Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 00:02:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mrw_23959/04_2023/7mrw_23959.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mrw_23959/04_2023/7mrw_23959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mrw_23959/04_2023/7mrw_23959.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mrw_23959/04_2023/7mrw_23959.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mrw_23959/04_2023/7mrw_23959.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mrw_23959/04_2023/7mrw_23959.pdb" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 119 5.16 5 C 15709 2.51 5 N 3882 2.21 5 O 4442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1034": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 24152 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1209, 10149 Classifications: {'peptide': 1209} Link IDs: {'PTRANS': 26, 'TRANS': 1182} Chain breaks: 6 Chain: "B" Number of atoms: 8123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 8123 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 19, 'TRANS': 952} Chain breaks: 3 Chain: "C" Number of atoms: 5880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5880 Classifications: {'peptide': 706} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 677} Chain breaks: 2 Time building chain proxies: 11.89, per 1000 atoms: 0.49 Number of scatterers: 24152 At special positions: 0 Unit cell: (97.76, 137.28, 173.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 119 16.00 O 4442 8.00 N 3882 7.00 C 15709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 407 " - pdb=" SG CYS A 413 " distance=2.02 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 71 " distance=2.02 Simple disulfide: pdb=" SG CYS B 233 " - pdb=" SG CYS B 240 " distance=2.03 Simple disulfide: pdb=" SG CYS B 791 " - pdb=" SG CYS B 851 " distance=2.02 Simple disulfide: pdb=" SG CYS B 871 " - pdb=" SG CYS B 912 " distance=2.03 Simple disulfide: pdb=" SG CYS B 947 " - pdb=" SG CYS B1034 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 231 " distance=2.02 Simple disulfide: pdb=" SG CYS C 244 " - pdb=" SG CYS C 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 620 " distance=2.02 Simple disulfide: pdb=" SG CYS C 475 " - pdb=" SG CYS C 536 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.09 Conformation dependent library (CDL) restraints added in 3.4 seconds 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 9 sheets defined 65.5% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.572A pdb=" N GLN A 58 " --> pdb=" O ASP A 54 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 85 removed outlier: 3.592A pdb=" N GLU A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 143 removed outlier: 3.717A pdb=" N LEU A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 160 Processing helix chain 'A' and resid 160 through 181 removed outlier: 4.053A pdb=" N THR A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE A 172 " --> pdb=" O LYS A 168 " (cutoff:3.500A) Proline residue: A 173 - end of helix removed outlier: 3.515A pdb=" N LYS A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.755A pdb=" N LEU A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 224 removed outlier: 4.195A pdb=" N ARG A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 removed outlier: 3.761A pdb=" N LYS A 242 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.851A pdb=" N PHE A 252 " --> pdb=" O ASN A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 272 Processing helix chain 'A' and resid 274 through 281 removed outlier: 3.546A pdb=" N ASN A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 299 removed outlier: 3.650A pdb=" N LYS A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 313 through 320 Processing helix chain 'A' and resid 321 through 333 removed outlier: 4.546A pdb=" N PHE A 326 " --> pdb=" O MET A 322 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 349 removed outlier: 3.516A pdb=" N THR A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 353 removed outlier: 3.747A pdb=" N ASP A 353 " --> pdb=" O LEU A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 353' Processing helix chain 'A' and resid 358 through 380 removed outlier: 3.715A pdb=" N LEU A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A 374 " --> pdb=" O TYR A 370 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 379 " --> pdb=" O GLN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 407 removed outlier: 3.630A pdb=" N PHE A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.749A pdb=" N HIS A 417 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 456 removed outlier: 3.670A pdb=" N TYR A 451 " --> pdb=" O TYR A 447 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 453 " --> pdb=" O ASN A 449 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 455 " --> pdb=" O TYR A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.688A pdb=" N VAL A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 removed outlier: 3.907A pdb=" N TYR A 479 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 487 Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 494 through 501 removed outlier: 3.713A pdb=" N VAL A 497 " --> pdb=" O TYR A 494 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 499 " --> pdb=" O ALA A 496 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE A 501 " --> pdb=" O GLU A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 522 removed outlier: 3.699A pdb=" N SER A 513 " --> pdb=" O LYS A 509 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 553 Processing helix chain 'A' and resid 561 through 572 removed outlier: 4.044A pdb=" N VAL A 568 " --> pdb=" O GLN A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 