 0.8818 (mtpp) cc_final: 0.8473 (mtmm) REVERT: A 973 LEU cc_start: 0.8976 (tp) cc_final: 0.8756 (tp) REVERT: A 1012 GLU cc_start: 0.8300 (mp0) cc_final: 0.7868 (mp0) REVERT: A 1036 GLU cc_start: 0.7941 (mp0) cc_final: 0.7688 (mp0) REVERT: A 1104 LEU cc_start: 0.8247 (mp) cc_final: 0.8020 (mp) REVERT: A 1157 GLU cc_start: 0.8671 (tp30) cc_final: 0.8312 (tp30) REVERT: A 1328 MET cc_start: 0.8793 (mmp) cc_final: 0.8417 (mmm) REVERT: B 163 ASP cc_start: 0.9073 (m-30) cc_final: 0.8794 (m-30) REVERT: B 225 ILE cc_start: 0.8019 (tp) cc_final: 0.7803 (tp) REVERT: B 346 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8607 (mp0) REVERT: B 428 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7447 (tm-30) REVERT: B 464 GLU cc_start: 0.8732 (tp30) cc_final: 0.8438 (tp30) REVERT: B 494 SER cc_start: 0.9442 (p) cc_final: 0.9209 (p) REVERT: B 580 MET cc_start: 0.6109 (mtp) cc_final: 0.5757 (mtt) REVERT: B 729 ASN cc_start: 0.7146 (t0) cc_final: 0.6660 (m110) REVERT: B 758 MET cc_start: 0.0362 (ptt) cc_final: -0.0001 (ppp) REVERT: B 812 GLN cc_start: 0.8111 (tp-100) cc_final: 0.7378 (mp10) REVERT: B 933 LYS cc_start: 0.8283 (mmmt) cc_final: 0.7936 (mmmt) REVERT: B 946 ILE cc_start: 0.8422 (tp) cc_final: 0.8094 (tp) REVERT: B 966 ASP cc_start: 0.7572 (t70) cc_final: 0.7295 (t70) REVERT: B 1021 GLU cc_start: 0.8085 (tp30) cc_final: 0.7850 (tp30) REVERT: B 1036 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7859 (mm-30) REVERT: B 1123 CYS cc_start: 0.8333 (t) cc_final: 0.7878 (t) REVERT: B 1169 GLU cc_start: 0.8428 (tt0) cc_final: 0.8180 (tt0) REVERT: B 1180 ASN cc_start: 0.9132 (m-40) cc_final: 0.8928 (m110) REVERT: B 1186 ARG cc_start: 0.8680 (mtp-110) cc_final: 0.8225 (mtp-110) REVERT: B 1286 GLU cc_start: 0.8497 (mp0) cc_final: 0.8189 (mp0) outliers start: 0 outliers final: 0 residues processed: 683 average time/residue: 0.5972 time to fit residues: 645.0726 Evaluate side-chains 597 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 597 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 209 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 212 optimal weight: 0.9990 chunk 225 optimal weight: 0.6980 chunk 111 optimal weight: 0.1980 chunk 201 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 HIS A1038 ASN A1326 ASN B 212 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1154 GLN ** B1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19136 Z= 0.197 Angle : 0.519 6.506 25829 Z= 0.282 Chirality : 0.034 0.142 3082 Planarity : 0.004 0.062 3232 Dihedral : 4.838 28.350 2457 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2299 helix: 0.64 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.27 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 470 HIS 0.004 0.001 HIS A 720 PHE 0.019 0.001 PHE B 101 TYR 0.022 0.001 TYR B1115 ARG 0.004 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 664 time to evaluate : 3.090 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: A 20 ILE cc_start: 0.8354 (mm) cc_final: 0.8106 (mm) REVERT: A 21 ASN cc_start: 0.8999 (t0) cc_final: 0.8684 (m-40) REVERT: A 84 ASN cc_start: 0.8551 (t0) cc_final: 0.8085 (m110) REVERT: A 208 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6786 (mm-30) REVERT: A 372 ASP cc_start: 0.7811 (p0) cc_final: 0.7564 (p0) REVERT: A 393 LEU cc_start: 0.8964 (tp) cc_final: 0.8672 (tp) REVERT: A 397 GLN cc_start: 0.8621 (tp40) cc_final: 0.8300 (tp40) REVERT: A 487 ASN cc_start: 0.8063 (m-40) cc_final: 0.7471 (m-40) REVERT: A 495 ILE cc_start: 0.8560 (mm) cc_final: 0.8319 (mm) REVERT: A 562 GLU cc_start: 0.7641 (tt0) cc_final: 0.7233 (mm-30) REVERT: A 586 PHE cc_start: 0.7808 (m-10) cc_final: 0.7513 (m-10) REVERT: A 597 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8721 (tm-30) REVERT: A 611 ILE cc_start: 0.8607 (mm) cc_final: 0.8330 (mm) REVERT: A 795 ASP cc_start: 0.7259 (m-30) cc_final: 0.6982 (m-30) REVERT: A 806 ASP cc_start: 0.8973 (m-30) cc_final: 0.8744 (m-30) REVERT: A 817 ILE cc_start: 0.8999 (tp) cc_final: 0.8794 (tp) REVERT: A 832 HIS cc_start: 0.8969 (m-70) cc_final: 0.8681 (m170) REVERT: A 889 MET cc_start: 0.7094 (pmm) cc_final: 0.6841 (pmm) REVERT: A 936 LYS cc_start: 0.8860 (mtpp) cc_final: 0.8520 (mtmm) REVERT: A 973 LEU cc_start: 0.9000 (tp) cc_final: 0.8779 (tp) REVERT: A 1012 GLU cc_start: 0.8345 (mp0) cc_final: 0.7871 (mp0) REVERT: A 1036 GLU cc_start: 0.7839 (mp0) cc_final: 0.7590 (mp0) REVERT: A 1157 GLU cc_start: 0.8727 (tp30) cc_final: 0.8335 (tp30) REVERT: A 1287 ILE cc_start: 0.8372 (tt) cc_final: 0.8159 (tt) REVERT: A 1328 MET cc_start: 0.8922 (mmp) cc_final: 0.8596 (mmm) REVERT: B 163 ASP cc_start: 0.9074 (m-30) cc_final: 0.8788 (m-30) REVERT: B 225 ILE cc_start: 0.8034 (tp) cc_final: 0.7788 (tp) REVERT: B 335 TYR cc_start: 0.8379 (t80) cc_final: 0.7822 (t80) REVERT: B 346 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8632 (mp0) REVERT: B 361 GLU cc_start: 0.7758 (mp0) cc_final: 0.7481 (mp0) REVERT: B 464 GLU cc_start: 0.8737 (tp30) cc_final: 0.8423 (tp30) REVERT: B 729 ASN cc_start: 0.7125 (t0) cc_final: 0.6590 (m110) REVERT: B 844 CYS cc_start: 0.9056 (m) cc_final: 0.8838 (m) REVERT: B 856 LEU cc_start: 0.8992 (tp) cc_final: 0.8791 (tt) REVERT: B 933 LYS cc_start: 0.8295 (mmmt) cc_final: 0.7957 (mmmt) REVERT: B 966 ASP cc_start: 0.7565 (t70) cc_final: 0.7284 (t70) REVERT: B 1021 GLU cc_start: 0.8029 (tp30) cc_final: 0.7706 (tp30) REVERT: B 1036 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7968 (mm-30) REVERT: B 1056 ASN cc_start: 0.7855 (t0) cc_final: 0.7568 (t0) REVERT: B 1123 CYS cc_start: 0.8063 (t) cc_final: 0.7550 (t) REVERT: B 1186 ARG cc_start: 0.8745 (mtp-110) cc_final: 0.8007 (mtp-110) REVERT: B 1191 MET cc_start: 0.7733 (mmt) cc_final: 0.7492 (mmt) REVERT: B 1193 GLU cc_start: 0.7712 (mp0) cc_final: 0.7384 (mp0) REVERT: B 1286 GLU cc_start: 0.8544 (mp0) cc_final: 0.8203 (mp0) outliers start: 0 outliers final: 0 residues processed: 664 average time/residue: 0.6034 time to fit residues: 643.9709 Evaluate side-chains 595 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 595 time to evaluate : 2.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 187 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 167 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 192 optimal weight: 0.0980 chunk 155 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN A1038 ASN B 212 ASN B 422 ASN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19136 Z= 0.196 Angle : 0.525 6.323 25829 Z= 0.285 Chirality : 0.035 0.141 3082 Planarity : 0.004 0.060 3232 Dihedral : 4.802 26.220 2457 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.35 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.17), residues: 2299 helix: 0.68 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.31 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B1220 HIS 0.004 0.001 HIS A 720 PHE 0.022 0.001 PHE B 101 TYR 0.017 0.001 TYR A 703 ARG 0.008 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 670 time to evaluate : 3.216 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: A 21 ASN cc_start: 0.9139 (t0) cc_final: 0.8802 (t0) REVERT: A 84 ASN cc_start: 0.8515 (t0) cc_final: 0.8101 (m110) REVERT: A 372 ASP cc_start: 0.7833 (p0) cc_final: 0.7521 (p0) REVERT: A 393 LEU cc_start: 0.8928 (tp) cc_final: 0.8583 (tp) REVERT: A 397 GLN cc_start: 0.8636 (tp40) cc_final: 0.8299 (tp40) REVERT: A 435 PHE cc_start: 0.8129 (m-10) cc_final: 0.7761 (m-80) REVERT: A 467 SER cc_start: 0.8985 (p) cc_final: 0.8762 (p) REVERT: A 487 ASN cc_start: 0.8141 (m-40) cc_final: 0.7785 (m-40) REVERT: A 495 ILE cc_start: 0.8803 (mm) cc_final: 0.8571 (mm) REVERT: A 531 ASP cc_start: 0.8323 (m-30) cc_final: 0.8033 (m-30) REVERT: A 562 GLU cc_start: 0.7746 (tt0) cc_final: 0.7293 (mm-30) REVERT: A 597 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8741 (tm-30) REVERT: A 611 ILE cc_start: 0.8486 (mm) cc_final: 0.8251 (mm) REVERT: A 639 ASP cc_start: 0.8560 (m-30) cc_final: 0.8308 (m-30) REVERT: A 718 LYS cc_start: 0.6876 (pptt) cc_final: 0.6567 (tptm) REVERT: A 795 ASP cc_start: 0.7266 (m-30) cc_final: 0.7015 (m-30) REVERT: A 806 ASP cc_start: 0.8913 (m-30) cc_final: 0.8657 (m-30) REVERT: A 889 MET cc_start: 0.7083 (pmm) cc_final: 0.6820 (pmm) REVERT: A 936 LYS cc_start: 0.8897 (mtpp) cc_final: 0.8553 (mtmm) REVERT: A 973 LEU cc_start: 0.8969 (tp) cc_final: 0.8731 (tp) REVERT: A 1012 GLU cc_start: 0.8505 (mp0) cc_final: 0.8016 (mp0) REVERT: A 1036 GLU cc_start: 0.7848 (mp0) cc_final: 0.7615 (mp0) REVERT: A 1157 GLU cc_start: 0.8744 (tp30) cc_final: 0.8352 (tp30) REVERT: A 1328 MET cc_start: 0.8974 (mmp) cc_final: 0.8508 (mmm) REVERT: B 163 ASP cc_start: 0.9066 (m-30) cc_final: 0.8769 (m-30) REVERT: B 361 GLU cc_start: 0.8203 (mp0) cc_final: 0.7817 (mp0) REVERT: B 372 ASP cc_start: 0.8157 (t0) cc_final: 0.7672 (t0) REVERT: B 464 GLU cc_start: 0.8735 (tp30) cc_final: 0.8385 (tp30) REVERT: B 580 MET cc_start: 0.6769 (mtm) cc_final: 0.6201 (mtt) REVERT: B 729 ASN cc_start: 0.7173 (t0) cc_final: 0.6596 (m110) REVERT: B 844 CYS cc_start: 0.8980 (m) cc_final: 0.8769 (m) REVERT: B 933 LYS cc_start: 0.8309 (mmmt) cc_final: 0.7980 (mmmt) REVERT: B 966 ASP cc_start: 0.7586 (t70) cc_final: 0.7314 (t70) REVERT: B 1021 GLU cc_start: 0.7984 (tp30) cc_final: 0.7668 (tp30) REVERT: B 1036 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7963 (mm-30) REVERT: B 1038 ASN cc_start: 0.8981 (m110) cc_final: 0.8765 (m110) REVERT: B 1056 ASN cc_start: 0.7843 (t0) cc_final: 0.7521 (t0) REVERT: B 1123 CYS cc_start: 0.7977 (t) cc_final: 0.7498 (t) REVERT: B 1186 ARG cc_start: 0.8945 (mtp-110) cc_final: 0.8735 (mtm110) REVERT: B 1191 MET cc_start: 0.7805 (mmt) cc_final: 0.7453 (mmt) REVERT: B 1193 GLU cc_start: 0.7676 (mp0) cc_final: 0.7251 (mp0) REVERT: B 1227 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7907 (mt-10) REVERT: B 1231 MET cc_start: 0.8791 (mmt) cc_final: 0.8540 (mmm) REVERT: B 1300 ASN cc_start: 0.7244 (t0) cc_final: 0.7031 (t0) outliers start: 0 outliers final: 0 residues processed: 670 average time/residue: 0.6041 time to fit residues: 644.0058 Evaluate side-chains 595 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 595 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 75 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 132 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 225 optimal weight: 0.0370 chunk 187 optimal weight: 0.9980 chunk 104 optimal weight: 0.3980 chunk 18 optimal weight: 0.0000 chunk 74 optimal weight: 0.7980 chunk 118 optimal weight: 0.3980 overall best weight: 0.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1369 HIS B 212 ASN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 19136 Z= 0.138 Angle : 0.496 7.834 25829 Z= 0.263 Chirality : 0.034 0.133 3082 Planarity : 0.004 0.061 3232 Dihedral : 4.617 23.661 2457 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.61 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.18), residues: 2299 helix: 0.80 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.22 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 470 HIS 0.003 0.000 HIS A1369 PHE 0.022 0.001 PHE B 125 TYR 0.017 0.001 TYR B1115 ARG 0.004 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 671 time to evaluate : 3.177 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: A 20 ILE cc_start: 0.8271 (mm) cc_final: 0.8054 (mm) REVERT: A 21 ASN cc_start: 0.8945 (t0) cc_final: 0.8713 (t0) REVERT: A 84 ASN cc_start: 0.8510 (t0) cc_final: 0.8087 (m110) REVERT: A 107 THR cc_start: 0.7931 (m) cc_final: 0.7730 (m) REVERT: A 208 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7479 (mm-30) REVERT: A 372 ASP cc_start: 0.7807 (p0) cc_final: 0.7540 (p0) REVERT: A 376 LEU cc_start: 0.8936 (mp) cc_final: 0.8691 (mp) REVERT: A 393 LEU cc_start: 0.8910 (tp) cc_final: 0.8569 (tp) REVERT: A 397 GLN cc_start: 0.8634 (tp40) cc_final: 0.8317 (tp40) REVERT: A 435 PHE cc_start: 0.8152 (m-10) cc_final: 0.7782 (m-80) REVERT: A 487 