Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 13 12:18:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ojs_3824/07_2023/5ojs_3824.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ojs_3824/07_2023/5ojs_3824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ojs_3824/07_2023/5ojs_3824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ojs_3824/07_2023/5ojs_3824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ojs_3824/07_2023/5ojs_3824.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ojs_3824/07_2023/5ojs_3824.pdb" } resolution = 3.7 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= 0.001 sd= 0.006 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 120 5.16 5 C 18391 2.51 5 N 4718 2.21 5 O 5178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "T PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 288": "NH1" <-> "NH2" Residue "T TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 352": "NH1" <-> "NH2" Residue "T TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 474": "NH1" <-> "NH2" Residue "T PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 712": "NH1" <-> "NH2" Residue "T ARG 813": "NH1" <-> "NH2" Residue "T ARG 817": "NH1" <-> "NH2" Residue "T ARG 1123": "NH1" <-> "NH2" Residue "T ARG 1170": "NH1" <-> "NH2" Residue "T TYR 1206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 1272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 1304": "NH1" <-> "NH2" Residue "T PHE 1370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 1437": "NH1" <-> "NH2" Residue "T ARG 1520": "NH1" <-> "NH2" Residue "T ARG 1585": "NH1" <-> "NH2" Residue "T PHE 1592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 1861": "NH1" <-> "NH2" Residue "T PHE 1988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 2093": "NH1" <-> "NH2" Residue "T ARG 2432": "NH1" <-> "NH2" Residue "T ARG 2445": "NH1" <-> "NH2" Residue "T ARG 2456": "NH1" <-> "NH2" Residue "T ARG 2482": "NH1" <-> "NH2" Residue "T TYR 2492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 2681": "NH1" <-> "NH2" Residue "T ARG 2715": "NH1" <-> "NH2" Residue "T TYR 2721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 2807": "NH1" <-> "NH2" Residue "T TYR 2859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 2887": "NH1" <-> "NH2" Residue "T TYR 2916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 2969": "NH1" <-> "NH2" Residue "T PHE 3014": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 3034": "NH1" <-> "NH2" Residue "T ARG 3172": "NH1" <-> "NH2" Residue "T TYR 3291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 3313": "NH1" <-> "NH2" Residue "T ARG 3320": "NH1" <-> "NH2" Residue "T ARG 3373": "NH1" <-> "NH2" Residue "T ARG 3382": "NH1" <-> "NH2" Residue "T ARG 3424": "NH1" <-> "NH2" Residue "T ARG 3438": "NH1" <-> "NH2" Residue "T PHE 3464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 3545": "NH1" <-> "NH2" Residue "T PHE 3622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 3689": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 28407 Number of models: 1 Model: "" Number of chains: 1 Chain: "T" Number of atoms: 28407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3473, 28407 Classifications: {'peptide': 3473} Link IDs: {'CIS': 4, 'PTRANS': 146, 'TRANS': 3322} Chain breaks: 14 Time building chain proxies: 13.58, per 1000 atoms: 0.48 Number of scatterers: 28407 At special positions: 0 Unit cell: (134.62, 204.58, 139.92, 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 120 16.00 O 5178 8.00 N 4718 7.00 C 18391 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.25 Conformation dependent library (CDL) restraints added in 3.9 seconds 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6780 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 4 sheets defined 64.5% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.40 Creating SS restraints... Processing helix chain 'T' and resid 3 through 8 removed outlier: 4.196A pdb=" N ILE T 7 " --> pdb=" O LEU T 3 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 14 removed outlier: 4.391A pdb=" N SER T 12 " --> pdb=" O GLN T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 26 removed outlier: 3.699A pdb=" N SER T 23 " --> pdb=" O THR T 20 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ARG T 24 " --> pdb=" O LEU T 21 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR T 25 " --> pdb=" O GLN T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 34 Processing helix chain 'T' and resid 43 through 59 removed outlier: 3.989A pdb=" N PHE T 47 " --> pdb=" O ASP T 43 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLN T 49 " --> pdb=" O HIS T 45 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA T 50 " --> pdb=" O PHE T 46 " (cutoff:3.500A) Proline residue: T 53 - end of helix Processing helix chain 'T' and resid 73 through 84 removed outlier: 3.924A pdb=" N ASN T 77 " --> pdb=" O GLN T 73 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 100 removed outlier: 5.199A pdb=" N GLU T 98 " --> pdb=" O PRO T 94 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU T 100 " --> pdb=" O ALA T 96 " (cutoff:3.500A) Processing helix chain 'T' and resid 116 through 131 removed outlier: 3.970A pdb=" N THR T 124 " --> pdb=" O LYS T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 141 through 158 Proline residue: T 152 - end of helix removed outlier: 3.531A pdb=" N THR T 158 " --> pdb=" O LEU T 154 " (cutoff:3.500A) Processing helix chain 'T' and resid 217 through 221 removed outlier: 3.944A pdb=" N SER T 220 " --> pdb=" O SER T 217 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE T 221 " --> pdb=" O MET T 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 217 through 221' Processing helix chain 'T' and resid 231 through 240 Processing helix chain 'T' and resid 248 through 254 removed outlier: 3.966A pdb=" N LEU T 252 " --> pdb=" O GLU T 248 " (cutoff:3.500A) Processing helix chain 'T' and resid 292 through 309 Processing helix chain 'T' and resid 324 through 335 removed outlier: 3.753A pdb=" N LEU T 328 " --> pdb=" O PHE T 324 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP T 335 " --> pdb=" O ARG T 331 " (cutoff:3.500A) Processing helix chain 'T' and resid 341 through 357 removed outlier: 3.512A pdb=" N LYS T 345 " --> pdb=" O SER T 341 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU T 346 " --> pdb=" O SER T 342 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE T 354 " --> pdb=" O ALA T 350 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR T 357 " --> pdb=" O HIS T 353 " (cutoff:3.500A) Processing helix chain 'T' and resid 362 through 368 removed outlier: 3.598A pdb=" N LYS T 366 " --> pdb=" O LEU T 362 " (cutoff:3.500A) Processing helix chain 'T' and resid 374 through 379 removed outlier: 4.132A pdb=" N ASN T 379 " --> pdb=" O LEU T 376 " (cutoff:3.500A) Processing helix chain 'T' and resid 387 through 403 removed outlier: 3.566A pdb=" N TYR T 392 " --> pdb=" O ARG T 388 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR T 394 " --> pdb=" O LEU T 390 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL T 395 " --> pdb=" O ALA T 391 " (cutoff:3.500A) Processing helix chain 'T' and resid 407 through 424 removed outlier: 4.742A pdb=" N GLY T 420 " --> pdb=" O LYS T 416 " (cutoff:3.500A) Processing helix chain 'T' and resid 429 through 442 Processing helix chain 'T' and resid 442 through 453 removed