585 through 596 removed outlier: 4.090A pdb=" N ASP A 591 " --> pdb=" O ASP A 587 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 611 removed outlier: 4.147A pdb=" N TYR A 603 " --> pdb=" O ASP A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 removed outlier: 3.637A pdb=" N TYR A 627 " --> pdb=" O ALA A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 removed outlier: 3.654A pdb=" N VAL A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 641 " --> pdb=" O ASN A 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 636 through 641' Processing helix chain 'A' and resid 665 through 674 Processing helix chain 'A' and resid 678 through 684 Processing helix chain 'A' and resid 691 through 700 removed outlier: 3.758A pdb=" N GLN A 697 " --> pdb=" O ASN A 693 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 698 " --> pdb=" O SER A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 732 removed outlier: 3.835A pdb=" N PHE A 725 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 729 " --> pdb=" O PHE A 725 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN A 730 " --> pdb=" O LYS A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 removed outlier: 3.605A pdb=" N TYR A 737 " --> pdb=" O PRO A 733 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 756 removed outlier: 3.968A pdb=" N ASP A 749 " --> pdb=" O TYR A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 784 removed outlier: 3.544A pdb=" N TRP A 767 " --> pdb=" O LYS A 763 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS A 769 " --> pdb=" O ASN A 765 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 770 " --> pdb=" O GLN A 766 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 792 removed outlier: 3.823A pdb=" N ASN A 790 " --> pdb=" O ARG A 786 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 791 " --> pdb=" O HIS A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 817 removed outlier: 4.231A pdb=" N ILE A 811 " --> pdb=" O MET A 807 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A 816 " --> pdb=" O ASP A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 891 removed outlier: 4.252A pdb=" N GLU A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 914 removed outlier: 3.651A pdb=" N TYR A 905 " --> pdb=" O LEU A 901 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU A 912 " --> pdb=" O PHE A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 928 removed outlier: 3.930A pdb=" N ASN A 927 " --> pdb=" O LYS A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 976 removed outlier: 3.811A pdb=" N ILE A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 956 " --> pdb=" O ASN A 952 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG A 957 " --> pdb=" O SER A 953 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 959 " --> pdb=" O ALA A 955 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LYS A 961 " --> pdb=" O ARG A 957 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR A 962 " --> pdb=" O TYR A 958 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET A 969 " --> pdb=" O ALA A 965 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 973 " --> pdb=" O MET A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 988 removed outlier: 4.229A pdb=" N ALA A 985 " --> pdb=" O ASN A 981 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TYR A 986 " --> pdb=" O LEU A 982 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 995 removed outlier: 3.808A pdb=" N VAL A 994 " --> pdb=" O ASN A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1011 removed outlier: 3.557A pdb=" N THR A1003 " --> pdb=" O SER A 999 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A1004 " --> pdb=" O ALA A1000 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN A1009 " --> pdb=" O ALA A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1021 Processing helix chain 'A' and resid 1028 through 1032 removed outlier: 3.599A pdb=" N LEU A1032 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1054 removed outlier: 3.813A pdb=" N MET A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A1047 " --> pdb=" O TYR A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1069 removed outlier: 3.926A pdb=" N GLU A1064 " --> pdb=" O SER A1060 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN A1066 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1083 removed outlier: 4.009A pdb=" N LYS A1077 " --> pdb=" O PHE A1073 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY A1080 " --> pdb=" O ALA A1076 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN A1081 " --> pdb=" O LYS A1077 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE A1082 " --> pdb=" O LYS A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1101 removed outlier: 3.804A pdb=" N TRP A1101 " --> pdb=" O MET A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1109 removed outlier: 3.519A pdb=" N GLY A1108 " --> pdb=" O PHE A1105 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN A1109 " --> pdb=" O THR A1106 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1105 through 1109' Processing helix chain 'A' and resid 1141 through 1167 removed outlier: 3.693A pdb=" N ALA A1145 " --> pdb=" O HIS A1141 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A1157 " --> pdb=" O PHE A1153 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP A1162 " --> pdb=" O ASN A1158 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A1165 " --> pdb=" O LEU A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1218 removed outlier: 3.522A pdb=" N GLY A1207 " --> pdb=" O GLU A1203 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR A1210 " --> pdb=" O ASN A1206 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A1212 " --> pdb=" O PHE