Starting phenix.real_space_refine on Mon Sep 14 08:56:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d0b_27104/09_2026/8d0b_27104.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d0b_27104/09_2026/8d0b_27104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d0b_27104/09_2026/8d0b_27104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d0b_27104/09_2026/8d0b_27104.map" model { file = "/net/cci-nas-00/data/ceres_data/8d0b_27104/09_2026/8d0b_27104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d0b_27104/09_2026/8d0b_27104.cif" } resolution = 3.43 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.021 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 152 5.16 5 C 18708 2.51 5 N 5041 2.21 5 O 5451 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29367 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8734 Classifications: {'peptide': 1116} Link IDs: {'PCIS': 5, 'PTRANS': 87, 'TRANS': 1023} Chain breaks: 4 Chain: "B" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2923 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 348} Chain: "C" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 954 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 114} Chain: "D" Number of atoms: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3514 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 402} Chain: "E" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1995 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "F" Number of atoms: 7389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7389 Classifications: {'peptide': 915} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 868} Chain breaks: 2 Chain: "G" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3541 Classifications: {'peptide': 456} Modifications used: {'COO': 1} Link IDs: {'PCIS': 5, 'PTRANS': 28, 'TRANS': 422} Chain: "H" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 317 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Time building chain proxies: 5.93, per 1000 atoms: 0.20 Number of scatterers: 29367 At special positions: 0 Unit cell: (123.2, 168.3, 242, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 152 16.00 P 15 15.00 O 5451 8.00 N 5041 7.00 C 18708 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.3 seconds 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6900 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 37 sheets defined 37.6% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 9 through 27 removed outlier: 3.910A pdb=" N GLN A 13 " --> pdb=" O PRO A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 53 removed outlier: 4.184A pdb=" N GLN A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 88 through 100 Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.760A pdb=" N LEU A 154 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 266 through 274 removed outlier: 4.296A pdb=" N VAL A 270 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 449 through 459 removed outlier: 3.856A pdb=" N TYR A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 482 Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 501 through 515 Proline residue: A 509 - end of helix removed outlier: 3.725A pdb=" N LEU A 513 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 529 Processing helix chain 'A' and resid 551 through 566 removed outlier: 3.650A pdb=" N SER A 566 " --> pdb=" O LYS A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 573 removed outlier: 3.507A pdb=" N LEU A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 removed outlier: 4.022A pdb=" N LEU A 581 " --> pdb=" O ALA A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 590 Processing helix chain 'A' and resid 644 through 648 removed outlier: 4.105A pdb=" N LEU A 647 " --> pdb=" O ASP A 644 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE A 648 " --> pdb=" O PRO A 645 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 644 through 648' Processing helix chain 'A' and resid 801 through 811 removed outlier: 4.171A pdb=" N VAL A 805 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG A 806 " --> pdb=" O SER A 803 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLU A 809 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 811 " --> pdb=" O PHE A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 846 removed outlier: 3.944A pdb=" N ALA A 846 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 873 Processing helix chain 'A' and resid 882 through 887 Processing helix chain 'A' and resid 951 through 955 Processing helix chain 'A' and resid 1013 through 1017 Processing helix chain 'A' and resid 1090 through 1098 removed outlier: 4.087A pdb=" N ALA A1094 " --> pdb=" O ASN A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1112 Processing helix chain 'A' and resid 1137 through 1148 removed outlier: 3.534A pdb=" N THR A1147 " --> pdb=" O TRP A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 25 Proline residue: B 21 - end of helix removed outlier: 3.557A pdb=" N LEU B 24 " --> pdb=" O PRO B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 37 Processing helix chain 'B' and resid 103 through 124 Processing helix chain 'B' and resid 161 through 177 Proline residue: B 171 - end of helix Processing helix chain 'B' and resid 200 through 220 Processing helix chain 'B' and resid 226 through 232 removed outlier: 3.830A pdb=" N VAL B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 254 through 278 Processing helix chain 'B' and resid 297 through 310 removed outlier: 3.613A pdb=" N GLN B 310 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 Processing helix chain 'B' and resid 340 through 354 Processing helix chain 'C' and resid 11 through 16 Processing helix chain 'C' and resid 101 through 121 Processing helix chain 'D' and resid 5 through 7 No H-bonds generated for 'chain 'D' and resid 5 through 7' Processing helix chain 'D' and resid 8 through 20 removed outlier: 3.714A pdb=" N LEU D 12 " --> pdb=" O GLU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 30 Processing helix chain 'D' and resid 31 through 35 removed outlier: 3.900A pdb=" N VAL D 35 " --> pdb=" O TYR D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 41 No H-bonds generated for 'chain 'D' and resid 39 through 41' Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 111 through 115 removed outlier: 3.670A pdb=" N ASP D 114 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 149 removed outlier: 4.239A pdb=" N MET D 135 " --> pdb=" O CYS D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 209 through 228 removed outlier: 4.318A pdb=" N LYS D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR D 222 " --> pdb=" O ILE D 218 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU D 224 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLU D 225 " --> pdb=" O LYS D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 244 removed outlier: 3.593A pdb=" N TRP D 240 " --> pdb=" O ASN D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 264 through 281 removed outlier: 3.785A pdb=" N ASN D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 302 Processing helix chain 'D' and resid 306 through 312 removed outlier: 4.149A pdb=" N SER D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY D 312 " --> pdb=" O ASN D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 347 Processing helix chain 'D' and resid 349 through 368 removed outlier: 3.942A pdb=" N GLU D 366 " --> pdb=" O THR D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 386 Processing helix chain 'D' and resid 388 through 418 Processing