outlier: 3.791A pdb=" N ASN T 453 " --> pdb=" O LEU T 449 " (cutoff:3.500A) Processing helix chain 'T' and resid 454 through 456 No H-bonds generated for 'chain 'T' and resid 454 through 456' Processing helix chain 'T' and resid 457 through 497 removed outlier: 4.139A pdb=" N ILE T 467 " --> pdb=" O LEU T 463 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE T 468 " --> pdb=" O LEU T 464 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU T 478 " --> pdb=" O ARG T 474 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN T 479 " --> pdb=" O PHE T 475 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG T 480 " --> pdb=" O LYS T 476 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASP T 483 " --> pdb=" O ASN T 479 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N THR T 484 " --> pdb=" O ARG T 480 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS T 487 " --> pdb=" O ASP T 483 " (cutoff:3.500A) Processing helix chain 'T' and resid 501 through 506 removed outlier: 3.648A pdb=" N ASN T 505 " --> pdb=" O LYS T 502 " (cutoff:3.500A) Processing helix chain 'T' and resid 511 through 522 removed outlier: 3.630A pdb=" N PHE T 517 " --> pdb=" O GLU T 513 " (cutoff:3.500A) Processing helix chain 'T' and resid 563 through 567 removed outlier: 3.847A pdb=" N ALA T 567 " --> pdb=" O LYS T 564 " (cutoff:3.500A) Processing helix chain 'T' and resid 578 through 601 removed outlier: 4.532A pdb=" N THR T 596 " --> pdb=" O SER T 592 " (cutoff:3.500A) Processing helix chain 'T' and resid 602 through 605 removed outlier: 4.207A pdb=" N ASN T 605 " --> pdb=" O LYS T 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 602 through 605' Processing helix chain 'T' and resid 607 through 612 removed outlier: 3.855A pdb=" N TYR T 611 " --> pdb=" O PRO T 607 " (cutoff:3.500A) Processing helix chain 'T' and resid 615 through 619 Processing helix chain 'T' and resid 627 through 643 removed outlier: 4.654A pdb=" N VAL T 633 " --> pdb=" O GLU T 629 " (cutoff:3.500A) Processing helix chain 'T' and resid 644 through 648 removed outlier: 3.667A pdb=" N PHE T 647 " --> pdb=" O GLY T 644 " (cutoff:3.500A) Processing helix chain 'T' and resid 677 through 690 removed outlier: 3.796A pdb=" N LEU T 682 " --> pdb=" O ASP T 678 " (cutoff:3.500A) Processing helix chain 'T' and resid 698 through 714 removed outlier: 3.721A pdb=" N GLN T 704 " --> pdb=" O GLU T 700 " (cutoff:3.500A) Proline residue: T 707 - end of helix Processing helix chain 'T' and resid 719 through 728 Processing helix chain 'T' and resid 732 through 747 removed outlier: 4.730A pdb=" N GLY T 738 " --> pdb=" O PRO T 734 " (cutoff:3.500A) Processing helix chain 'T' and resid 755 through 771 removed outlier: 3.760A pdb=" N LYS T 767 " --> pdb=" O ILE T 763 " (cutoff:3.500A) Processing helix chain 'T' and resid 780 through 784 Processing helix chain 'T' and resid 788 through 801 removed outlier: 3.678A pdb=" N SER T 799 " --> pdb=" O SER T 795 " (cutoff:3.500A) Processing helix chain 'T' and resid 805 through 817 removed outlier: 4.210A pdb=" N PHE T 809 " --> pdb=" O PRO T 805 " (cutoff:3.500A) Processing helix chain 'T' and resid 823 through 827 removed outlier: 3.752A pdb=" N ASN T 826 " --> pdb=" O ARG T 823 " (cutoff:3.500A) Processing helix chain 'T' and resid 831 through 841 removed outlier: 3.906A pdb=" N LEU T 838 " --> pdb=" O ILE T 834 " (cutoff:3.500A) Processing helix chain 'T' and resid 855 through 864 removed outlier: 3.594A pdb=" N THR T 864 " --> pdb=" O GLU T 860 " (cutoff:3.500A) Processing helix chain 'T' and resid 879 through 890 removed outlier: 3.755A pdb=" N VAL T 884 " --> pdb=" O MET T 880 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE T 885 " --> pdb=" O LYS T 881 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU T 887 " --> pdb=" O LEU T 883 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR T 890 " --> pdb=" O ALA T 886 " (cutoff:3.500A) Processing helix chain 'T' and resid 893 through 903 removed outlier: 3.943A pdb=" N LEU T 903 " --> pdb=" O ARG T 899 " (cutoff:3.500A) Processing helix chain 'T' and resid 917 through 919 No H-bonds generated for 'chain 'T' and resid 917 through 919' Processing helix chain 'T' and resid 920 through 932 removed outlier: 3.913A pdb=" N LYS T 926 " --> pdb=" O ASP T 922 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE T 929 " --> pdb=" O SER T 925 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU T 932 " --> pdb=" O LEU T 928 " (cutoff:3.500A) Processing helix chain 'T' and resid 940 through 952 Processing helix chain 'T' and resid 998 through 1006 removed outlier: 3.739A pdb=" N GLN T1005 " --> pdb=" O LEU T1001 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER T1006 " --> pdb=" O ASN T1002 " (cutoff:3.500A) Processing helix chain 'T' and resid 1010 through 1029 removed outlier: 3.965A pdb=" N TYR T1020 " --> pdb=" O SER T1016 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR T1022 " --> pdb=" O TYR T1018 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N CYS T1023 " --> pdb=" O LYS T1019 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL T1024 " --> pdb=" O TYR T1020 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU T1025 " --> pdb=" O LEU T1021 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR T1029 " --> pdb=" O LEU T1025 " (cutoff:3.500A) Processing helix chain 'T' and resid 1030 through 1033 Processing helix chain 'T' and resid 1041 through 1048 removed outlier: 3.660A pdb=" N THR T1045 " --> pdb=" O GLU T1041 " (cutoff:3.500A) Processing helix chain 'T' and resid 1068 through 1090 removed outlier: 4.732A pdb=" N ASN T1074 " --> pdb=" O ARG T1070 " (cutoff:3.500A) Processing helix chain 'T' and resid 1095 through 1110 Processing helix chain 'T' and resid 1112 through 1121 removed outlier: 4.097A pdb=" N ASN T1116 " --> pdb=" O LEU T1112 " (cutoff:3.500A) Processing helix chain 'T' and resid 1144 through 1148 Processing helix chain 'T' and resid 1159 through 1179 removed outlier: 3.960A pdb=" N VAL T1163 " --> pdb=" O GLU T1159 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR T1179 " --> pdb=" O SER T1175 " (cutoff:3.500A) Processing helix chain 'T' and resid 1183 through 1188 Processing helix chain 'T' and resid 1188 through 1200 removed outlier: 4.050A pdb=" N GLU T1192 " --> pdb=" O SER T1188 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN T1196 " --> pdb=" O GLU T1192 " (cutoff:3.500A) Processing helix chain 'T' and resid 1201 through 1203 No H-bonds generated for 'chain 'T' and resid 1201 through 1203' Processing helix chain 'T' and resid 1206 through 1221 removed outlier: 3.696A pdb=" N LEU T1214 " --> pdb=" O ARG T1210 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP T1221 " --> pdb=" O LYS T1217 " (cutoff:3.500A) Processing helix chain 'T' and resid 1228 through 1233 removed outlier: 3.707A pdb=" N LYS T1232 " --> pdb=" O VAL T1228 " (cutoff:3.500A) Processing helix chain 'T' and resid 1233 through 1247 removed outlier: 3.646A pdb=" N LEU T1237 " --> pdb=" O TYR T1233 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN T1239 " --> pdb=" O TYR T1235 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU T1245 " --> pdb=" O LEU T1241 " (cutoff:3.500A) Processing helix chain 'T' and resid 1260 through 1271 Processing helix chain 'T' and resid 1283 through 1294 Processing helix chain 'T' and resid 1301 through 1314 Processing helix chain 'T' and