A1208 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE A1214 " --> pdb=" O TYR A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1223 removed outlier: 3.503A pdb=" N TYR A1223 " --> pdb=" O MET A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1256 removed outlier: 3.624A pdb=" N ARG A1240 " --> pdb=" O ARG A1236 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A1242 " --> pdb=" O LEU A1238 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A1244 " --> pdb=" O ARG A1240 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A1255 " --> pdb=" O ASN A1251 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A1256 " --> pdb=" O TYR A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1281 removed outlier: 3.606A pdb=" N ILE A1266 " --> pdb=" O SER A1262 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A1269 " --> pdb=" O LEU A1265 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A1275 " --> pdb=" O GLU A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1287 Processing helix chain 'A' and resid 1288 through 1290 No H-bonds generated for 'chain 'A' and resid 1288 through 1290' Processing helix chain 'A' and resid 1296 through 1301 removed outlier: 3.667A pdb=" N HIS A1301 " --> pdb=" O MET A1297 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1318 removed outlier: 3.830A pdb=" N ASN A1310 " --> pdb=" O ASP A1306 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A1312 " --> pdb=" O MET A1308 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A1314 " --> pdb=" O ASN A1310 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET A1316 " --> pdb=" O ARG A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1346 removed outlier: 3.600A pdb=" N LEU A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN A1345 " --> pdb=" O GLN A1342 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 54 removed outlier: 3.559A pdb=" N SER B 47 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 82 removed outlier: 3.626A pdb=" N ALA B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN B 73 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY B 76 " --> pdb=" O HIS B 72 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN B 80 " --> pdb=" O GLY B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 105 removed outlier: 3.566A pdb=" N LEU B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 131 removed outlier: 3.642A pdb=" N SER B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 161 removed outlier: 3.627A pdb=" N LEU B 161 " --> pdb=" O ASN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 169 removed outlier: 3.985A pdb=" N ILE B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 197 removed outlier: 3.559A pdb=" N PHE B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.890A pdb=" N TYR B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE B 202 " --> pdb=" O GLN B 198 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 230 through 236 removed outlier: 4.217A pdb=" N SER B 234 " --> pdb=" O GLN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 258 removed outlier: 3.525A pdb=" N SER B 248 " --> pdb=" O TYR B 244 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR B 250 " --> pdb=" O SER B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 268 removed outlier: 3.855A pdb=" N ASP B 265 " --> pdb=" O PRO B 261 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 281 Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 357 through 376 Processing helix chain 'B' and resid 380 through 388 Processing helix chain 'B' and resid 390 through 408 removed outlier: 3.504A pdb=" N ARG B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 433 removed outlier: 3.811A pdb=" N TYR B 432 " --> pdb=" O TYR B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 447 removed outlier: 3.663A pdb=" N LEU B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 464 removed outlier: 3.589A pdb=" N PHE B 460 " --> pdb=" O ARG B 456 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG B 462 " --> pdb=" O HIS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 479 removed outlier: 3.729A pdb=" N LYS B 476 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP B 477 " --> pdb=" O MET B 473 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 478 " --> pdb=" O ILE B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 500 removed outlier: 3.564A pdb=" N GLU B 497 " --> pdb=" O LYS B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 513 through 528 removed outlier: 3.530A pdb=" N ILE B 517 " --> pdb=" O ASP B 513 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'B' and resid 540 through 556 removed outlier: 3.817A pdb=" N PHE B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 569 removed outlier: 3.969A pdb=" N ILE B 566 " --> pdb=" O PRO B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 587 removed outlier: 3.503A pdb=" N LEU B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 611 removed outlier: 3.921A pdb=" N THR B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 601 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE B 602 " --> pdb=" O GLN B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 657 removed outlier: 3.960A pdb=" N TYR B 650 " --> pdb=" O THR B 646 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 651 " --> pdb=" O SER B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 700 removed outlier: 3.726A pdb=" N GLN B 690 " --> pdb=" O SER B 686 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN B 700 " --> pdb=" O ALA B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 727 removed outlier: 3.960A pdb=" N THR B 721 " --> pdb=" O TYR B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 735 Processing helix chain 'B' and resid 740 through 