ASN cc_start: 0.8150 (m-40) cc_final: 0.7770 (m-40) REVERT: A 495 ILE cc_start: 0.8803 (mm) cc_final: 0.8547 (mm) REVERT: A 562 GLU cc_start: 0.7791 (tt0) cc_final: 0.7295 (mm-30) REVERT: A 597 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8712 (tm-30) REVERT: A 611 ILE cc_start: 0.8510 (mm) cc_final: 0.8279 (mm) REVERT: A 785 GLU cc_start: 0.7372 (pm20) cc_final: 0.6611 (tm-30) REVERT: A 795 ASP cc_start: 0.7238 (m-30) cc_final: 0.6912 (m-30) REVERT: A 889 MET cc_start: 0.7079 (pmm) cc_final: 0.6831 (pmm) REVERT: A 936 LYS cc_start: 0.8897 (mtpp) cc_final: 0.8560 (mtmm) REVERT: A 973 LEU cc_start: 0.8947 (tp) cc_final: 0.8724 (tp) REVERT: A 1012 GLU cc_start: 0.8420 (mp0) cc_final: 0.7967 (mp0) REVERT: A 1036 GLU cc_start: 0.7851 (mp0) cc_final: 0.7622 (mp0) REVERT: A 1157 GLU cc_start: 0.8786 (tp30) cc_final: 0.8416 (tp30) REVERT: B 163 ASP cc_start: 0.9078 (m-30) cc_final: 0.8760 (m-30) REVERT: B 218 MET cc_start: 0.8179 (tpp) cc_final: 0.7922 (tpp) REVERT: B 222 THR cc_start: 0.7946 (m) cc_final: 0.7529 (m) REVERT: B 225 ILE cc_start: 0.7976 (tp) cc_final: 0.7776 (tp) REVERT: B 335 TYR cc_start: 0.8162 (t80) cc_final: 0.7633 (t80) REVERT: B 342 LEU cc_start: 0.8931 (tp) cc_final: 0.8720 (tp) REVERT: B 361 GLU cc_start: 0.8052 (mp0) cc_final: 0.7736 (mp0) REVERT: B 372 ASP cc_start: 0.8167 (t0) cc_final: 0.7687 (t0) REVERT: B 464 GLU cc_start: 0.8753 (tp30) cc_final: 0.8384 (tp30) REVERT: B 493 VAL cc_start: 0.8591 (m) cc_final: 0.8383 (m) REVERT: B 580 MET cc_start: 0.6697 (mtm) cc_final: 0.6207 (mtt) REVERT: B 729 ASN cc_start: 0.7154 (t0) cc_final: 0.6574 (m110) REVERT: B 812 GLN cc_start: 0.8569 (tp40) cc_final: 0.7884 (mp10) REVERT: B 933 LYS cc_start: 0.8288 (mmmt) cc_final: 0.7980 (mmmt) REVERT: B 966 ASP cc_start: 0.7543 (t70) cc_final: 0.7265 (t70) REVERT: B 1036 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7915 (mm-30) REVERT: B 1038 ASN cc_start: 0.8933 (m110) cc_final: 0.8727 (m110) REVERT: B 1056 ASN cc_start: 0.7802 (t0) cc_final: 0.7483 (t0) REVERT: B 1123 CYS cc_start: 0.7858 (t) cc_final: 0.7314 (t) REVERT: B 1169 GLU cc_start: 0.8443 (tt0) cc_final: 0.8214 (tt0) REVERT: B 1191 MET cc_start: 0.8527 (mmt) cc_final: 0.8206 (mmt) REVERT: B 1193 GLU cc_start: 0.7720 (mp0) cc_final: 0.7241 (mp0) REVERT: B 1227 GLU cc_start: 0.8503 (mt-10) cc_final: 0.7962 (mt-10) REVERT: B 1231 MET cc_start: 0.8761 (mmt) cc_final: 0.8515 (mmm) REVERT: B 1300 ASN cc_start: 0.7322 (t0) cc_final: 0.7024 (t0) outliers start: 0 outliers final: 0 residues processed: 671 average time/residue: 0.6006 time to fit residues: 640.2065 Evaluate side-chains 601 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 601 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 217 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 189 optimal weight: 0.9980 chunk 125 optimal weight: 0.3980 chunk 224 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN A1038 ASN ** A1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN B 422 ASN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19136 Z= 0.188 Angle : 0.510 6.763 25829 Z= 0.276 Chirality : 0.034 0.139 3082 Planarity : 0.004 0.060 3232 Dihedral : 4.632 23.759 2457 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.70 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.18), residues: 2299 helix: 0.82 (0.14), residues: 1463 sheet: None (None), residues: 0 loop : -1.37 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 470 HIS 0.004 0.001 HIS A1369 PHE 0.022 0.001 PHE A 125 TYR 0.017 0.001 TYR B1115 ARG 0.006 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 658 time to evaluate : 3.011 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: A 84 ASN cc_start: 0.8498 (t0) cc_final: 0.8079 (m110) REVERT: A 208 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7524 (mm-30) REVERT: A 372 ASP cc_start: 0.7806 (p0) cc_final: 0.7567 (p0) REVERT: A 376 LEU cc_start: 0.9094 (mp) cc_final: 0.8889 (mp) REVERT: A 393 LEU cc_start: 