resid 1334 through 1340 removed outlier: 4.606A pdb=" N LYS T1340 " --> pdb=" O PRO T1336 " (cutoff:3.500A) Processing helix chain 'T' and resid 1346 through 1355 removed outlier: 3.895A pdb=" N GLN T1350 " --> pdb=" O PRO T1346 " (cutoff:3.500A) Processing helix chain 'T' and resid 1355 through 1362 removed outlier: 4.204A pdb=" N PHE T1359 " --> pdb=" O ASP T1355 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS T1360 " --> pdb=" O ALA T1356 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU T1361 " --> pdb=" O ILE T1357 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER T1362 " --> pdb=" O THR T1358 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 1355 through 1362' Processing helix chain 'T' and resid 1372 through 1384 Processing helix chain 'T' and resid 1403 through 1425 removed outlier: 4.105A pdb=" N ALA T1420 " --> pdb=" O ILE T1416 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE T1421 " --> pdb=" O LYS T1417 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN T1425 " --> pdb=" O ILE T1421 " (cutoff:3.500A) Processing helix chain 'T' and resid 1436 through 1447 removed outlier: 3.906A pdb=" N VAL T1443 " --> pdb=" O ARG T1439 " (cutoff:3.500A) Processing helix chain 'T' and resid 1448 through 1450 No H-bonds generated for 'chain 'T' and resid 1448 through 1450' Processing helix chain 'T' and resid 1452 through 1467 removed outlier: 3.614A pdb=" N ILE T1456 " --> pdb=" O SER T1452 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR T1458 " --> pdb=" O GLU T1454 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY T1465 " --> pdb=" O GLU T1461 " (cutoff:3.500A) Processing helix chain 'T' and resid 1476 through 1481 removed outlier: 3.915A pdb=" N ASN T1480 " --> pdb=" O GLU T1476 " (cutoff:3.500A) Processing helix chain 'T' and resid 1482 through 1488 Processing helix chain 'T' and resid 1497 through 1507 removed outlier: 3.860A pdb=" N LEU T1503 " --> pdb=" O GLY T1499 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS T1505 " --> pdb=" O ASP T1501 " (cutoff:3.500A) Processing helix chain 'T' and resid 1517 through 1529 Processing helix chain 'T' and resid 1531 through 1537 removed outlier: 3.760A pdb=" N LEU T1535 " --> pdb=" O ARG T1531 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR T1537 " --> pdb=" O GLU T1533 " (cutoff:3.500A) Processing helix chain 'T' and resid 1546 through 1557 Processing helix chain 'T' and resid 1570 through 1584 removed outlier: 3.926A pdb=" N LEU T1574 " --> pdb=" O LEU T1570 " (cutoff:3.500A) Processing helix chain 'T' and resid 1593 through 1601 Processing helix chain 'T' and resid 1604 through 1614 removed outlier: 3.526A pdb=" N THR T1608 " --> pdb=" O HIS T1604 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU T1609 " --> pdb=" O ASN T1605 " (cutoff:3.500A) Processing helix chain 'T' and resid 1617 through 1629 removed outlier: 3.754A pdb=" N ASN T1626 " --> pdb=" O LEU T1622 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE T1627 " --> pdb=" O PHE T1623 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL T1628 " --> pdb=" O MET T1624 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN T1629 " --> pdb=" O CYS T1625 " (cutoff:3.500A) Processing helix chain 'T' and resid 1639 through 1642 removed outlier: 3.757A pdb=" N LYS T1642 " --> pdb=" O ASP T1639 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 1639 through 1642' Processing helix chain 'T' and resid 1643 through 1654 removed outlier: 3.699A pdb=" N TYR T1648 " --> pdb=" O LEU T1644 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP T1649 " --> pdb=" O ASP T1645 " (cutoff:3.500A) Processing helix chain 'T' and resid 1662 through 1679 removed outlier: 4.152A pdb=" N ASN T1668 " --> pdb=" O SER T1664 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET T1669 " --> pdb=" O PHE T1665 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE T1678 " --> pdb=" O ASN T1674 " (cutoff:3.500A) Processing helix chain 'T' and resid 1692 through 1709 removed outlier: 3.505A pdb=" N ASN T1709 " --> pdb=" O THR T1705 " (cutoff:3.500A) Processing helix chain 'T' and resid 1715 through 1734 removed outlier: 4.075A pdb=" N ALA T1723 " --> pdb=" O ASN T1719 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA T1727 " --> pdb=" O ALA T1723 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU T1734 " --> pdb=" O LEU T1730 " (cutoff:3.500A) Processing helix chain 'T' and resid 1741 through 1750 removed outlier: 3.867A pdb=" N LEU T1745 " --> pdb=" O ASN T1741 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP T1746 " --> pdb=" O PRO T1742 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE T1747 " --> pdb=" O LEU T1743 " (cutoff:3.500A) Processing helix chain 'T' and resid 1762 through 1769 removed outlier: 3.802A pdb=" N ILE T1766 " --> pdb=" O LEU T1762 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS T1768 " --> pdb=" O LYS T1764 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN T1769 " --> pdb=" O PHE T1765 " (cutoff:3.500A) Processing helix chain 'T' and resid 1778 through 1791 removed outlier: 3.518A pdb=" N LEU T1791 " --> pdb=" O THR T1787 " (cutoff:3.500A) Processing helix chain 'T' and resid 1796 through 1817 Processing helix chain 'T' and resid 1833 through 1842 Processing helix chain 'T' and resid 1858 through 1875 removed outlier: 4.232A pdb=" N PHE T1862 " --> pdb=" O ASP T1858 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE T1871 " --> pdb=" O LEU T1867 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE T1872 " --> pdb=" O SER T1868 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS T1873 " --> pdb=" O ALA T1869 " (cutoff:3.500A) Processing helix chain 'T' and resid 1879 through 1891 removed outlier: 3.569A pdb=" N LYS T1883 " --> pdb=" O ILE T1879 " (cutoff:3.500A) Processing helix chain 'T' and resid 1892 through 1896 Processing helix chain 'T' and resid 1901 through 1913 Processing helix chain 'T' and resid 1922 through 1929 Processing helix chain 'T' and resid 1938 through 1956 Proline residue: T1951 - end of helix Processing helix chain 'T' and resid 1964 through 1977 removed outlier: 4.151A pdb=" N VAL T1970 " --> pdb=" O TRP T1966 " (cutoff:3.500A) Processing helix chain 'T' and resid 1980 through 1988 removed outlier: 3.559A pdb=" N TYR T1986 " --> pdb=" O ASN T1982 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE T1988 " --> pdb=" O ILE T1984 " (cutoff:3.500A) Processing helix chain 'T' and resid 1989 through 1991 No H-bonds generated for 'chain 'T' and resid 1989 through 1991' Processing helix chain 'T' and resid 2001 through 2014 removed outlier: 4.730A pdb=" N SER T2005 " --> pdb=" O ASP T2001 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN T2006 " --> pdb=" O LEU T2002 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE T2007 " --> pdb=" O PHE T2003 " (cutoff:3.500A) Processing helix chain 'T' and resid 2024 through 2042 removed outlier: 3.560A pdb=" N ALA T2028 " --> pdb=" O SER T2024 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA T2032 " --> pdb=" O ALA T2028 " (cutoff:3.500A) Processing helix chain 'T' and resid 2090 through 2107 Processing helix chain 'T' and resid 2116 through 2128 removed outlier: 3.587A pdb=" N ILE T2128 " --> pdb=" O LEU T2124 " (cutoff:3.500A) Processing helix chain 'T' and resid 2140 through 2145 removed outlier: 3.520A pdb=" N PHE T2143 " --> pdb=" O LEU T2140 " (cutoff:3.500A) Processing