helix chain 'E' and resid 17 through 22 Processing helix chain 'E' and resid 38 through 63 Processing helix chain 'E' and resid 68 through 81 Processing helix chain 'E' and resid 92 through 110 Processing helix chain 'E' and resid 113 through 134 Processing helix chain 'E' and resid 136 through 147 Processing helix chain 'E' and resid 155 through 162 Processing helix chain 'E' and resid 162 through 170 Processing helix chain 'E' and resid 191 through 197 removed outlier: 4.342A pdb=" N GLY E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 236 removed outlier: 3.931A pdb=" N SER E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 241 Processing helix chain 'E' and resid 246 through 255 removed outlier: 3.697A pdb=" N HIS E 255 " --> pdb=" O ASN E 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 426 removed outlier: 4.229A pdb=" N ALA F 422 " --> pdb=" O ASP F 418 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N THR F 423 " --> pdb=" O GLU F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 491 Processing helix chain 'F' and resid 522 through 524 No H-bonds generated for 'chain 'F' and resid 522 through 524' Processing helix chain 'F' and resid 597 through 606 Processing helix chain 'F' and resid 614 through 630 Processing helix chain 'F' and resid 642 through 655 Processing helix chain 'F' and resid 658 through 663 removed outlier: 3.718A pdb=" N LYS F 661 " --> pdb=" O HIS F 658 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 684 Processing helix chain 'F' and resid 693 through 701 Processing helix chain 'F' and resid 707 through 715 Processing helix chain 'F' and resid 724 through 731 removed outlier: 3.865A pdb=" N ILE F 728 " --> pdb=" O PRO F 724 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN F 729 " --> pdb=" O MET F 725 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN F 730 " --> pdb=" O GLU F 726 " (cutoff:3.500A) Processing helix chain 'F' and resid 734 through 759 removed outlier: 3.561A pdb=" N LEU F 759 " --> pdb=" O ILE F 755 " (cutoff:3.500A) Processing helix chain 'F' and resid 760 through 773 Processing helix chain 'F' and resid 775 through 780 removed outlier: 3.687A pdb=" N THR F 779 " --> pdb=" O ILE F 775 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU F 780 " --> pdb=" O MET F 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 775 through 780' Processing helix chain 'F' and resid 783 through 798 Processing helix chain 'F' and resid 863 through 873 Processing helix chain 'F' and resid 909 through 930 removed outlier: 3.629A pdb=" N LYS F 930 " --> pdb=" O LYS F 926 " (cutoff:3.500A) Processing helix chain 'F' and resid 935 through 955 Processing helix chain 'F' and resid 955 through 962 removed outlier: 3.811A pdb=" N LEU F 960 " --> pdb=" O MET F 956 " (cutoff:3.500A) Processing helix chain 'F' and resid 969 through 994 Processing helix chain 'F' and resid 1014 through 1033 removed outlier: 3.898A pdb=" N LEU F1032 " --> pdb=" O GLU F1028 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR F1033 " --> pdb=" O VAL F1029 " (cutoff:3.500A) Processing helix chain 'F' and resid 1268 through 1273 Processing helix chain 'F' and resid 1318 through 1321 Processing helix chain 'F' and resid 1322 through 1343 Processing helix chain 'F' and resid 1384 through 1398 Processing helix chain 'F' and resid 1400 through 1407 Processing helix chain 'F' and resid 1410 through 1421 Processing helix chain 'F' and resid 1423 through 1442 removed outlier: 3.642A pdb=" N ALA F1437 " --> pdb=" O LEU F1433 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE F1440 " --> pdb=" O THR F1436 " (cutoff:3.500A) Processing helix chain 'F' and resid 1443 through 1448 removed outlier: 6.120A pdb=" N TYR F1446 " --> pdb=" O ARG F1443 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER F1447 " --> pdb=" O SER F1444 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU F1448 " --> pdb=" O GLY F1445 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1443 through 1448' Processing helix chain 'F' and resid 1451 through 1455 Processing helix chain 'G' and resid 147 through 152 Processing helix chain 'G' and resid 158 through 163 removed outlier: 3.670A pdb=" N ASN G 162 " --> pdb=" O SER G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 236 removed outlier: 3.511A pdb=" N ILE G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 280 Processing helix chain 'G' and resid 331 through 337 removed outlier: 4.165A pdb=" N PHE G 337 " --> pdb=" O GLU G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 371 Processing helix chain 'G' and resid 386 through 391 Processing helix chain 'G' and resid 397 through 414 Processing helix chain 'G' and resid 446 through 451 removed outlier: 4.105A pdb=" N LYS G 451 " --> pdb=" O ARG G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 483 Processing helix chain 'G' and resid 493 through 505 Processing helix chain 'G' and resid 521 through 529 Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 67 removed outlier: 6.722A pdb=" N SER A 66 " --> pdb=" O LEU A 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 removed outlier: 6.636A pdb=" N CYS A 82 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N LEU A 179 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER A 143 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 115 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 238 removed outlier: 3.592A pdb=" N VAL A 237 " --> pdb=" O TYR A 244 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 244 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 232 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLY A 250 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU A 230 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU A 226 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR A 284 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLY A 228 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL A 282 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU A 230 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA A 280 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 237 through 238 removed outlier: 3.592A pdb=" N VAL A 237 " --> pdb=" O TYR A 244 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 244 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 10.630A pdb=" N HIS A 297 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER A 260 " --> pdb=" O HIS A 297 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TRP A 299 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR A 301 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 351 through 352 removed outlier: 3.613A pdb=" N TYR A 540 " --> pdb=" O ARG A 351 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.609A pdb=" N ARG A 354 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 408 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 420 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY A 380 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU A 372 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY A 364 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 399 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N CYS A 400 " --> pdb=" O GLN A 432 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 428 " --> pdb=" O GLN A 404 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 547 through 548 Processing sheet with id=AA8, first strand: chain 'A' and resid 592 through 597 removed outlier: 4.124A pdb=" N LYS A 683 " --> pdb=" O ARG A 666 " (cutoff:3.500A) removed outlier: 13.871A pdb=" N