0.8919 (tp) cc_final: 0.8627 (tp) REVERT: A 435 PHE cc_start: 0.8171 (m-10) cc_final: 0.7841 (m-80) REVERT: A 487 ASN cc_start: 0.7852 (m-40) cc_final: 0.7525 (m-40) REVERT: A 495 ILE cc_start: 0.8746 (mm) cc_final: 0.8484 (mm) REVERT: A 551 MET cc_start: 0.6141 (mpp) cc_final: 0.5606 (mpp) REVERT: A 562 GLU cc_start: 0.7899 (tt0) cc_final: 0.7343 (mm-30) REVERT: A 597 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8693 (tm-30) REVERT: A 611 ILE cc_start: 0.8447 (mm) cc_final: 0.8201 (mm) REVERT: A 718 LYS cc_start: 0.6894 (pptt) cc_final: 0.6585 (tptm) REVERT: A 785 GLU cc_start: 0.7406 (pm20) cc_final: 0.6729 (tm-30) REVERT: A 806 ASP cc_start: 0.8631 (m-30) cc_final: 0.8356 (m-30) REVERT: A 889 MET cc_start: 0.6863 (pmm) cc_final: 0.6599 (pmm) REVERT: A 936 LYS cc_start: 0.8931 (mtpp) cc_final: 0.8586 (mtmm) REVERT: A 973 LEU cc_start: 0.8975 (tp) cc_final: 0.8750 (tp) REVERT: A 1012 GLU cc_start: 0.8372 (mp0) cc_final: 0.7971 (mp0) REVERT: A 1036 GLU cc_start: 0.7778 (mp0) cc_final: 0.7515 (mp0) REVERT: A 1157 GLU cc_start: 0.8752 (tp30) cc_final: 0.8374 (tp30) REVERT: A 1163 PHE cc_start: 0.8464 (m-80) cc_final: 0.8213 (m-80) REVERT: B 163 ASP cc_start: 0.9030 (m-30) cc_final: 0.8775 (m-30) REVERT: B 342 LEU cc_start: 0.8942 (tp) cc_final: 0.8733 (tp) REVERT: B 361 GLU cc_start: 0.8062 (mp0) cc_final: 0.7761 (mp0) REVERT: B 372 ASP cc_start: 0.8190 (t0) cc_final: 0.7702 (t0) REVERT: B 464 GLU cc_start: 0.8756 (tp30) cc_final: 0.8350 (tp30) REVERT: B 580 MET cc_start: 0.6763 (mtm) cc_final: 0.6297 (mtt) REVERT: B 600 PHE cc_start: 0.8871 (t80) cc_final: 0.8670 (t80) REVERT: B 921 ASN cc_start: 0.8409 (m110) cc_final: 0.7979 (m110) REVERT: B 933 LYS cc_start: 0.8262 (mmmt) cc_final: 0.7934 (mmmt) REVERT: B 966 ASP cc_start: 0.7588 (t70) cc_final: 0.7308 (t70) REVERT: B 1036 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7928 (mm-30) REVERT: B 1038 ASN cc_start: 0.8983 (m110) cc_final: 0.8746 (m110) REVERT: B 1056 ASN cc_start: 0.7730 (t0) cc_final: 0.7487 (t0) REVERT: B 1123 CYS cc_start: 0.7917 (t) cc_final: 0.7398 (t) REVERT: B 1169 GLU cc_start: 0.8475 (tt0) cc_final: 0.8237 (tt0) REVERT: B 1193 GLU cc_start: 0.7682 (mp0) cc_final: 0.7346 (mp0) REVERT: B 1300 ASN cc_start: 0.7285 (t0) cc_final: 0.7040 (t0) outliers start: 0 outliers final: 0 residues processed: 658 average time/residue: 0.6186 time to fit residues: 653.1422 Evaluate side-chains 596 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 596 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 138 optimal weight: 0.0770 chunk 89 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 0.0970 chunk 43 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1038 ASN ** A1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN B 422 ASN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19136 Z= 0.186 Angle : 0.522 7.373 25829 Z= 0.281 Chirality : 0.035 0.156 3082 Planarity : 0.004 0.059 3232 Dihedral : 4.653 24.628 2457 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.22 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.18), residues: 2299 helix: 0.83 (0.14), residues: 1464 sheet: None (None), residues: 0 loop : -1.34 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 773 HIS 0.003 0.001 HIS A 720 PHE 0.015 0.001 PHE B 126 TYR 0.016 0.001 TYR B1115 ARG 0.004 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 655 time to evaluate : 3.034 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: A 20 ILE cc_start: 0.8310 (mm) cc_final: 0.8093 (mm) REVERT: A 72 PHE cc_start: 0.6787 (t80) cc_final: 0.6516 (t80) REVERT: A 84 ASN cc_start: 0.8511 (t0) cc_final: 0.8074 (m110) REVERT: A 208 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7510 (mm-30) REVERT: A 376 LEU cc_start: 0.9000 (mp) cc_final: 0.8776 (mp) REVERT: A 393 LEU cc_start: 0.8920 (tp) cc_final: 0.8623 (tp) REVERT: A 435 PHE cc_start: 0.8190 (m-10) cc_final: 0.7854 (m-80) REVERT: A 467 SER cc_start: 0.8936 (p) cc_final: 0.8677 (p) REVERT: A 487 ASN cc_start: 0.7999 (m-40) cc_final: 0.7655 (m-40) REVERT: A 531 ASP cc_start: 0.8283 (m-30) cc_final: 0.7954 (m-30) REVERT: A 562 GLU cc_start: 0.7941 (tt0) cc_final: 0.7368 (mm-30) REVERT: A 597 GLU cc_start: 0.9182 (tm-30) cc_final: 0.8767 (tm-30) REVERT: A 611 ILE cc_start: 0.8452 (mm) cc_final: 0.8211 (mm) REVERT: A 718 LYS cc_start: 0.6915 (pptt) cc_final: 0.6590 (tptm) REVERT: A 852 ASP cc_start: 0.8170 (t70) cc_final: 0.7951 (t70) REVERT: A 889 MET cc_start: 0.6857 (pmm) cc_final: 0.6597 (pmm) REVERT: A 936 LYS cc_start: 0.9024 (mtpp) cc_final: 0.8671 (mtmm) REVERT: A 973 LEU cc_start: 0.8987 (tp) cc_final: 0.8759 (tp) REVERT: A 1012 GLU cc_start: 0.8382 (mp0) cc_final: 0.7986 (mp0) REVERT: A 1036 GLU cc_start: 0.7786 (mp0) cc_final: 0.7509 (mp0) REVERT: A 1163 PHE cc_start: 0.8460 (m-80) cc_final: 0.8196 (m-80) REVERT: B 126 PHE cc_start: 0.7919 (t80) cc_final: 0.7708 (t80) REVERT: B 163 ASP cc_start: 0.9024 (m-30) cc_final: 0.8754 (m-30) REVERT: B 342 LEU cc_start: 0.8860 (tp) cc_final: 0.8632 (tp) REVERT: B 361 GLU cc_start: 0.8221 (mp0) cc_final: 0.7802 (mp0) REVERT: B 372 ASP cc_start: 0.8211 (t0) cc_final: 0.7727 (t0) REVERT: B 464 GLU cc_start: 0.8765 (tp30) cc_final: 0.8331 (tp30) REVERT: B 580 MET cc_start: 0.6773 (mtm) cc_final: 0.6307 (mtt) REVERT: B 600 PHE cc_start: 0.8888 (t80) cc_final: 0.8634 (t80) REVERT: B 921 ASN cc_start: 0.8402 (m110) cc_final: 0.7979 (m110) REVERT: B 933 LYS cc_start: 0.8254 (mmmt) cc_final: 0.7927 (mmmt) REVERT: B 966 ASP cc_start: 0.7594 (t70) cc_final: 0.7306 (t70) REVERT: B 1036 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7991 (mm-30) REVERT: B 1056 ASN cc_start: 0.7619 (t0) cc_final: 0.7372 (t0) REVERT: B 1123 CYS cc_start: 0.7855 (t) cc_final: 0.7324 (t) REVERT: B 1169 GLU cc_start: 0.8369 (tt0) cc_final: 0.8078 (tt0) REVERT: B 1191 MET cc_start: 0.8504 (mmt) cc_final: 0.7979 (mmt) REVERT: B 1193 GLU cc_start: 0.7399 (mp0) cc_final: 0.6692 (mp0) REVERT: B 1300 ASN cc_start: 0.7311 (t0) cc_final: 0.7049 (t0) outliers start: 0 outliers final: 0 residues processed: 655 average time/residue: 0.5967 time to fit residues: 623.5803 Evaluate side-chains 590 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 590 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 204 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 196 optimal weight: 0.9990 chunk 209 optimal weight: 0.7980 chunk 125 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 164 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 197 optimal weight: 0.0980 chunk 208 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1038 ASN ** A1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN B 422 ASN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19136 Z= 0.191 Angle : 0.520 7.737 25829 Z= 0.281 Chirality : 0.035 0.137 3082 Planarity : 0.004 0.057 3232 Dihedral : 4.636 24.690 2457 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.52 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.18), residues: 2299 helix: 0.81 (0.14), residues: 1465 sheet: None (None), residues: 0 loop : -1.35 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 773 HIS 0.003 0.001 HIS A 720 PHE 0.021 0.001 PHE A 699 TYR 0.016 0.002 TYR A1062 ARG 0.006 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 645 time to evaluate : 3.308 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: A 20 ILE cc_start: 0.8302 (mm) cc_final: 0.8053 (mm) REVERT: A 84 ASN cc_start: 0.8568 (t0) cc_final: 0.8112 (m110) REVERT: A 208 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7522 (mm-30) REVERT: A 376 LEU cc_start: 0.8998 (mp) cc_final: 0.8782 (mp) REVERT: A 393 LEU cc_start: 0.8934 (tp) cc_final: 0.8590 (tp) REVERT: A 397 GLN cc_start: 0.8637 (tp40) cc_final: 0.8332 (tp40) REVERT: A 424 GLN cc_start: 0.8173 (pt0) cc_final: 0.7958 (mt0) REVERT: A 435 PHE cc_start: 0.8185 (m-10) cc_final: 0.7902 (m-80) REVERT: A 467 SER cc_start: 0.8963 (p) cc_final: 0.8695 (p) REVERT: A 487 ASN