helix chain 'T' and resid 2157 through 2174 removed outlier: 3.572A pdb=" N LYS T2173 " --> pdb=" O TYR T2169 " (cutoff:3.500A) Processing helix chain 'T' and resid 2183 through 2192 removed outlier: 3.734A pdb=" N ILE T2187 " --> pdb=" O ASN T2183 " (cutoff:3.500A) Processing helix chain 'T' and resid 2196 through 2200 removed outlier: 3.861A pdb=" N HIS T2199 " --> pdb=" O LYS T2196 " (cutoff:3.500A) Processing helix chain 'T' and resid 2203 through 2218 removed outlier: 5.346A pdb=" N GLN T2211 " --> pdb=" O GLN T2207 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N VAL T2212 " --> pdb=" O LYS T2208 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS T2218 " --> pdb=" O MET T2214 " (cutoff:3.500A) Processing helix chain 'T' and resid 2229 through 2244 removed outlier: 3.982A pdb=" N MET T2238 " --> pdb=" O THR T2234 " (cutoff:3.500A) Processing helix chain 'T' and resid 2249 through 2252 removed outlier: 3.642A pdb=" N SER T2252 " --> pdb=" O GLU T2249 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 2249 through 2252' Processing helix chain 'T' and resid 2253 through 2265 removed outlier: 3.705A pdb=" N VAL T2257 " --> pdb=" O VAL T2253 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR T2258 " --> pdb=" O THR T2254 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA T2260 " --> pdb=" O GLY T2256 " (cutoff:3.500A) Processing helix chain 'T' and resid 2275 through 2287 removed outlier: 3.714A pdb=" N MET T2279 " --> pdb=" O LEU T2275 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS T2287 " --> pdb=" O SER T2283 " (cutoff:3.500A) Processing helix chain 'T' and resid 2289 through 2294 Processing helix chain 'T' and resid 2302 through 2321 removed outlier: 4.369A pdb=" N THR T2308 " --> pdb=" O ALA T2304 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER T2319 " --> pdb=" O LEU T2315 " (cutoff:3.500A) Processing helix chain 'T' and resid 2328 through 2342 removed outlier: 3.809A pdb=" N VAL T2336 " --> pdb=" O PHE T2332 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N HIS T2342 " --> pdb=" O LEU T2338 " (cutoff:3.500A) Processing helix chain 'T' and resid 2346 through 2361 removed outlier: 3.708A pdb=" N LYS T2351 " --> pdb=" O ASN T2347 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE T2352 " --> pdb=" O PHE T2348 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE T2361 " --> pdb=" O ARG T2357 " (cutoff:3.500A) Processing helix chain 'T' and resid 2368 through 2377 removed outlier: 4.393A pdb=" N LYS T2372 " --> pdb=" O THR T2368 " (cutoff:3.500A) Processing helix chain 'T' and resid 2380 through 2386 removed outlier: 4.227A pdb=" N ILE T2384 " --> pdb=" O LEU T2380 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY T2386 " --> pdb=" O PHE T2382 " (cutoff:3.500A) Processing helix chain 'T' and resid 2390 through 2404 removed outlier: 3.947A pdb=" N PHE T2394 " --> pdb=" O LEU T2390 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN T2404 " --> pdb=" O LYS T2400 " (cutoff:3.500A) Processing helix chain 'T' and resid 2428 through 2441 Processing helix chain 'T' and resid 2447 through 2456 removed outlier: 4.496A pdb=" N TYR T2453 " --> pdb=" O GLU T2449 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE T2455 " --> pdb=" O LEU T2451 " (cutoff:3.500A) Processing helix chain 'T' and resid 2468 through 2478 removed outlier: 3.708A pdb=" N ALA T2472 " --> pdb=" O TRP T2468 " (cutoff:3.500A) Processing helix chain 'T' and resid 2498 through 2502 removed outlier: 3.517A pdb=" N GLU T2502 " --> pdb=" O ILE T2499 " (cutoff:3.500A) Processing helix chain 'T' and resid 2518 through 2534 removed outlier: 4.980A pdb=" N LYS T2524 " --> pdb=" O SER T2520 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY T2525 " --> pdb=" O ASN T2521 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS T2526 " --> pdb=" O PHE T2522 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE T2527 " --> pdb=" O VAL T2523 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY T2532 " --> pdb=" O ALA T2528 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS T2534 " --> pdb=" O MET T2530 " (cutoff:3.500A) Processing helix chain 'T' and resid 2537 through 2543 Processing helix chain 'T' and resid 2545 through 2550 removed outlier: 3.603A pdb=" N PHE T2549 " --> pdb=" O LEU T2545 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR T2550 " --> pdb=" O ILE T2546 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 2545 through 2550' Processing helix chain 'T' and resid 2554 through 2568 removed outlier: 3.703A pdb=" N ARG T2558 " --> pdb=" O LYS T2554 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR T2562 " --> pdb=" O ARG T2558 " (cutoff:3.500A) Proline residue: T2565 - end of helix Processing helix chain 'T' and resid 2569 through 2571 No H-bonds generated for 'chain 'T' and resid 2569 through 2571' Processing helix chain 'T' and resid 2575 through 2588 removed outlier: 3.685A pdb=" N PHE T2579 " --> pdb=" O GLU T2575 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR T2585 " --> pdb=" O ARG T2581 " (cutoff:3.500A) Processing helix chain 'T' and resid 2604 through 2612 removed outlier: 3.554A pdb=" N SER T2609 " --> pdb=" O MET T2605 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE T2610 " --> pdb=" O LEU T2606 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER T2611 " --> pdb=" O LEU T2607 " (cutoff:3.500A) Processing helix chain 'T' and resid 2622 through 2627 removed outlier: 3.597A pdb=" N ALA T2627 " --> pdb=" O VAL T2623 " (cutoff:3.500A) Processing helix chain 'T' and resid 2636 through 2642 Processing helix chain 'T' and resid 2643 through 2646 Processing helix chain 'T' and resid 2651 through 2670 removed outlier: 3.907A pdb=" N ILE T2655 " --> pdb=" O ASN T2651 " (cutoff:3.500A) Processing helix chain 'T' and resid 2672 through 2681 removed outlier: 4.217A pdb=" N GLY T2677 " --> pdb=" O ASP T2673 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU T2678 " --> pdb=" O MET T2674 " (cutoff:3.500A) Processing helix chain 'T' and resid 2685 through 2696 removed outlier: 4.175A pdb=" N ASN T2689 " --> pdb=" O TYR T2685 " (cutoff:3.500A) Processing helix chain 'T' and resid 2699 through 2714 removed outlier: 3.759A pdb=" N VAL T2712 " --> pdb=" O GLU T2708 " (cutoff:3.500A) Processing helix chain 'T' and resid 2720 through 2723 removed outlier: 3.630A pdb=" N GLN T2723 " --> pdb=" O PRO T2720 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 2720 through 2723' Processing helix chain 'T' and resid 2724 through 2741 removed outlier: 4.192A pdb=" N LEU T2740 " --> pdb=" O CYS T2736 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN T2741 " --> pdb=" O ALA T2737 " (cutoff:3.500A) Processing helix chain 'T' and resid 2744 through 2747 removed outlier: 3.845A pdb=" N THR T2747 " --> pdb=" O ASP T2744 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 2744 through 2747' Processing helix chain 'T' and resid 2748 through 2753 removed outlier: 3.512A pdb=" N GLU T2753 " --> pdb=" O LEU T2749 " (cutoff:3.500A) Processing helix chain 'T' and resid 2754 through 2759 removed outlier: 4.311A pdb=" N LEU T2759 " --> pdb=" O PHE T2755 " (cutoff:3.500A) Processing helix chain 'T' and resid 2776 through 2781 Processing helix chain 'T' and resid 2788 through 2806 removed outlier: 3.881A pdb=" N ALA T2799 " --> pdb=" O LYS T2795 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA T2804 " --> pdb=" O LEU T2800 " (cutoff:3.500A) Processing helix chain 'T' and resid 2812 through 2816 removed outlier: 3.590A pdb=" N LYS T2815 " --> pdb=" O GLU T2812 " (cutoff:3.500A) Processing helix chain 'T' and resid 2817 through 2831 removed outlier: 3.583A pdb=" N SER T2824 " --> pdb=" O GLY T2820 " (cutoff:3.500A) Processing helix chain 'T' and resid 2837 through 2859 removed outlier: 4.268A pdb=" N TRP T2841 " --> pdb=" O PRO T2837 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU T2842 " --> pdb=" O ALA T2838 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU T2851 " --> pdb=" O GLN T2847 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU T2854 " --> pdb=" O MET T2850 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR T2859 " --> pdb=" O ALA T2855 " (cutoff:3.500A) Processing helix chain 'T' and resid 2859 through 2864 Processing helix chain 'T' and resid 2875 through 2883 Processing helix chain 'T' and resid 2884 through 2886 No H-bonds generated for 'chain 'T' and resid 2884 through 2886' Processing helix chain 'T' and resid 2894 through 2915 Processing helix chain 'T' and resid 2943 through 2957 Processing helix chain 'T' and resid 2959 through 2966 removed outlier: 3.752A pdb=" N CYS T2963 " --> pdb=" O MET T2959 " (cutoff:3.500A) Processing helix chain 'T' and resid 2979 through 2991 Processing helix chain 'T' and resid 2992 through 2994 No H-bonds generated for 'chain 'T' and resid 2992 through 2994' Processing helix chain 'T' and resid 2995 through 3001 removed outlier: 3.978A pdb=" N THR T3000 " --> pdb=" O ASN T2997 " (cutoff:3.500A) Processing helix chain 'T' and resid 3015 through 3018 removed outlier: 4.651A pdb=" N GLN T3018 " --> pdb=" O GLY T3015 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 3015 through 3018' Processing helix chain 'T' and resid 3019 through 3033 removed outlier: 4.274A pdb=" N GLY T3027 " --> pdb=" O PHE T3023 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU T3033 " --> pdb=" O PHE T3029 " (cutoff:3.500A) Processing helix chain 'T' and resid 3037 through 3051 removed outlier: 4.131A pdb=" N GLN T3048 " --> pdb=" O ALA T3044 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP T3050 " --> pdb=" O ALA T3046 " (cutoff:3.500A) Processing helix chain 'T' and resid 3054 through 3069 removed outlier: 3.963A pdb=" N TRP T3060 " --> pdb=" O ALA T3056 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY T3061 " --> pdb=" O TRP T3057 " (cutoff:3.500A) Processing helix chain 'T' and resid 3075 through 3077 No H-bonds generated for 'chain 'T' and resid 3075 through 3077' Processing helix chain 'T' and resid 3078 through 3087 Processing helix chain 'T' and resid 3097 through 3108 removed outlier: 3.666A pdb=" N TRP T3106 " --> pdb=" O CYS T3102 " (cutoff:3.500A) Processing helix chain 'T' and resid 3115 through 3123 Processing helix chain 'T' and resid 3133 through 3135 No H-bonds generated for 'chain 'T' and resid 3133 through 3135' Processing helix chain 'T' and resid 3136 through 3142 Processing helix chain 'T' and resid 3151 through 3162 removed outlier: 4.015A pdb=" N ILE T3155 " --> pdb=" O MET T3151 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG T3158 " --> pdb=" O HIS T3154 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE T3159 " --> pdb=" O ILE T3155 " (cutoff:3.500A) Processing helix chain 'T' and resid 3164 through 3182 removed outlier: 4.807A pdb=" N PHE T3169 " --> pdb=" O GLN T3165 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN T3170 " --> pdb=" O ALA T3166 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR T3173 " --> pdb=" O PHE T3169 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL T3180 " --> pdb=" O GLU T3176 " (cutoff:3.500A) Processing helix chain 'T' and resid 3203 through 3218 removed outlier: 3.808A pdb=" N GLU T3210 " --> pdb=" O GLU T3206 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU T3211 " --> pdb=" O TYR T3207 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN T3212 " --> pdb=" O LEU T3208 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA T3218 " --> pdb=" O ILE T3214 " (cutoff:3.500A) Processing helix chain 'T' and resid 3219 through 3237 removed outlier: 3.506A pdb=" N ALA T3223 " --> pdb=" O TYR T3219 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU T3229 " --> pdb=" O SER T3225 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE T3237 " --> pdb=" O ILE T3233 " (cutoff:3.500A) Processing helix chain 'T' and resid 3242 through 3261 removed outlier: 3.617A pdb=" N LEU T3258 " --> pdb=" O ILE T3254 " (cutoff:3.500A) Processing helix chain 'T' and resid 3273 through 3283 removed outlier: 3.759A pdb=" N GLU T3277 " --> pdb=" O PRO T3273 " (cutoff:3.500A) Processing helix chain 'T' and resid 3284 through 3287 Processing helix chain 'T' and resid 3292 through 3298 Processing helix chain 'T' and resid 3308 through 3325 removed outlier: 3.692A pdb=" N LYS T3312 " --> pdb=" O GLU T3308 " (cutoff:3.500A) Processing helix chain 'T' and resid 3333 through 3338 Processing helix chain 'T' and resid 3412 through 3423 removed outlier: 3.642A pdb=" N GLU T3416 " --> pdb=" O HIS T3412 " (cutoff:3.500A) Processing helix chain 'T' and resid 3426 through 3433 removed outlier: 3.708A pdb=" N ASN T3433 " --> pdb=" O SER T3429 " (cutoff:3.500A) Processing helix chain 'T' and resid 3467 through 3478 Processing helix chain 'T' and resid 3482 through 3496 removed outlier: 4.089A pdb=" N GLN T3486 " --> pdb=" O PRO T3482 " (cutoff:3.500A) Processing helix chain 'T' and resid 3506 through 3521 removed outlier: 3.672A pdb=" N GLU T3512 " --> pdb=" O ILE T3508 " (cutoff:3.500A) Processing helix chain 'T' and resid 3525 through 3532 Processing helix chain 'T' and resid 3538 through 3561 removed outlier: 3.531A pdb=" N PHE T3544 " --> pdb=" O ASP T3540 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN T3547 " --> pdb=" O LEU T3543 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER T3550 " --> pdb=" O LYS T3546 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER T3553 " --> pdb=" O ALA T3549 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET T3558 " --> pdb=" O SER T3554 " (cutoff:3.500A) Processing helix chain 'T' and resid 3625 through 3633 removed outlier: 4.741A pdb=" N LEU T3631 " --> pdb=" O ASN T3627 " (cutoff:3.500A) Processing helix chain 'T' and resid 3635 through 3640 Processing helix chain 'T' and resid 3640 through 3653 removed outlier: 4.219A pdb=" N SER T3649 " --> pdb=" O LEU T3645 " (cutoff:3.500A) Processing helix chain 'T' and resid 3657 through 3678 removed outlier: 3.571A pdb=" N THR T3661 " --> pdb=" O ASN T3657 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU T3665 " --> pdb=" O THR T3661 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU T3670 " --> pdb=" O PHE T3666 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU T3678 " --> pdb=" O TRP T3674 " (cutoff:3.500A) Processing helix chain 'T' and resid 3686 through 3703 removed outlier: 4.529A pdb=" N GLU T3690 " --> pdb=" O PRO T3686 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN T3695 " --> pdb=" O MET T3691 " (cutoff:3.500A) Processing helix chain 'T' and resid 3717 through 3728 Processing helix chain 'T' and resid 3729 through 3735 removed outlier: 3.913A pdb=" N ARG T3735 " --> pdb=" O ARG T3731 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'T' and resid 3331 through 3332 Processing sheet with id=AA2, first strand: chain 'T' and resid 3371 through 3374 Processing sheet with id=AA3, first strand: chain 'T' and resid 3371 through 3374 removed outlier: 3.575A pdb=" N ARG T3389 " --> pdb=" O VAL T3405 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN T3406 " --> pdb=" O ARG T3456 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG T3456 " --> pdb=" O GLN T3406 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE T3449 " --> pdb=" O ILE T3457 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'T' and resid 3572 through 3574 1254 hydrogen bonds defined for protein. 