SER A 629 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N VAL A 688 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 692 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 635 " --> pdb=" O PHE A 692 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 592 through 597 removed outlier: 4.124A pdb=" N LYS A 683 " --> pdb=" O ARG A 666 " (cutoff:3.500A) removed outlier: 13.871A pdb=" N SER A 629 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N VAL A 688 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 692 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 635 " --> pdb=" O PHE A 692 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS A 632 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LEU A 621 " --> pdb=" O CYS A 632 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 742 through 744 removed outlier: 3.772A pdb=" N MET A 742 " --> pdb=" O SER A 762 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N TYR A 764 " --> pdb=" O LYS A 738 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LYS A 738 " --> pdb=" O TYR A 764 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU A 766 " --> pdb=" O CYS A 736 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 780 through 781 removed outlier: 6.953A pdb=" N LEU A 766 " --> pdb=" O CYS A 736 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LYS A 738 " --> pdb=" O TYR A 764 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N TYR A 764 " --> pdb=" O LYS A 738 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 760 through 769 current: chain 'A' and resid 860 through 862 Processing sheet with id=AB3, first strand: chain 'A' and resid 991 through 996 removed outlier: 6.710A pdb=" N ARG A 966 " --> pdb=" O LEU A 995 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A 973 " --> pdb=" O CYS A 985 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N HIS A 945 " --> pdb=" O VAL A 982 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N CYS A 984 " --> pdb=" O HIS A 945 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP A 947 " --> pdb=" O CYS A 984 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 950 " --> pdb=" O VAL A 929 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 904 " --> pdb=" O THR A 932 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA A 934 " --> pdb=" O ILE A 902 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE A 902 " --> pdb=" O ALA A 934 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE A 898 " --> pdb=" O SER A 970 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N SER A 970 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA A 900 " --> pdb=" O HIS A 968 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N HIS A 968 " --> pdb=" O ALA A 900 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE A 902 " --> pdb=" O ARG A 966 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG A 966 " --> pdb=" O ILE A 902 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1024 through 1027 removed outlier: 3.521A pdb=" N SER A1200 " --> pdb=" O SER A1158 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLU A1160 " --> pdb=" O CYS A1198 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N CYS A1198 " --> pdb=" O GLU A1160 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU A1194 " --> pdb=" O GLU A1083 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A1087 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ARG A1089 " --> pdb=" O CYS A1198 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N SER A1200 " --> pdb=" O ARG A1089 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A1086 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE A1068 " --> pdb=" O PHE A1040 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE A1040 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLN A1070 " --> pdb=" O GLN A1038 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLN A1038 " --> pdb=" O GLN A1070 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE A1072 " --> pdb=" O SER A1036 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N SER A1036 " --> pdb=" O ILE A1072 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ARG A1074 " --> pdb=" O VAL A1034 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N VAL A1034 " --> pdb=" O ARG A1074 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU A1076 " --> pdb=" O VAL A1032 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1175 through 1177 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 28 removed outlier: 6.490A pdb=" N ALA B 27 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N LEU B 60 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR B 131 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LYS B 154 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ARG B 133 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR B 152 " --> pdb=" O ARG B 133 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ARG B 135 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER B 137 " --> pdb=" O HIS B 148 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N VAL B 83 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 9.353A pdb=" N ILE B 147 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN B 85 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ALA B 149 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE B 87 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N THR B 151 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N TRP B 89 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 10.686A pdb=" N TYR B 153 " --> pdb=" O TRP B 89 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N PHE B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU B 68 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER B 74 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL B 66 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLY B 76 " --> pdb=" O ILE B 64 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 38 through 39 removed outlier: 3.894A pdb=" N LYS B 38 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 223 through 225 Processing sheet with id=AB9, first strand: chain 'B' and resid 322 through 323 Processing sheet with id=AC1, first strand: chain 'C' and resid 8 through 9 removed outlier: 6.334A pdb=" N THR C 8 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N PHE C 29 " --> pdb=" O THR C 8 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU C 72 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N CYS C 96 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE C 74 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU C 94 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU C 76 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 14.114A pdb=" N SER C 87 " --> pdb=" O GLN C 52 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N GLN C 54 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL C 89 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU C 56 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ALA C 91 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N CYS C 58 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N VAL C 93 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N HIS C 53 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG C 41 " --> pdb=" O TYR C 35 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR C 35 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR C 43 " --> pdb=" O CYS C 33 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLN C 47 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 