cc_start: 0.8028 (m-40) cc_final: 0.7644 (m-40) REVERT: A 531 ASP cc_start: 0.8287 (m-30) cc_final: 0.7953 (m-30) REVERT: A 562 GLU cc_start: 0.8057 (tt0) cc_final: 0.7425 (mm-30) REVERT: A 597 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8781 (tm-30) REVERT: A 611 ILE cc_start: 0.8457 (mm) cc_final: 0.8220 (mm) REVERT: A 718 LYS cc_start: 0.6967 (pptt) cc_final: 0.6611 (tptm) REVERT: A 806 ASP cc_start: 0.8915 (m-30) cc_final: 0.8651 (m-30) REVERT: A 889 MET cc_start: 0.6849 (pmm) cc_final: 0.6583 (pmm) REVERT: A 936 LYS cc_start: 0.8941 (mtpp) cc_final: 0.8603 (mtmm) REVERT: A 973 LEU cc_start: 0.8965 (tp) cc_final: 0.8731 (tp) REVERT: A 1012 GLU cc_start: 0.8393 (mp0) cc_final: 0.7996 (mp0) REVERT: A 1036 GLU cc_start: 0.7787 (mp0) cc_final: 0.7519 (mp0) REVERT: A 1163 PHE cc_start: 0.8451 (m-80) cc_final: 0.8210 (m-80) REVERT: A 1287 ILE cc_start: 0.8570 (tt) cc_final: 0.8359 (tt) REVERT: B 163 ASP cc_start: 0.9000 (m-30) cc_final: 0.8741 (m-30) REVERT: B 342 LEU cc_start: 0.8847 (tp) cc_final: 0.8634 (tp) REVERT: B 361 GLU cc_start: 0.8176 (mp0) cc_final: 0.7692 (mp0) REVERT: B 464 GLU cc_start: 0.8775 (tp30) cc_final: 0.8313 (tp30) REVERT: B 600 PHE cc_start: 0.8879 (t80) cc_final: 0.8565 (t80) REVERT: B 859 ASP cc_start: 0.8189 (t70) cc_final: 0.7972 (t0) REVERT: B 921 ASN cc_start: 0.8381 (m110) cc_final: 0.7940 (m110) REVERT: B 934 ASP cc_start: 0.8998 (t0) cc_final: 0.8299 (t70) REVERT: B 946 ILE cc_start: 0.8147 (tp) cc_final: 0.7925 (tp) REVERT: B 954 TYR cc_start: 0.8036 (t80) cc_final: 0.7801 (t80) REVERT: B 966 ASP cc_start: 0.7618 (t70) cc_final: 0.7342 (t70) REVERT: B 1036 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7984 (mm-30) REVERT: B 1038 ASN cc_start: 0.9036 (m110) cc_final: 0.8745 (m110) REVERT: B 1056 ASN cc_start: 0.7614 (t0) cc_final: 0.7386 (t0) REVERT: B 1062 TYR cc_start: 0.7092 (m-80) cc_final: 0.6838 (m-10) REVERT: B 1123 CYS cc_start: 0.8015 (t) cc_final: 0.7477 (t) REVERT: B 1169 GLU cc_start: 0.8503 (tt0) cc_final: 0.8265 (tt0) REVERT: B 1300 ASN cc_start: 0.7198 (t0) cc_final: 0.6880 (t0) outliers start: 0 outliers final: 0 residues processed: 645 average time/residue: 0.5934 time to fit residues: 612.3588 Evaluate side-chains 597 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 597 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 137 optimal weight: 0.0870 chunk 221 optimal weight: 0.0470 chunk 135 optimal weight: 1.9990 chunk 104 optimal weight: 0.1980 chunk 153 optimal weight: 0.9980 chunk 232 optimal weight: 0.4980 chunk 213 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1038 ASN ** A1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN B 422 ASN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19136 Z= 0.145 Angle : 0.499 8.152 25829 Z= 0.265 Chirality : 0.034 0.143 3082 Planarity : 0.004 0.056 3232 Dihedral : 4.510 24.669 2457 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.31 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.18), residues: 2299 helix: 0.94 (0.14), residues: 1468 sheet: None (None), residues: 0 loop : -1.28 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 470 HIS 0.002 0.000 HIS A 720 PHE 0.028 0.001 PHE A 125 TYR 0.022 0.001 TYR A 703 ARG 0.005 0.000 ARG A 490 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4598 Ramachandran restraints generated. 2299 Oldfield, 0 Emsley, 2299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 654 time to evaluate : 3.040 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: A 20 ILE cc_start: 0.8166 (mm) cc_final: 0.7286 (mm) REVERT: A 84 ASN cc_start: 0.8563 (t0) cc_final: 0.8109 (m110) REVERT: A 208 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7278 (mm-30) REVERT: A 227 SER cc_start: 0.8807 (m) cc_final: 0.8579 (p) REVERT: A 393 LEU cc_start: 0.8896 (tp) cc_final: 0.8537 (tp) REVERT: A 397 GLN cc_start: 0.8644 (tp40) cc_final: 0.8345 (tp40) REVERT: A 424 GLN cc_start: 0.7941 (pt0) cc_final: 0.7666 (mt0) REVERT: A 435 PHE