755 removed outlier: 4.004A pdb=" N LEU B 748 " --> pdb=" O TYR B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 779 No H-bonds generated for 'chain 'B' and resid 777 through 779' Processing helix chain 'B' and resid 780 through 798 removed outlier: 3.519A pdb=" N LEU B 784 " --> pdb=" O TYR B 780 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS B 785 " --> pdb=" O HIS B 781 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR B 786 " --> pdb=" O LYS B 782 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 787 " --> pdb=" O ASP B 783 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 788 " --> pdb=" O LEU B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 829 Processing helix chain 'B' and resid 842 through 854 removed outlier: 3.507A pdb=" N LYS B 846 " --> pdb=" O SER B 842 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 850 " --> pdb=" O LYS B 846 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 853 " --> pdb=" O VAL B 849 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN B 854 " --> pdb=" O SER B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 871 removed outlier: 3.540A pdb=" N ALA B 864 " --> pdb=" O GLN B 860 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS B 869 " --> pdb=" O ASN B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 876 Processing helix chain 'B' and resid 882 through 892 Processing helix chain 'B' and resid 897 through 919 removed outlier: 3.670A pdb=" N LYS B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET B 914 " --> pdb=" O LEU B 910 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 917 " --> pdb=" O LYS B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 937 removed outlier: 3.905A pdb=" N LEU B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 966 removed outlier: 3.599A pdb=" N THR B 944 " --> pdb=" O ASP B 940 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS B 949 " --> pdb=" O TYR B 945 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 962 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 985 removed outlier: 3.643A pdb=" N ALA B 975 " --> pdb=" O ARG B 971 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR B 979 " --> pdb=" O ALA B 975 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 984 " --> pdb=" O ASP B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1002 Processing helix chain 'B' and resid 1002 through 1018 removed outlier: 3.538A pdb=" N LEU B1011 " --> pdb=" O GLU B1007 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B1013 " --> pdb=" O LYS B1009 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B1016 " --> pdb=" O GLU B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1032 removed outlier: 3.539A pdb=" N TYR B1032 " --> pdb=" O LEU B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1039 removed outlier: 4.263A pdb=" N THR B1038 " --> pdb=" O CYS B1034 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER B1039 " --> pdb=" O HIS B1035 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1034 through 1039' Processing helix chain 'B' and resid 1039 through 1054 removed outlier: 4.927A pdb=" N LEU B1046 " --> pdb=" O ASN B1042 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N TRP B1047 " --> pdb=" O PHE B1043 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B1050 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1079 removed outlier: 3.506A pdb=" N PHE B1063 " --> pdb=" O TYR B1059 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B1064 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP B1068 " --> pdb=" O PHE B1064 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLN B1069 " --> pdb=" O SER B1065 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN B1070 " --> pdb=" O GLU B1066 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE B1073 " --> pdb=" O GLN B1069 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU B1074 " --> pdb=" O ASN B1070 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE B1075 " --> pdb=" O ILE B1071 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B1076 " --> pdb=" O ARG B1072 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER B1077 " --> pdb=" O PHE B1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 48 removed outlier: 3.615A pdb=" N LYS C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS C 42 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 removed outlier: 3.597A pdb=" N SER C 59 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE C 60 " --> pdb=" O ALA C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 60' Processing helix chain 'C' and resid 66 through 77 removed outlier: 3.818A pdb=" N PHE C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE C 77 " --> pdb=" O PHE C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 removed outlier: 3.792A pdb=" N ASP C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 100 removed outlier: 4.146A pdb=" N LEU C 100 " --> pdb=" O THR C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 112 removed outlier: 3.758A pdb=" N GLU C 107 " --> pdb=" O SER C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 137 removed outlier: 4.006A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 191 removed outlier: 3.515A pdb=" N LYS C 186 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 206 removed outlier: 4.106A pdb=" N SER C 204 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR C 205 " --> pdb=" O ASN C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.771A pdb=" N LEU C 214 " --> pdb=" O GLN C 210 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 244 Processing helix chain 'C' and resid 249 through 264 removed outlier: 4.116A pdb=" N ASP C 255 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS C 260 