11.295A pdb=" N PHE C 29 " --> pdb=" O GLN C 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 58 removed outlier: 6.226A pdb=" N TYR D 54 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU D 49 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ARG D 56 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE D 47 " --> pdb=" O ARG D 56 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLU D 44 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER D 46 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL D 83 " --> pdb=" O GLN D 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 58 removed outlier: 6.226A pdb=" N TYR D 54 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU D 49 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ARG D 56 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE D 47 " --> pdb=" O ARG D 56 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLU D 44 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER D 46 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU D 317 " --> pdb=" O ILE D 80 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 106 through 110 removed outlier: 3.636A pdb=" N CYS D 167 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 110 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL D 165 " --> pdb=" O ILE D 110 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TRP D 157 " --> pdb=" O ILE D 334 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 36 through 37 Processing sheet with id=AC6, first strand: chain 'E' and resid 184 through 187 removed outlier: 4.192A pdb=" N TYR E 201 " --> pdb=" O TYR E 208 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 332 through 333 removed outlier: 7.394A pdb=" N HIS F 342 " --> pdb=" O TRP F 366 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TRP F 366 " --> pdb=" O HIS F 342 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE F 362 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA F 348 " --> pdb=" O PHE F 360 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE F 360 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 9.734A pdb=" N VAL F 516 " --> pdb=" O HIS F 373 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N SER F 375 " --> pdb=" O VAL F 516 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N ALA F 518 " --> pdb=" O SER F 375 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N CYS F 377 " --> pdb=" O ALA F 518 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ALA F 520 " --> pdb=" O CYS F 377 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N MET F 379 " --> pdb=" O ALA F 520 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 332 through 333 removed outlier: 3.767A pdb=" N TRP F 498 " --> pdb=" O ILE F 529 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU F 500 " --> pdb=" O ASN F 527 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 431 through 438 removed outlier: 3.525A pdb=" N GLU F 454 " --> pdb=" O LYS F 433 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER F 450 " --> pdb=" O LYS F 437 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N GLU F 451 " --> pdb=" O PRO F 391 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR F 457 " --> pdb=" O ARG F 385 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N HIS F 475 " --> pdb=" O LEU F 390 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 394 through 396 removed outlier: 5.799A pdb=" N THR F 406 " --> pdb=" O LYS F 395 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 609 through 611 removed outlier: 8.989A pdb=" N GLU F 610 " --> pdb=" O HIS F 582 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N CYS F 584 " --> pdb=" O GLU F 610 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE F 558 " --> pdb=" O MET F 547 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N MET F 547 " --> pdb=" O ILE F 558 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N MET F 560 " --> pdb=" O LYS F 545 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS F 545 " --> pdb=" O MET F 560 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA F 562 " --> pdb=" O SER F 543 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N SER F 543 " --> pdb=" O ALA F 562 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL F 564 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ALA F 541 " --> pdb=" O VAL F 564 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS F 566 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL F 539 " --> pdb=" O HIS F 566 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL F 538 " --> pdb=" O ILE F 633 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL F 635 " --> pdb=" O VAL F 538 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N MET F 540 " --> pdb=" O VAL F 635 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 997 through 1002 removed outlier: 6.742A pdb=" N VAL F 998 " --> pdb=" O ASN F1009 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ASN F1009 " --> pdb=" O VAL F 998 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR F1000 " --> pdb=" O MET F1007 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP F 860 " --> pdb=" O ILE F1040 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE F1040 " --> pdb=" O ASP F 860 " (cutoff:3.500A) removed outlier: 11.590A pdb=" N GLY F1042 " --> pdb=" O PRO F1062 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE F1044 " --> pdb=" O VAL F1060 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL F1060 " --> pdb=" O PHE F1044 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER F1046 " --> pdb=" O LEU F1058 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR F1055 " --> pdb=" O LYS F1075 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS F1075 " --> pdb=" O TYR F1055 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 1279 through 1282 removed outlier: 3.528A pdb=" N PHE F1279 " --> pdb=" O TYR F1292 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS F1281 " --> pdb=" O ASN F1290 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 1356 through 1357 Processing sheet with id=AD6, first strand: chain 'G' and resid 170 through 175 removed outlier: 6.596A pdb=" N VAL G 170 " --> pdb=" O ARG G 597 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG G 597 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR G 172 " --> pdb=" O VAL G 595 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N CYS G 590 " --> pdb=" O ARG G 577 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG G 577 " --> pdb=" O CYS G 590 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA G 592 " --> pdb=" O TYR G 575 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL G 374 " --> pdb=" O MET G 341 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU G 420 " --> pdb=" O GLN G 454 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 193 through 196 removed outlier: 4.249A pdb=" N SER G 461 " --> pdb=" O LEU G 196 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE G 468 " --> pdb=" O VAL G 537 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE G 539 " --> pdb=" O ILE G 468 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLY G 470 " --> pdb=" O ILE G 539 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE G 547 " --> pdb=" O ASN G 558 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 250 through 259 removed outlier: 4.927A pdb=" N VAL G 270 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU G 314 " --> pdb=" O GLN G 283 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ALA G 316 " --> pdb=" O PRO G 285 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASP G 287 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LYS G 318 " --> pdb=" O ASP G 287 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL G 315 " --> pdb=" O ILE G 307 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE G 307 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLU G 305 " --> pdb=" O THR G 317 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU G 319 " --> pdb=" O ILE G 303 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE G 303 " --> pdb=" O LEU G 319 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 294 through 296 removed outlier: 3.656A pdb=" N TYR G 294 " --> pdb=" O SER G 487 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 563 through 564 1223 hydrogen bonds defined for protein. 