3666 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.97 Time building geometry restraints manager: 12.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7393 1.33 - 1.45: 5388 1.45 - 1.57: 16041 1.57 - 1.69: 1 1.69 - 1.81: 203 Bond restraints: 29026 Sorted by residual: bond pdb=" C VAL T 325 " pdb=" N PRO T 326 " ideal model delta sigma weight residual 1.334 1.417 -0.083 2.34e-02 1.83e+03 1.25e+01 bond pdb=" CB LYS T1804 " pdb=" CG LYS T1804 " ideal model delta sigma weight residual 1.520 1.434 0.086 3.00e-02 1.11e+03 8.26e+00 bond pdb=" C ILE T3137 " pdb=" N PRO T3138 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 8.07e+00 bond pdb=" CA MET T 254 " pdb=" C MET T 254 " ideal model delta sigma weight residual 1.523 1.557 -0.034 1.34e-02 5.57e+03 6.26e+00 bond pdb=" CB ASN T2163 " pdb=" CG ASN T2163 " ideal model delta sigma weight residual 1.516 1.577 -0.061 2.50e-02 1.60e+03 5.98e+00 ... (remaining 29021 not shown) Histogram of bond angle deviations from ideal: 95.63 - 104.83: 524 104.83 - 114.02: 16561 114.02 - 123.21: 20748 123.21 - 132.40: 1425 132.40 - 141.60: 65 Bond angle restraints: 39323 Sorted by residual: angle pdb=" C ILE T1157 " pdb=" N PRO T1158 " pdb=" CA PRO T1158 " ideal model delta sigma weight residual 119.84 139.17 -19.33 1.25e+00 6.40e-01 2.39e+02 angle pdb=" C LEU T2888 " pdb=" N PRO T2889 " pdb=" CA PRO T2889 " ideal model delta sigma weight residual 119.84 131.82 -11.98 1.25e+00 6.40e-01 9.19e+01 angle pdb=" CA LEU T3053 " pdb=" CB LEU T3053 " pdb=" CG LEU T3053 " ideal model delta sigma weight residual 116.30 141.60 -25.30 3.50e+00 8.16e-02 5.22e+01 angle pdb=" C VAL T3715 " pdb=" N THR T3716 " pdb=" CA THR T3716 " ideal model delta sigma weight residual 121.54 135.07 -13.53 1.91e+00 2.74e-01 5.01e+01 angle pdb=" CA LEU T1825 " pdb=" CB LEU T1825 " pdb=" CG LEU T1825 " ideal model delta sigma weight residual 116.30 140.90 -24.60 3.50e+00 8.16e-02 4.94e+01 ... (remaining 39318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 15947 16.84 - 33.67: 1351 33.67 - 50.51: 306 50.51 - 67.35: 14 67.35 - 84.18: 26 Dihedral angle restraints: 17644 sinusoidal: 7278 harmonic: 10366 Sorted by residual: dihedral pdb=" CA LEU T2888 " pdb=" C LEU T2888 " pdb=" N PRO T2889 " pdb=" CA PRO T2889 " ideal model delta harmonic sigma weight residual -180.00 -108.71 -71.29 0 5.00e+00 4.00e-02 2.03e+02 dihedral pdb=" CA ILE T1157 " pdb=" C ILE T1157 " pdb=" N PRO T1158 " pdb=" CA PRO T1158 " ideal model delta harmonic sigma weight residual -180.00 -111.71 -68.29 0 5.00e+00 4.00e-02 1.87e+02 dihedral pdb=" CA GLU T3618 " pdb=" C GLU T3618 " pdb=" N PRO T3619 " pdb=" CA PRO T3619 " ideal model delta harmonic sigma weight residual -180.00 -119.83 -60.17 0 5.00e+00 4.00e-02 1.45e+02 ... (remaining 17641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 3969 0.102 - 0.205: 483 0.205 - 0.307: 40 0.307 - 0.410: 6 0.410 - 0.512: 3 Chirality restraints: 4501 Sorted by residual: chirality pdb=" CG LEU T1825 " pdb=" CB LEU T1825 " pdb=" CD1 LEU T1825 " pdb=" CD2 LEU T1825 " both_signs ideal model delta sigma weight residual False -2.59 -2.08 -0.51 2.00e-01 2.50e+01 6.55e+00 chirality pdb=" CG LEU T 876 " pdb=" CB LEU T 876 " pdb=" CD1 LEU T 876 " pdb=" CD2 LEU T 876 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CG LEU T 440 " pdb=" CB LEU T 440 " pdb=" CD1 LEU T 440 " pdb=" CD2 LEU T 440 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.38e+00 ... (remaining 4498 not shown) Planarity restraints: 4969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU T 246 " 0.093 5.00e-02 4.00e+02 1.42e-01 3.23e+01 pdb=" N PRO T 247 " -0.246 5.00e-02 4.00e+02 pdb=" CA PRO T 247 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO T 247 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS T 227 " 0.075 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO T 228 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO T 228 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO T 228 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU T 851 " 0.075 5.00e-02 4.00e+02 1.15e-01 2.10e+01 pdb=" N PRO T 852 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO T 852 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO T 852 " 0.062 5.00e-02 4.00e+02 ... (remaining 4966 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3570 2.75 - 3.29: 28916 3.29 - 3.82: 46176 3.82 - 4.36: 55314 4.36 - 4.90: 88734 Nonbonded interactions: 222710 Sorted by model distance: nonbonded pdb=" O GLU T2303 " pdb=" OG1 THR T2307 " model vdw 2.211 2.440 nonbonded pdb=" O VAL T3643 " pdb=" OG1 THR T3647 " model vdw 2.242 2.440 nonbonded pdb=" O LEU T2168 " pdb=" NZ LYS T2215 " model vdw 2.273 2.520 nonbonded pdb=" OG SER T2693 " pdb=" O VAL T3715 " model vdw 2.273 2.440 nonbonded pdb=" O TYR T 585 " pdb=" OG1 THR T 589 " model vdw 2.278 2.440 ... (remaining 222705 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: 1.500 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: 7.470 Check model and map are aligned: 0.430 Set scattering table: 0.240 Process input model: 74.940 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.007 0.092 29026 Z= 0.463 Angle : 1.429 25.298 39323 Z= 0.714 Chirality : 0.071 0.512 4501 Planarity : 0.009 0.142 4969 Dihedral : 13.414 84.182 10864 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.64 % Allowed : 14.75 % Favored : 84.61 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 10.96 % Twisted General : 1.03 % 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: -5.58 (0.11), residues: 3443 helix: -3.55 (0.07), residues: 1969 sheet: -2.88 (0.70), residues: 33 loop : -3.82 (0.15), residues: 1441 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 618 time to evaluate : 3.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 20 residues processed: 672 average time/residue: 0.4404 time to fit residues: 459.4036 Evaluate side-chains 383 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 363 time to evaluate : 3.276 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2534 time to fit residues: 14.2188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 293 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 140 optimal weight: 0.0470 chunk 271 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 chunk 202 optimal weight: 0.8980 chunk 315 optimal weight: 0.4980 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 45 HIS T 58 GLN T 400 HIS T 401 ASN T 565 ASN T 639 HIS T 836 GLN ** T 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 956 ASN T1002 ASN T1114 GLN T1126 ASN T1234 GLN T1365 ASN ** T1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1488 ASN T1619 GLN T1626 ASN T1654 ASN T1690 ASN ** T1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1740 GLN T1775 ASN T1784 ASN ** T1983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2183 ASN ** T2289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2294 GLN T2362 ASN T2418 GLN T2474 GLN T2490 ASN T2501 GLN T2526 HIS T2574 ASN T2646 ASN ** T2670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T2741 GLN T2752 HIS ** T2822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T2839 HIS T2847 GLN T2861 ASN T2863 HIS T2869 ASN T2896 ASN T2899 ASN T2907 HIS T2975 ASN ** T3073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3080 ASN T3154 HIS T3297 ASN T3346 HIS T3361 ASN T3406 GLN T3497 HIS ** T3537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 29026 Z= 0.225 Angle : 0.908 14.444 39323 Z= 0.454 Chirality : 0.048 0.231 4501 Planarity : 0.007 0.135 4969 Dihedral : 8.355 64.625 3743 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.26 % Allowed : 13.19 % Favored : 86.55 % Rotamer Outliers : 4.