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU C 263 " --> pdb=" O ARG C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 286 removed outlier: 3.985A pdb=" N CYS C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 298 removed outlier: 3.649A pdb=" N ASP C 292 " --> pdb=" O ASN C 288 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE C 294 " --> pdb=" O TYR C 290 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET C 298 " --> pdb=" O PHE C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 369 through 376 removed outlier: 3.669A pdb=" N THR C 374 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 375 " --> pdb=" O SER C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 392 Processing helix chain 'C' and resid 399 through 407 removed outlier: 3.611A pdb=" N HIS C 405 " --> pdb=" O LYS C 401 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 424 removed outlier: 4.009A pdb=" N ASN C 423 " --> pdb=" O GLN C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 455 removed outlier: 3.534A pdb=" N GLY C 439 " --> pdb=" O GLU C 435 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 492 removed outlier: 3.520A pdb=" N ILE C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER C 479 " --> pdb=" O CYS C 475 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 514 removed outlier: 3.904A pdb=" N TYR C 507 " --> pdb=" O TYR C 503 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER C 514 " --> pdb=" O LYS C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 528 No H-bonds generated for 'chain 'C' and resid 526 through 528' Processing helix chain 'C' and resid 529 through 540 removed outlier: 3.532A pdb=" N ALA C 535 " --> pdb=" O ARG C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 548 removed outlier: 4.029A pdb=" N SER C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 570 removed outlier: 4.164A pdb=" N LEU C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 592 removed outlier: 3.645A pdb=" N ILE C 583 " --> pdb=" O GLU C 579 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR C 589 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS C 592 " --> pdb=" O THR C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 622 removed outlier: 4.295A pdb=" N LEU C 599 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE C 605 " --> pdb=" O PHE C 601 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR C 615 " --> pdb=" O ASN C 611 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 619 " --> pdb=" O TYR C 615 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS C 620 " --> pdb=" O GLU C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 630 removed outlier: 3.843A pdb=" N GLU C 627 " --> pdb=" O PRO C 623 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU C 628 " --> pdb=" O LYS C 624 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE C 629 " --> pdb=" O GLU C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 651 removed outlier: 3.512A pdb=" N ILE C 642 " --> pdb=" O ILE C 638 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 648 " --> pdb=" O LYS C 644 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 651 " --> pdb=" O ASP C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 666 removed outlier: 3.569A pdb=" N ARG C 659 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE C 665 " --> pdb=" O MET C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 690 removed outlier: 3.793A pdb=" N VAL C 676 " --> pdb=" O SER C 672 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE C 683 " --> pdb=" O ALA C 679 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS C 688 " --> pdb=" O ASP C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 728 removed outlier: 3.612A pdb=" N LEU C 723 " --> pdb=" O LYS C 719 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR C 726 " --> pdb=" O VAL C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 736 removed outlier: 3.626A pdb=" N ALA C 735 " --> pdb=" O THR C 731 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AA2, first strand: chain 'A' and resid 828 through 831 removed outlier: 3.577A pdb=" N SER A 858 " --> pdb=" O ARG A 831 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 206 through 209 Processing sheet with id=AA4, first strand: chain 'B' and resid 481 through 482 removed outlier: 4.013A pdb=" N THR B 481 " --> pdb=" O ASN B 489 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 234 through 238 removed outlier: 3.546A pdb=" N LYS C 339 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 152 through 153 Processing sheet with id=AA7, first strand: chain 'C' and resid 175 through 179 removed outlier: 5.146A pdb=" N LEU C 176 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR C 165 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 178 " --> pdb=" O ILE C 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 306 through 308 Processing sheet with id=AA9, first strand: chain 'C' and resid 310 through 311 removed outlier: 4.407A pdb=" N VAL C 706 " --> pdb=" O VAL C 311 " (cutoff:3.500A) 1057 hydrogen bonds defined for protein. 3087 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.71 Time building geometry restraints manager: 9.