3426 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: 7.75 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9469 1.34 - 1.46: 5555 1.46 - 1.58: 14814 1.58 - 1.70: 29 1.70 - 1.82: 207 Bond restraints: 30074 Sorted by residual: bond pdb=" C1' DT H 12 " pdb=" N1 DT H 12 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.78e+00 bond pdb=" C3' DT H 7 " pdb=" C2' DT H 7 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.41e+00 bond pdb=" C3' DT H 6 " pdb=" C2' DT H 6 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.94e+00 bond pdb=" C1' DT H 6 " pdb=" N1 DT H 6 " ideal model delta sigma weight residual 1.468 1.498 -0.030 1.40e-02 5.10e+03 4.57e+00 bond pdb=" C3' DG H 4 " pdb=" C2' DG H 4 " ideal model delta sigma weight residual 1.516 1.531 -0.015 8.00e-03 1.56e+04 3.45e+00 ... (remaining 30069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 40424 2.15 - 4.31: 336 4.31 - 6.46: 42 6.46 - 8.61: 11 8.61 - 10.76: 3 Bond angle restraints: 40816 Sorted by residual: angle pdb=" C LEU B 187 " pdb=" CA LEU B 187 " pdb=" CB LEU B 187 " ideal model delta sigma weight residual 116.54 110.08 6.46 1.15e+00 7.56e-01 3.15e+01 angle pdb=" C GLU A 951 " pdb=" N ASP A 952 " pdb=" CA ASP A 952 " ideal model delta sigma weight residual 120.09 125.89 -5.80 1.25e+00 6.40e-01 2.15e+01 angle pdb=" N3 DT H 12 " pdb=" C4 DT H 12 " pdb=" O4 DT H 12 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT H 13 " pdb=" C4 DT H 13 " pdb=" O4 DT H 13 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT H 6 " pdb=" C4 DT H 6 " pdb=" O4 DT H 6 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 ... (remaining 40811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 16063 17.94 - 35.88: 1774 35.88 - 53.82: 377 53.82 - 71.75: 59 71.75 - 89.69: 26 Dihedral angle restraints: 18299 sinusoidal: 7652 harmonic: 10647 Sorted by residual: dihedral pdb=" CA LEU A 955 " pdb=" C LEU A 955 " pdb=" N PRO A 956 " pdb=" CA PRO A 956 " ideal model delta harmonic sigma weight residual 180.00 140.76 39.24 0 5.00e+00 4.00e-02 6.16e+01 dihedral pdb=" CA ALA F 886 " pdb=" C ALA F 886 " pdb=" N GLN F 887 " pdb=" CA GLN F 887 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLN F 897 " pdb=" C GLN F 897 " pdb=" N ILE F 898 " pdb=" CA ILE F 898 " ideal model delta harmonic sigma weight residual 180.00 160.52 19.48 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 18296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3284 0.036 - 0.072: 864 0.072 - 0.108: 304 0.108 - 0.144: 86 0.144 - 0.179: 2 Chirality restraints: 4540 Sorted by residual: chirality pdb=" CB VAL E 215 " pdb=" CA VAL E 215 " pdb=" CG1 VAL E 215 " pdb=" CG2 VAL E 215 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" CA GLU B 210 " pdb=" N GLU B 210 " pdb=" C GLU B 210 " pdb=" CB GLU B 210 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CB VAL A1169 " pdb=" CA VAL A1169 " pdb=" CG1 VAL A1169 " pdb=" CG2 VAL A1169 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 4537 not shown) Planarity restraints: 5197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 955 " 0.038 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO A 956 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 956 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 956 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 828 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C MET A 828 " 0.032 2.00e-02 2.50e+03 pdb=" O MET A 828 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 829 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 215 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C VAL E 215 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL E 215 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA E 216 " 0.010 2.00e-02 2.50e+03 ... (remaining 5194 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 798 2.71 - 3.26: 27567 3.26 - 3.81: 45456 3.81 - 4.35: 53490 4.35 - 4.90: 93028 Nonbonded interactions: 220339 Sorted by model distance: nonbonded pdb=" O ARG E 235 " pdb=" NE ARG E 235 " model vdw 2.167 3.120 nonbonded pdb=" OH TYR D 279 " pdb=" OD2 ASP D 286 " model vdw 2.238 3.040 nonbonded pdb=" OH TYR D 26 " pdb=" OG SER D 319 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR A 358 " pdb=" OD2 ASP A 376 " model vdw 2.256 3.040 nonbonded pdb=" NE2 GLN D 25 " pdb=" OE1 GLU D 396 " model vdw 2.268 3.120 ... (remaining 220334 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic 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: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 28.710 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 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 : 0.002 0.054 30074 Z= 0.117 Angle : 0.489 10.763 40816 Z= 0.266 Chirality : 0.040 0.179 4540 Planarity : 0.003 0.060 5197 Dihedral : 15.429 89.693 11399 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Rotamer: Outliers : 0.06 % Allowed : 10.00 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.15), residues: 3604 helix: 2.40 (0.16), residues: 1223 sheet: 0.60 (0.21), residues: 675 loop : -0.30 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 139 TYR 0.018 0.001 TYR F1055 PHE 0.016 0.001 PHE B 215 TRP 0.018 0.001 TRP A 50 HIS 0.003 0.000 HIS D 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.12 (30074) covalent geometry : angle 0.48856 / 0.27 (40816) hydrogen bonds : bond 0.18680 / 12.33 ( 1195) hydrogen bonds : angle 6.58367 / 4.65 ( 3426) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 1.306 Fit side-chains revert: symmetry clash REVERT: D 4 PHE cc_start: 0.7142 (t80) cc_final: 0.6592 (t80) REVERT: F 929 MET cc_start: 0.8145 (mtt) cc_final: 0.7580 (mtp) outliers start: 2 outliers final: 0 residues processed: 93 average time/residue: 0.1892 time to fit residues: 30.5375 Evaluate side-chains 87 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 8.