cc_start: 0.8213 (m-10) cc_final: 0.7962 (m-80) REVERT: A 467 SER cc_start: 0.8930 (p) cc_final: 0.8686 (p) REVERT: A 487 ASN cc_start: 0.8037 (m-40) cc_final: 0.7662 (m-40) REVERT: A 531 ASP cc_start: 0.8274 (m-30) cc_final: 0.7939 (m-30) REVERT: A 562 GLU cc_start: 0.7656 (tt0) cc_final: 0.7004 (mm-30) REVERT: A 597 GLU cc_start: 0.9222 (tm-30) cc_final: 0.8791 (tm-30) REVERT: A 611 ILE cc_start: 0.8459 (mm) cc_final: 0.8216 (mm) REVERT: A 718 LYS cc_start: 0.7628 (pptt) cc_final: 0.7181 (tptm) REVERT: A 806 ASP cc_start: 0.8856 (m-30) cc_final: 0.8597 (m-30) REVERT: A 852 ASP cc_start: 0.8735 (t0) cc_final: 0.8454 (t0) REVERT: A 889 MET cc_start: 0.7123 (pmm) cc_final: 0.6888 (pmm) REVERT: A 936 LYS cc_start: 0.8940 (mtpp) cc_final: 0.8605 (mtmm) REVERT: A 973 LEU cc_start: 0.8952 (tp) cc_final: 0.8720 (tp) REVERT: A 1036 GLU cc_start: 0.7780 (mp0) cc_final: 0.7523 (mp0) REVERT: A 1038 ASN cc_start: 0.9009 (m110) cc_final: 0.8796 (m110) REVERT: A 1287 ILE cc_start: 0.8531 (tt) cc_final: 0.8314 (tt) REVERT: B 163 ASP cc_start: 0.9015 (m-30) cc_final: 0.8731 (m-30) REVERT: B 342 LEU cc_start: 0.8833 (tp) cc_final: 0.8606 (tp) REVERT: B 361 GLU cc_start: 0.8170 (mp0) cc_final: 0.7727 (mp0) REVERT: B 464 GLU cc_start: 0.8762 (tp30) cc_final: 0.8299 (tp30) REVERT: B 539 ILE cc_start: 0.8860 (mp) cc_final: 0.8529 (mp) REVERT: B 600 PHE cc_start: 0.8921 (t80) cc_final: 0.8653 (t80) REVERT: B 859 ASP cc_start: 0.8174 (t70) cc_final: 0.7964 (t0) REVERT: B 933 LYS cc_start: 0.8267 (mmmt) cc_final: 0.7973 (mmmt) REVERT: B 934 ASP cc_start: 0.8970 (t0) cc_final: 0.8256 (t0) REVERT: B 941 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8488 (tm-30) REVERT: B 946 ILE cc_start: 0.8159 (tp) cc_final: 0.7915 (tp) REVERT: B 954 TYR cc_start: 0.8088 (t80) cc_final: 0.7880 (t80) REVERT: B 966 ASP cc_start: 0.7599 (t70) cc_final: 0.7338 (t70) REVERT: B 1036 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8050 (mm-30) REVERT: B 1038 ASN cc_start: 0.8966 (m110) cc_final: 0.8737 (m110) REVERT: B 1056 ASN cc_start: 0.7608 (t0) cc_final: 0.7380 (t0) REVERT: B 1123 CYS cc_start: 0.7853 (t) cc_final: 0.7270 (t) REVERT: B 1191 MET cc_start: 0.8426 (mmt) cc_final: 0.7987 (mmt) REVERT: B 1193 GLU cc_start: 0.7461 (mp0) cc_final: 0.6864 (mp0) REVERT: B 1300 ASN cc_start: 0.7543 (t0) cc_final: 0.7232 (t0) outliers start: 0 outliers final: 0 residues processed: 654 average time/residue: 0.6061 time to fit residues: 634.6961 Evaluate side-chains 595 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 595 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 146 optimal weight: 1.9990 chunk 196 optimal weight: 0.0270 chunk 56 optimal weight: 0.5980 chunk 170 optimal weight: 0.0770 chunk 27 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 190 optimal weight: 0.0870 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN B 422 ASN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 GLN B1154 GLN ** B1297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.162866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.139054 restraints weight = 119792.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.144440 restraints weight = 58414.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.147878 restraints weight = 34515.810| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 19136 Z= 0.141 Angle : 0.497 8.181 25829 Z= 0.263 Chirality : 0.034 0.140 3082 Planarity : 0.003 0.058 3232 Dihedral : 4.446 24.449 2457 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.61 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.18), residues: 2299 helix: 0.98 (0.14), residues: 1469 sheet: None (None), residues: 0 loop : -1.23 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 470 HIS 0.002 0.000 HIS B 351 PHE 0.016 0.001 PHE B 101 TYR 0.022 0.001 TYR A 703 ARG 0.009 0.000 ARG A 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10713.82 seconds wall clock time: 188 minutes 13.55 seconds (11293.55 seconds total)