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7354 1.34 - 1.46: 6345 1.46 - 1.59: 10830 1.59 - 1.71: 0 1.71 - 1.83: 198 Bond restraints: 24727 Sorted by residual: bond pdb=" CA PHE B 739 " pdb=" CB PHE B 739 " ideal model delta sigma weight residual 1.530 1.455 0.076 1.50e-02 4.44e+03 2.54e+01 bond pdb=" CB THR A 163 " pdb=" CG2 THR A 163 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.44e+00 bond pdb=" CG1 ILE A 285 " pdb=" CD1 ILE A 285 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.74e+00 bond pdb=" CB ASN B 588 " pdb=" CG ASN B 588 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.37e+00 bond pdb=" CG LEU B 826 " pdb=" CD1 LEU B 826 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.35e+00 ... (remaining 24722 not shown) Histogram of bond angle deviations from ideal: 95.58 - 103.31: 205 103.31 - 111.03: 8805 111.03 - 118.75: 10408 118.75 - 126.48: 13695 126.48 - 134.20: 201 Bond angle restraints: 33314 Sorted by residual: angle pdb=" N VAL A 934 " pdb=" CA VAL A 934 " pdb=" C VAL A 934 " ideal model delta sigma weight residual 109.46 101.80 7.66 1.38e+00 5.25e-01 3.08e+01 angle pdb=" C PHE C 471 " pdb=" N ARG C 472 " pdb=" CA ARG C 472 " ideal model delta sigma weight residual 121.54 130.64 -9.10 1.91e+00 2.74e-01 2.27e+01 angle pdb=" C ILE C 93 " pdb=" N HIS C 94 " pdb=" CA HIS C 94 " ideal model delta sigma weight residual 121.31 128.10 -6.79 1.49e+00 4.50e-01 2.08e+01 angle pdb=" C ILE A 237 " pdb=" N LEU A 238 " pdb=" CA LEU A 238 " ideal model delta sigma weight residual 120.38 126.69 -6.31 1.46e+00 4.69e-01 1.87e+01 angle pdb=" C LYS B 966 " pdb=" N PHE B 967 " pdb=" CA PHE B 967 " ideal model delta sigma weight residual 124.31 131.51 -7.20 1.67e+00 3.59e-01 1.86e+01 ... (remaining 33309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.71: 14053 15.71 - 31.43: 743 31.43 - 47.14: 83 47.14 - 62.85: 12 62.85 - 78.56: 5 Dihedral angle restraints: 14896 sinusoidal: 6197 harmonic: 8699 Sorted by residual: dihedral pdb=" CA SER A1011 " pdb=" C SER A1011 " pdb=" N ILE A1012 " pdb=" CA ILE A1012 " ideal model delta harmonic sigma weight residual -180.00 -132.49 -47.51 0 5.00e+00 4.00e-02 9.03e+01 dihedral pdb=" CB CYS C 157 " pdb=" SG CYS C 157 " pdb=" SG CYS C 231 " pdb=" CB CYS C 231 " ideal model delta sinusoidal sigma weight residual -86.00 -164.56 78.56 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CA LEU C 286 " pdb=" C LEU C 286 " pdb=" N LYS C 287 " pdb=" CA LYS C 287 " ideal model delta harmonic sigma weight residual -180.00 -147.16 -32.84 0 5.00e+00 4.00e-02 4.31e+01 ... (remaining 14893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2493 0.054 - 0.108: 942 0.108 - 0.162: 128 0.162 - 0.215: 24 0.215 - 0.269: 7 Chirality restraints: 3594 Sorted by residual: chirality pdb=" CB ILE B 349 " pdb=" CA ILE B 349 " pdb=" CG1 ILE B 349 " pdb=" CG2 ILE B 349 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE C 93 " pdb=" CA ILE C 93 " pdb=" CG1 ILE C 93 " pdb=" CG2 ILE C 93 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE A 145 " pdb=" CA ILE A 145 " pdb=" CG1 ILE A 145 " pdb=" CG2 ILE A 145 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 3591 not shown) Planarity restraints: 4182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 253 " -0.013 2.00e-02 2.50e+03 2.37e-02 9.82e+00 pdb=" CG PHE A 253 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE A 253 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE A 253 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 253 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 253 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 253 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 583 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.94e+00 pdb=" CG ASN B 583 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN B 583 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN B 583 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 705 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.34e+00 pdb=" N PRO B 706 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 706 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 706 " 0.038 5.00e-02 4.00e+02 ... (remaining 4179 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4723 2.75 - 3.29: 22870 3.29 - 3.83: 38978 3.83 - 4.36: 49364 4.36 - 4.90: 81513 Nonbonded interactions: 197448 Sorted by model distance: nonbonded pdb=" O PRO A 838 " pdb=" OH TYR B 441 " model vdw 2.217 2.440 nonbonded pdb=" O LEU A 704 " pdb=" OH TYR B 689 " model vdw 2.238 2.440 nonbonded pdb=" OH TYR A1024 " pdb=" OD2 ASP A1315 " model vdw 2.249 2.440 nonbonded pdb=" O ASP C 433 " pdb=" OG1 THR C 436 " model vdw 2.249 2.440 nonbonded pdb=" OG1 THR A1326 " pdb=" O ILE C 498 " model vdw 2.260 2.440 ... (remaining 197443 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.660 Check model and map are aligned: 0.370 Set scattering table: 0.210 Process input model: 60.050 Find NCS groups from input model: 0.630 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.085 24727 Z= 0.560 Angle : 1.001 10.885 33314 Z= 0.559 Chirality : 0.054 0.269 3594 Planarity : 0.006 0.068 4182 Dihedral : 9.641 77.618 9235 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.81 % Favored : 96.12 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (0.11), residues: 2859 helix: -3.74 (0.07), residues: 1661 sheet: -0.93 (0.76), residues: 53 loop : -1.66 (0.15), residues: 1145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 565 time to evaluate : 2.962 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 outliers start: 6 outliers final: 0 residues processed: 568 average time/residue: 0.3614 time to fit residues: 323.3107 Evaluate side-chains 259 residues out of total 2716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 3.100 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 1.9990 chunk 217 optimal weight: 0.0060 chunk 120 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 224 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 chunk 167 optimal weight: 0.9990 chunk 260 optimal weight: 6.