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN G 404 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.073258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.049815 restraints weight = 130438.000| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 4.26 r_work: 0.2862 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 30074 Z= 0.231 Angle : 0.570 10.004 40816 Z= 0.295 Chirality : 0.042 0.156 4540 Planarity : 0.004 0.055 5197 Dihedral : 7.637 88.639 4108 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.36 % Favored : 95.59 % Rotamer: Outliers : 0.98 % Allowed : 10.61 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.15), residues: 3604 helix: 2.37 (0.16), residues: 1211 sheet: 0.38 (0.21), residues: 663 loop : -0.41 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 85 TYR 0.014 0.001 TYR F 957 PHE 0.017 0.001 PHE A 986 TRP 0.012 0.001 TRP A 50 HIS 0.005 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (30074) covalent geometry : angle 0.56955 / 0.30 (40816) hydrogen bonds : bond 0.05096 / 3.38 ( 1195) hydrogen bonds : angle 5.16819 / 3.63 ( 3426) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: A 639 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.7906 (p) REVERT: A 1108 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8752 (mm) REVERT: B 217 MET cc_start: 0.9452 (tpt) cc_final: 0.9196 (mmp) REVERT: F 731 MET cc_start: 0.9296 (mmm) cc_final: 0.8841 (mmm) REVERT: F 929 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7908 (mtp) REVERT: F 990 MET cc_start: 0.8824 (ttt) cc_final: 0.8491 (ttt) REVERT: F 994 MET cc_start: 0.8836 (ptt) cc_final: 0.8491 (ptp) REVERT: F 1303 MET cc_start: 0.8427 (mmp) cc_final: 0.8169 (mmp) outliers start: 32 outliers final: 16 residues processed: 117 average time/residue: 0.1803 time to fit residues: 36.7458 Evaluate side-chains 108 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 HIS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1085 VAL Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain F residue 560 MET Chi-restraints excluded: chain F residue 929 MET Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 472 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 130 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 319 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 308 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 HIS C 81 HIS E 88 ASN F 475 HIS F 505 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.074342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.051029 restraints weight = 129851.629| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 4.29 r_work: 0.2891 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30074 Z= 0.106 Angle : 0.479 8.329 40816 Z= 0.250 Chirality : 0.040 0.152 4540 Planarity : 0.004 0.059 5197 Dihedral : 7.595 89.096 4108 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.78 % Rotamer: Outliers : 0.77 % Allowed : 11.19 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.15), residues: 3604 helix: 2.45 (0.16), residues: 1211 sheet: 0.51 (0.21), residues: 662 loop : -0.37 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 418 TYR 0.015 0.001 TYR D 383 PHE 0.015 0.001 PHE E 42 TRP 0.012 0.001 TRP A 50 HIS 0.004 0.000 HIS A 812 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (30074) covalent geometry : angle 0.47910 / 0.25 (40816) hydrogen bonds : bond 0.04050 / 2.69 ( 1195) hydrogen bonds : angle 4.80057 / 3.37 ( 3426) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8270 (m) REVERT: A 1042 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8834 (p) REVERT: B 217 MET cc_start: 0.9451 (tpt) cc_final: 0.9144 (mmp) REVERT: F 731 MET cc_start: 0.9261 (mmm) cc_final: 0.8868 (mmm) REVERT: F 756 MET cc_start: 0.9098 (tmm) cc_final: 0.8891 (tmm) REVERT: F 929 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7893 (mtp) REVERT: F 1303 MET cc_start: 0.8513 (mmp) cc_final: 0.8307 (mmp) outliers start: 25 outliers final: 11 residues processed: 110 average time/residue: 0.1776 time to fit residues: 33.9383 Evaluate side-chains 101 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 442 HIS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain F residue 560 MET Chi-restraints excluded: chain F residue 929 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 251 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 307 optimal weight: 5.9990 chunk 269 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 354 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.073829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.050405 restraints weight = 129480.741| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 4.28 r_work: 0.2875 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30074 Z= 0.166 Angle : 0.501 8.569 40816 Z= 0.259 Chirality : 0.040 0.149 4540 Planarity : 0.004 0.058 5197 Dihedral : 7.637 88.778 4108 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.02 % Favored : 95.92 % Rotamer: Outliers : 1.26 % Allowed : 11.35 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.15), residues: 3604 helix: 2.45 (0.16), residues: 1210 sheet: 0.41 (0.21), residues: 664 loop : -0.41 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 418 TYR 0.016 0.001 TYR D 383 PHE 0.014 0.001 PHE E 42 TRP 0.012 0.001 TRP D 240 HIS 0.006 0.001 HIS A 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (30074) covalent geometry : angle 0.50074 / 0.26 (40816) hydrogen bonds : bond 0.04051 / 2.70 ( 1195) hydrogen bonds : angle 4.67659 / 3.28 ( 3426) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 88 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 637 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7616 (pptt) REVERT: A 1108 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8748 (mm) REVERT: B 217 MET cc_start: 0.9458 (tpt) cc_final: 0.9149 (mmp) REVERT: D 371 GLU cc_start: -0.1419 (OUTLIER) cc_final: -0.1744 (pt0) REVERT: F 394 MET cc_start: 0.7548 (tpt) cc_final: 0.7118 (tpt) REVERT: F 731 MET cc_start: 0.9253 (mmm) cc_final: 0.8601 (mmm) REVERT: F 756 MET cc_start: 0.9131 (tmm) cc_final: 0.8883 (tmm) REVERT: F 929 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.7891 (mtp) outliers start: 41 outliers final: 24 residues processed: 125 average time/residue: 0.1846 time to fit residues: 39.7169 Evaluate side-chains 116 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1085 VAL Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain D residue 170 CYS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain F residue 560 MET Chi-restraints excluded: chain F residue 929 MET Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 570 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 10 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 178 optimal weight: 0.4980 chunk 286 optimal weight: 5.9990 chunk 235 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 284 optimal weight: 9.9990 chunk 321 optimal weight: 0.9990 chunk 358 optimal weight: 0.0670 chunk 289 optimal weight: 30.0000 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 442 HIS A 691 GLN B 240 ASN C 81 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.074278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.050937 restraints weight = 129589.744| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 4.29 r_work: 0.2890 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30074 Z= 0.110 Angle : 0.470 8.017 40816 Z= 0.243 Chirality : 0.040 0.145 4540 Planarity : 0.004 0.059 5197 Dihedral : 7.597 87.527 4108 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.30 % Favored : 96.67 % Rotamer: Outliers : 1.26 % Allowed : 11.68 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.15), residues: 3604 helix: 2.49 (0.16), residues: 1213 sheet: 0.49 (0.21), residues: 655 loop : -0.39 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 135 TYR 0.016 0.001 TYR D 383 PHE 0.014 0.001 PHE E 42 TRP 0.012 0.001 TRP D 240 HIS 0.002 0.000 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (30074) covalent geometry : angle 0.47008 / 0.24 (40816) hydrogen bonds : bond 0.03576 / 2.38 ( 1195) hydrogen bonds : angle 4.49702 / 3.15 ( 3426) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 90 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7960 (tt) REVERT: A 637 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7487 (pptt) REVERT: A 639 SER cc_start: 0.8109 (OUTLIER) cc_final: 0.7892 (p) REVERT: A 1042 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8873 (p) REVERT: A 1108 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8743 (mm) REVERT: B 217 MET cc_start: 0.9468 (tpt) cc_final: 0.9149 (mmp) REVERT: E 230 LEU cc_start: 0.9109 (tp) cc_final: 0.8860 (tp) REVERT: E 235 ARG cc_start: 0.8891 (tpm170) cc_final: 0.8653 (tpm170) REVERT: F 394 MET cc_start: 0.7699 (tpt) cc_final: 0.7337 (tpt) REVERT: F 756 MET cc_start: 0.9098 (tmm) cc_final: 0.8875 (tmm) REVERT: F 929 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7876 (mtp) REVERT: F 985 MET cc_start: 0.8965 (mmm) cc_final: 0.8536 (mpp) REVERT: F 1303 MET cc_start: 0.8557 (mmp) cc_final: 0.8341 (mmp) outliers start: 41 outliers final: 21 residues processed: 127 average time/residue: 0.1833 time to fit residues: 40.3112 Evaluate side-chains 116 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 442 HIS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain D residue 170 CYS Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 560 MET Chi-restraints excluded: chain F residue 929 MET Chi-restraints excluded: chain G residue 431 HIS Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 570 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 235 optimal weight: 5.9990 chunk 239 optimal weight: 8.9990 chunk 310 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 356 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 262 optimal weight: 0.9980 chunk 178 optimal weight: 0.1980 chunk 319 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 272 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.074624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.051379 restraints weight = 128589.664| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 4.28 r_work: 0.2901 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 30074 Z= 0.095 Angle : 0.466 10.602 40816 Z= 0.240 Chirality : 0.039 0.152 4540 Planarity : 0.004 0.058 5197 Dihedral : 7.575 86.829 4108 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 1.10 % Allowed : 12.14 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.15), residues: 3604 helix: 2.53 (0.16), residues: 1213 sheet: 0.46 (0.21), residues: 655 loop : -0.37 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 445 TYR 0.016 0.001 TYR D 383 PHE 0.013 0.001 PHE E 42 TRP 0.012 0.001 TRP D 240 HIS 0.006 0.000 HIS A 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (30074) covalent geometry : angle 0.46632 / 0.24 (40816) hydrogen bonds : bond 0.03390 / 2.26 ( 1195) hydrogen bonds : angle 4.40176 / 3.08 ( 3426) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7962 (tt) REVERT: A 399 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8255 (m) REVERT: A 639 SER cc_start: 0.8102 (OUTLIER) cc_final: 0.7896 (p) REVERT: A 1042 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8898 (p) REVERT: A 1108 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8757 (mm) REVERT: B 217 MET cc_start: 0.9466 (tpt) cc_final: 0.9138 (mmp) REVERT: C 45 MET cc_start: 0.8816 (mtm) cc_final: 0.8513 (mtm) REVERT: E 230 LEU cc_start: 0.9106 (tp) cc_final: 0.8849 (tp) REVERT: E 235 ARG cc_start: 0.8852 (tpm170) cc_final: 0.8598 (tpm170) REVERT: F 394 MET cc_start: 0.7638 (tpt) cc_final: 0.7296 (tpp) REVERT: F 756 MET cc_start: 0.9097 (tmm) cc_final: 0.8877 (tmm) REVERT: F 929 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7877 (mtp) REVERT: F 985 MET cc_start: 0.8958 (mmm) cc_final: 0.8525 (mpp) REVERT: F 990 MET cc_start: 0.8841 (ttt) cc_final: 0.8313 (ptp) REVERT: F 1303 MET cc_start: 0.8611 (mmp) cc_final: 0.8340 (mmp) outliers start: 36 outliers final: 25 residues processed: 123 average time/residue: 0.1636 time to fit residues: 34.8148 Evaluate side-chains 119 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1085 VAL Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain D residue 170 CYS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 560 MET Chi-restraints excluded: chain F residue 877 THR Chi-restraints excluded: chain F residue 929 MET Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 431 HIS Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 570 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 125 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 307 optimal weight: 5.9990 chunk 172 optimal weight: 0.5980 chunk 272 optimal weight: 30.0000 chunk 239 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.073881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.050623 restraints weight = 129761.037| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 4.56 r_work: 0.2862 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30074 Z= 0.164 Angle : 0.496 9.570 40816 Z= 0.254 Chirality : 0.040 0.143 4540 Planarity : 0.004 0.057 5197 Dihedral : 7.617 87.364 4108 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.97 % Favored : 96.00 % Rotamer: Outliers : 1.26 % Allowed : 12.39 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.15), residues: 3604 helix: 2.51 (0.16), residues: 1214 sheet: 0.36 (0.21), residues: 663 loop : -0.42 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 418 TYR 0.016 0.001 TYR D 383 PHE 0.016 0.001 PHE B 215 TRP 0.011 0.001 TRP D 240 HIS 0.004 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (30074) covalent geometry : angle 0.49609 / 0.25 (40816) hydrogen bonds : bond 0.03716 / 2.48 ( 1195) hydrogen bonds : angle 4.40558 / 3.08 ( 3426) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 90 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7917 (tt) REVERT: A 399 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8234 (m) REVERT: A 639 SER cc_start: 0.8154 (OUTLIER) cc_final: 0.7910 (p) REVERT: A 1042 VAL cc_start: 0.9097 (OUTLIER) cc_final: 0.8834 (p) REVERT: A 1108 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8775 (mm) REVERT: B 217 MET cc_start: 0.9487 (tpt) cc_final: 0.9158 (mmp) REVERT: E 230 LEU cc_start: 0.9106 (tp) cc_final: 0.8857 (tp) REVERT: F 394 MET cc_start: 0.7573 (tpt) cc_final: 0.7199 (tpp) REVERT: F 756 MET cc_start: 0.9128 (tmm) cc_final: 0.8885 (tmm) REVERT: F 929 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.7939 (mtp) REVERT: F 985 MET cc_start: 0.8947 (mmm) cc_final: 0.8516 (mpp) REVERT: F 1303 MET cc_start: 0.8652 (mmp) cc_final: 0.8422 (mmp) outliers start: 41 outliers final: 31 residues processed: 127 average time/residue: 0.1795 time to fit residues: 39.0655 Evaluate side-chains 126 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1085 VAL Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain D residue 170 CYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 560 MET Chi-restraints excluded: chain F residue 585 VAL Chi-restraints excluded: chain F residue 651 ILE Chi-restraints excluded: chain F residue 877 THR Chi-restraints excluded: chain F residue 929 MET Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 570 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 145 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 153 optimal weight: 0.0370 chunk 81 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 337 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 32 optimal weight: 0.0670 chunk 241 optimal weight: 5.