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 8.90 % Twisted General : 0.51 % 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: -4.11 (0.13), residues: 3443 helix: -2.11 (0.10), residues: 2071 sheet: -2.49 (0.75), residues: 33 loop : -3.66 (0.16), residues: 1339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 446 time to evaluate : 3.454 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 outliers start: 133 outliers final: 46 residues processed: 543 average time/residue: 0.4087 time to fit residues: 360.2324 Evaluate side-chains 392 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 346 time to evaluate : 3.496 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.2816 time to fit residues: 29.2202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 175 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 262 optimal weight: 7.9990 chunk 214 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 315 optimal weight: 9.9990 chunk 341 optimal weight: 7.9990 chunk 281 optimal weight: 3.9990 chunk 313 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 253 optimal weight: 9.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 69 HIS T 565 ASN ** T 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 896 GLN ** T1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1700 ASN ** T1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1784 ASN ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2418 GLN T2490 ASN T2811 GLN T3064 ASN ** T3073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3346 HIS T3385 HIS ** T3537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3547 GLN T3551 GLN ** T3573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T3580 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 29026 Z= 0.301 Angle : 0.903 11.695 39323 Z= 0.451 Chirality : 0.050 0.262 4501 Planarity : 0.007 0.142 4969 Dihedral : 7.993 63.514 3743 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.55 % Favored : 85.22 % Rotamer Outliers : 3.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 8.90 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.13), residues: 3443 helix: -1.40 (0.11), residues: 2079 sheet: -1.99 (0.80), residues: 33 loop : -3.64 (0.16), residues: 1331 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 380 time to evaluate : 3.229 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 outliers start: 124 outliers final: 47 residues processed: 481 average time/residue: 0.4003 time to fit residues: 314.6887 Evaluate side-chains 369 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 322 time to evaluate : 3.422 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.3154 time to fit residues: 31.4239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 311 optimal weight: 5.9990 chunk 237 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 34 optimal weight: 0.1980 chunk 150 optimal weight: 0.3980 chunk 211 optimal weight: 3.9990 chunk 316 optimal weight: 0.7980 chunk 335 optimal weight: 0.7980 chunk 165 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 565 ASN T 753 ASN ** T 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 956 ASN ** T1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T3018 GLN ** T3073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T3213 ASN ** T3346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 29026 Z= 0.198 Angle : 0.840 12.393 39323 Z= 0.413 Chirality : 0.047 0.337 4501 Planarity : 0.006 0.140 4969 Dihedral : 7.566 61.042 3743 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.24 % Favored : 86.55 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 8.22 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.14), residues: 3443 helix: -0.97 (0.11), residues: 2089 sheet: -1.95 (0.71), residues: 43 loop : -3.60 (0.16), residues: 1311 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 384 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 36 residues processed: 453 average time/residue: 0.3720 time to fit residues: 280.3749 Evaluate side-chains 364 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 328 time to evaluate : 3.200 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2649 time to fit residues: 22.3607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 279 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 249 optimal weight: 4.9990 chunk 138 optimal weight: 0.0870 chunk 286 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 301 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1983 ASN T2199 HIS ** T2342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2418 GLN T2474 GLN ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 29026 Z= 0.235 Angle : 0.849 14.166 39323 Z= 0.415 Chirality : 0.048 0.346 4501 Planarity : 0.006 0.146 4969 Dihedral : 7.399 62.332 3743 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 14.41 % Favored : 85.39 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 7.53 % Twisted General : 0.24 % 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: -2.68 (0.14), residues: 3443 helix: -0.74 (0.11), residues: 2085 sheet: -1.71 (0.74), residues: 43 loop : -3.53 (0.16), residues: 1315 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 373 time to evaluate : 3.710 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: 84 outliers final: 34 residues processed: 441 average time/residue: 0.3733 time to fit residues: 277.0241 Evaluate side-chains 361 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 327 time to evaluate : 3.346 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2652 time to fit residues: 21.7128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 112 optimal weight: 0.0070 chunk 302 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 335 optimal weight: 0.6980 chunk 278 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 150 ASN T 400 HIS ** T 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1109 HIS ** T1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 29026 Z= 0.230 Angle : 0.839 16.250 39323 Z= 0.409 Chirality : 0.048 0.355 4501 Planarity : 0.006 0.132 4969 Dihedral : 7.226 61.255 3743 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.32 % Favored : 85.51 % Rotamer Outliers : 2.