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 241 ASN A 247 ASN A 279 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN A 478 ASN A 621 ASN A 730 ASN A 787 HIS A 801 ASN A 816 ASN A 933 ASN A 937 ASN ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN ** A1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN B 157 ASN B 223 ASN B 286 HIS B 450 ASN B 588 ASN B 693 ASN ** B 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 GLN ** B 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN ** B1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 225 ASN C 468 HIS C 486 ASN C 572 ASN C 617 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 24727 Z= 0.196 Angle : 0.604 10.134 33314 Z= 0.320 Chirality : 0.040 0.182 3594 Planarity : 0.004 0.060 4182 Dihedral : 5.503 40.366 3158 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: -2.27 (0.13), residues: 2859 helix: -1.59 (0.10), residues: 1705 sheet: -0.30 (0.75), residues: 53 loop : -1.15 (0.17), residues: 1101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 353 time to evaluate : 3.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 29 residues processed: 399 average time/residue: 0.3459 time to fit residues: 223.0247 Evaluate side-chains 271 residues out of total 2716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 242 time to evaluate : 3.227 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2285 time to fit residues: 16.8519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 144 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 216 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 282 optimal weight: 0.8980 chunk 232 optimal weight: 4.9990 chunk 258 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 209 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN A 564 GLN A 978 ASN ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1251 ASN B 73 ASN B 77 ASN B 583 ASN B 704 ASN ** B 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 854 ASN ** B 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 24727 Z= 0.178 Angle : 0.545 12.392 33314 Z= 0.282 Chirality : 0.040 0.213 3594 Planarity : 0.003 0.058 4182 Dihedral : 4.914 37.396 3158 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.94 % Favored : 97.03 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: -1.14 (0.15), residues: 2859 helix: -0.54 (0.12), residues: 1703 sheet: -0.33 (0.72), residues: 53 loop : -0.90 (0.17), residues: 1103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 303 time to evaluate : 3.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 23 residues processed: 335 average time/residue: 0.3319 time to fit residues: 186.5997 Evaluate side-chains 276 residues out of total 2716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 253 time to evaluate : 3.539 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2424 time to fit residues: 14.9915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 257 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 175 optimal weight: 0.8980 chunk 262 optimal weight: 0.8980 chunk 277 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 ASN A 942 ASN ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN ** B 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 24727 Z= 0.179 Angle : 0.527 9.367 33314 Z= 0.273 Chirality : 0.039 0.182 3594 Planarity : 0.003 0.061 4182 Dihedral : 4.706 36.045 3158 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: -0.54 (0.15), residues: 2859 helix: -0.00 (0.12), residues: 1711 sheet: -0.32 (0.70), residues: 53 loop : -0.76 (0.18), residues: 1095 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 287 time to evaluate : 3.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 306 average time/residue: 0.3046 time to fit residues: 157.8689 Evaluate side-chains 259 residues out of total 2716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 244 time to evaluate : 2.722 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2217 time to fit residues: 9.7872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 231 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 206 optimal weight: 0.7980 chunk 114 optimal weight: 0.0040 chunk 236 optimal weight: 0.5980 chunk 191 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 249 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1318 ASN A1322 ASN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN ** B 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 ASN ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 24727 Z= 0.166 Angle : 0.514 8.687 33314 Z= 0.263 Chirality : 0.039 0.198 3594 Planarity : 0.003 0.062 4182 Dihedral : 4.520 34.962 3158 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: -0.10 (0.15), residues: 2859 helix: 0.43 (0.13), residues: 1687 sheet: -0.36 (0.70), residues: 53 loop : -0.68 (0.18), residues: 1119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 283 time to evaluate : 3.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 14 residues processed: 305 average time/residue: 0.3271 time to fit residues: 169.5036 Evaluate side-chains 256 residues out of total 2716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 242 time to evaluate : 2.952 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2306 time to fit residues: 10.2789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 93 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 ASN ** B 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 HIS ** B 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 24727 Z= 0.296 Angle : 0.596 8.966 33314 Z= 0.306 Chirality : 0.042 0.226 3594 Planarity : 0.003 0.068 4182 Dihedral : 4.681 35.290 3158 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.01 (0.15), residues: 2859 helix: 0.57 (0.13), residues: 1686 sheet: -0.45 (0.71), residues: 53 loop : -0.72 (0.18), residues: 1120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 236 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 17 residues