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 7.53 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.14), residues: 3443 helix: -0.53 (0.11), residues: 2079 sheet: -1.40 (0.77), residues: 43 loop : -3.45 (0.17), residues: 1321 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 371 time to evaluate : 3.482 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 outliers start: 66 outliers final: 32 residues processed: 418 average time/residue: 0.3780 time to fit residues: 264.0210 Evaluate side-chains 361 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 329 time to evaluate : 3.341 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2683 time to fit residues: 20.6862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 323 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 245 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 282 optimal weight: 9.9990 chunk 187 optimal weight: 3.9990 chunk 334 optimal weight: 0.2980 chunk 209 optimal weight: 6.9990 chunk 203 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T2183 ASN T2199 HIS ** T2289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2732 ASN ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 29026 Z= 0.215 Angle : 0.839 14.446 39323 Z= 0.408 Chirality : 0.047 0.355 4501 Planarity : 0.006 0.132 4969 Dihedral : 7.073 58.585 3743 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.17 % Favored : 85.65 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 7.53 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.14), residues: 3443 helix: -0.37 (0.12), residues: 2064 sheet: -1.10 (0.85), residues: 43 loop : -3.37 (0.17), residues: 1336 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 381 time to evaluate : 3.445 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: 39 outliers final: 12 residues processed: 412 average time/residue: 0.3915 time to fit residues: 266.1041 Evaluate side-chains 347 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 335 time to evaluate : 3.531 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2642 time to fit residues: 10.8532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 206 optimal weight: 0.0020 chunk 133 optimal weight: 0.4980 chunk 199 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 212 optimal weight: 0.9980 chunk 227 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 262 optimal weight: 2.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T1805 ASN ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3468 HIS ** T3573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 29026 Z= 0.204 Angle : 0.836 13.471 39323 Z= 0.405 Chirality : 0.047 0.285 4501 Planarity : 0.006 0.137 4969 Dihedral : 6.921 56.537 3743 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.65 % Favored : 86.17 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 6.85 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.15), residues: 3443 helix: -0.27 (0.12), residues: 2067 sheet: -1.04 (0.83), residues: 43 loop : -3.32 (0.17), residues: 1333 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 382 time to evaluate : 3.475 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 outliers start: 36 outliers final: 14 residues processed: 410 average time/residue: 0.3924 time to fit residues: 269.2329 Evaluate side-chains 358 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 344 time to evaluate : 3.227 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2842 time to fit residues: 11.7837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 304 optimal weight: 10.0000 chunk 320 optimal weight: 0.8980 chunk 292 optimal weight: 1.9990 chunk 311 optimal weight: 4.9990 chunk 187 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 281 optimal weight: 4.9990 chunk 294 optimal weight: 1.9990 chunk 310 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2658 ASN ** T2696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T2890 ASN ** T3048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 29026 Z= 0.246 Angle : 0.864 13.036 39323 Z= 0.418 Chirality : 0.048 0.311 4501 Planarity : 0.006 0.137 4969 Dihedral : 6.943 55.834 3743 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.55 % Favored : 85.27 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 7.53 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.14), residues: 3443 helix: -0.28 (0.12), residues: 2072 sheet: -1.05 (0.81), residues: 43 loop : -3.27 (0.17), residues: 1328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 365 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 375 average time/residue: 0.3943 time to fit residues: 246.5832 Evaluate side-chains 349 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 342 time to evaluate : 3.341 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2593 time to fit residues: 8.1452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 204 optimal weight: 2.9990 chunk 329 optimal weight: 0.9980 chunk 201 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 345 optimal weight: 4.9990 chunk 318 optimal weight: 0.0980 chunk 275 optimal weight: 6.9990 chunk 28 optimal weight: 0.0570 chunk 212 optimal weight: 0.5980 chunk 168 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1983 ASN ** T2289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2696 GLN ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3073 ASN ** T3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.088 29026 Z= 0.206 Angle : 0.852 13.408 39323 Z= 0.409 Chirality : 0.047 0.305 4501 Planarity : 0.006 0.136 4969 Dihedral : 6.775 55.049 3743 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.53 % Favored : 86.26 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 6.16 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.15), residues: 3443 helix: -0.20 (0.12), residues: 2073 sheet: -0.80 (0.83), residues: 43 loop : -3.24 (0.17), residues: 1327 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 377 time to evaluate : 3.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 381 average time/residue: 0.3861 time to fit residues: 246.6521 Evaluate side-chains 349 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 347 time to evaluate : 3.439 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3236 time to fit residues: 5.8231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 218 optimal weight: 0.0970 chunk 293 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 253 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 76 optimal weight: 0.1980 chunk 275 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 283 optimal weight: 0.7980 chunk 34 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1397 GLN ** T1541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2847 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.138482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.117632 restraints weight = 70827.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.118683 restraints weight = 46039.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.119713 restraints weight = 32695.122| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 29026 Z= 0.199 Angle : 0.853 13.679 39323 Z= 0.409 Chirality : 0.047 0.276 4501 Planarity : 0.006 0.134 4969 Dihedral : 6.642 54.913 3743 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.53 % Favored : 86.26 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 6.16 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.15), residues: 3443 helix: -0.17 (0.12), residues: 2075 sheet: -0.69 (0.82), residues: 43 loop : -3.18 (0.17), residues: 1325 =============================================================================== Job complete usr+sys time: 5919.74 seconds wall clock time: 108 minutes 22.54 seconds (6502.54 seconds total)