processed: 258 average time/residue: 0.3317 time to fit residues: 145.3628 Evaluate side-chains 239 residues out of total 2716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 222 time to evaluate : 3.310 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2246 time to fit residues: 11.4284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 267 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 276 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 24727 Z= 0.229 Angle : 0.555 9.764 33314 Z= 0.281 Chirality : 0.040 0.228 3594 Planarity : 0.003 0.067 4182 Dihedral : 4.579 34.236 3158 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.18 (0.16), residues: 2859 helix: 0.73 (0.13), residues: 1698 sheet: -0.47 (0.72), residues: 53 loop : -0.71 (0.19), residues: 1108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 253 time to evaluate : 3.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 270 average time/residue: 0.3276 time to fit residues: 150.1572 Evaluate side-chains 236 residues out of total 2716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 226 time to evaluate : 2.877 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2260 time to fit residues: 8.2368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 171 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 217 optimal weight: 5.9990 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 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN A 522 HIS ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 24727 Z= 0.165 Angle : 0.529 11.404 33314 Z= 0.267 Chirality : 0.039 0.240 3594 Planarity : 0.003 0.063 4182 Dihedral : 4.437 33.000 3158 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.39 (0.16), residues: 2859 helix: 0.91 (0.13), residues: 1694 sheet: -0.41 (0.71), residues: 53 loop : -0.63 (0.19), residues: 1112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 257 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 268 average time/residue: 0.3458 time to fit residues: 153.4002 Evaluate side-chains 247 residues out of total 2716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 240 time to evaluate : 3.040 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2440 time to fit residues: 7.2959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 251 optimal weight: 3.9990 chunk 265 optimal weight: 5.9990 chunk 241 optimal weight: 0.0270 chunk 257 optimal weight: 2.9990 chunk 264 optimal weight: 0.8980 chunk 155 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 232 optimal weight: 7.9990 chunk 243 optimal weight: 2.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 778 HIS ** B 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 24727 Z= 0.169 Angle : 0.538 11.447 33314 Z= 0.269 Chirality : 0.039 0.260 3594 Planarity : 0.003 0.059 4182 Dihedral : 4.367 32.231 3158 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.54 (0.16), residues: 2859 helix: 1.05 (0.13), residues: 1688 sheet: -0.46 (0.71), residues: 53 loop : -0.58 (0.19), residues: 1118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 258 time to evaluate : 3.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 262 average time/residue: 0.3461 time to fit residues: 151.6727 Evaluate side-chains 246 residues out of total 2716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 237 time to evaluate : 3.346 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2445 time to fit residues: 8.5593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 256 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 272 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 chunk 285 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 175 optimal weight: 0.0770 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN A 522 HIS ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 24727 Z= 0.194 Angle : 0.560 12.752 33314 Z= 0.280 Chirality : 0.041 0.335 3594 Planarity : 0.003 0.059 4182 Dihedral : 4.365 35.157 3158 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.60 (0.16), residues: 2859 helix: 1.09 (0.13), residues: 1690 sheet: -0.46 (0.71), residues: 53 loop : -0.55 (0.19), residues: 1116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5718 Ramachandran restraints generated. 2859 Oldfield, 0 Emsley, 2859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 240 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 245 average time/residue: 0.3339 time to fit residues: 137.8139 Evaluate side-chains 240 residues out of total 2716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 236 time to evaluate : 2.841 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2513 time to fit residues: 5.8000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 139 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 242 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 891 ASN ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.100668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.085082 restraints weight = 59599.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.087712 restraints weight = 30453.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.089466 restraints weight = 19126.555| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 24727 Z= 0.175 Angle : 0.554 12.114 33314 Z= 0.274 Chirality : 0.040 0.317 3594 Planarity : 0.003 0.058 4182 Dihedral : 4.314 32.026 3158 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.66 (0.16), residues: 2859 helix: 1.15 (0.13), residues: 1692 sheet: -0.47 (0.71), residues: 53 loop : -0.54 (0.19), residues: 1114 =============================================================================== Job complete usr+sys time: 4310.07 seconds wall clock time: 81 minutes 32.71 seconds (4892.71 seconds total)