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 442 HIS A 446 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.074635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.051367 restraints weight = 128454.337| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 4.29 r_work: 0.2902 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 30074 Z= 0.095 Angle : 0.469 9.820 40816 Z= 0.241 Chirality : 0.040 0.167 4540 Planarity : 0.004 0.058 5197 Dihedral : 7.568 86.511 4108 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.56 % Rotamer: Outliers : 1.13 % Allowed : 12.63 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.15), residues: 3604 helix: 2.54 (0.16), residues: 1213 sheet: 0.49 (0.21), residues: 654 loop : -0.39 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 135 TYR 0.015 0.001 TYR D 383 PHE 0.014 0.001 PHE E 42 TRP 0.012 0.001 TRP D 240 HIS 0.002 0.000 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 (30074) covalent geometry : angle 0.46871 / 0.24 (40816) hydrogen bonds : bond 0.03318 / 2.22 ( 1195) hydrogen bonds : angle 4.30067 / 3.01 ( 3426) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 1.275 Fit side-chains revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7952 (tt) REVERT: A 399 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8287 (m) REVERT: A 637 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7705 (pptt) REVERT: A 1042 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8900 (p) REVERT: B 217 MET cc_start: 0.9499 (tpt) cc_final: 0.9133 (mmp) REVERT: E 93 TYR cc_start: 0.6717 (t80) cc_final: 0.6493 (t80) REVERT: E 235 ARG cc_start: 0.8900 (tpm170) cc_final: 0.8649 (tpm170) REVERT: F 394 MET cc_start: 0.7543 (tpt) cc_final: 0.7218 (tpp) REVERT: F 756 MET cc_start: 0.9103 (tmm) cc_final: 0.8873 (tmm) REVERT: F 929 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.7907 (mtp) REVERT: F 985 MET cc_start: 0.8950 (mmm) cc_final: 0.8507 (mpp) REVERT: F 990 MET cc_start: 0.8865 (ttt) cc_final: 0.8140 (ptp) REVERT: F 994 MET cc_start: 0.8740 (ptp) cc_final: 0.7896 (pmm) REVERT: F 1303 MET cc_start: 0.8617 (mmp) cc_final: 0.8386 (mmp) outliers start: 37 outliers final: 27 residues processed: 122 average time/residue: 0.1796 time to fit residues: 38.0887 Evaluate side-chains 119 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1085 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 170 CYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 560 MET Chi-restraints excluded: chain F residue 877 THR Chi-restraints excluded: chain F residue 929 MET Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 431 HIS Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 570 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 66 optimal weight: 8.9990 chunk 271 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 301 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 316 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 284 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.074355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.051084 restraints weight = 128574.113| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 4.28 r_work: 0.2895 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30074 Z= 0.113 Angle : 0.475 10.781 40816 Z= 0.243 Chirality : 0.040 0.157 4540 Planarity : 0.003 0.057 5197 Dihedral : 7.559 86.214 4108 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.34 % Rotamer: Outliers : 1.13 % Allowed : 12.57 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.15), residues: 3604 helix: 2.56 (0.15), residues: 1213 sheet: 0.49 (0.21), residues: 655 loop : -0.39 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 135 TYR 0.016 0.001 TYR D 383 PHE 0.018 0.001 PHE B 215 TRP 0.012 0.001 TRP D 240 HIS 0.003 0.000 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (30074) covalent geometry : angle 0.47502 / 0.24 (40816) hydrogen bonds : bond 0.03377 / 2.27 ( 1195) hydrogen bonds : angle 4.26916 / 2.99 ( 3426) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7969 (tt) REVERT: A 399 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8239 (m) REVERT: A 1042 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8908 (p) REVERT: B 217 MET cc_start: 0.9487 (tpt) cc_final: 0.9165 (mmp) REVERT: E 230 LEU cc_start: 0.9100 (tp) cc_final: 0.8845 (tp) REVERT: E 235 ARG cc_start: 0.8888 (tpm170) cc_final: 0.8612 (tpm170) REVERT: F 394 MET cc_start: 0.7554 (tpt) cc_final: 0.7241 (tpp) REVERT: F 756 MET cc_start: 0.9106 (tmm) cc_final: 0.8873 (tmm) REVERT: F 929 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.7912 (mtp) REVERT: F 985 MET cc_start: 0.8952 (mmm) cc_final: 0.8719 (tpp) REVERT: F 990 MET cc_start: 0.8857 (ttt) cc_final: 0.8042 (ptp) REVERT: F 994 MET cc_start: 0.8750 (ptp) cc_final: 0.7685 (pmm) REVERT: F 1303 MET cc_start: 0.8619 (mmp) cc_final: 0.8392 (mmp) outliers start: 37 outliers final: 29 residues processed: 122 average time/residue: 0.1696 time to fit residues: 36.0571 Evaluate side-chains 121 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1085 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 170 CYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 560 MET Chi-restraints excluded: chain F residue 585 VAL Chi-restraints excluded: chain F residue 877 THR Chi-restraints excluded: chain F residue 929 MET Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 431 HIS Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 570 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 165 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 305 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 114 optimal weight: 0.0770 chunk 324 optimal weight: 6.9990 chunk 227 optimal weight: 0.9980 chunk 143 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.075048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.051888 restraints weight = 127731.395| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 4.27 r_work: 0.2917 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 30074 Z= 0.087 Angle : 0.466 11.467 40816 Z= 0.238 Chirality : 0.039 0.176 4540 Planarity : 0.003 0.057 5197 Dihedral : 7.507 85.273 4108 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.81 % Rotamer: Outliers : 0.95 % Allowed : 12.82 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.15), residues: 3604 helix: 2.60 (0.15), residues: 1213 sheet: 0.59 (0.21), residues: 661 loop : -0.34 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 135 TYR 0.015 0.001 TYR D 383 PHE 0.015 0.001 PHE E 42 TRP 0.012 0.001 TRP D 240 HIS 0.002 0.000 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 (30074) covalent geometry : angle 0.46622 / 0.24 (40816) hydrogen bonds : bond 0.03052 / 2.05 ( 1195) hydrogen bonds : angle 4.17991 / 2.92 ( 3426) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7208 Ramachandran restraints generated. 3604 Oldfield, 0 Emsley, 3604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8049 (tt) REVERT: A 399 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8182 (m) REVERT: A 1042 VAL cc_start: 0.9101 (OUTLIER) cc_final: 0.8880 (p) REVERT: B 217 MET cc_start: 0.9481 (tpt) cc_final: 0.9160 (mmp) REVERT: E 235 ARG cc_start: 0.8829 (tpm170) cc_final: 0.8576 (tpm170) REVERT: F 394 MET cc_start: 0.7596 (tpt) cc_final: 0.7327 (tpp) REVERT: F 756 MET cc_start: 0.9110 (tmm) cc_final: 0.8903 (tmm) REVERT: F 929 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.7905 (mtp) REVERT: F 985 MET cc_start: 0.8962 (mmm) cc_final: 0.8732 (tpp) REVERT: F 990 MET cc_start: 0.8863 (ttt) cc_final: 0.8338 (ptp) REVERT: F 994 MET cc_start: 0.8729 (ptp) cc_final: 0.8435 (ptp) REVERT: F 1303 MET cc_start: 0.8610 (mmp) cc_final: 0.8373 (mmp) outliers start: 31 outliers final: 24 residues processed: 120 average time/residue: 0.1846 time to fit residues: 38.2553 Evaluate side-chains 117 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1085 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 560 MET Chi-restraints excluded: chain F residue 585 VAL Chi-restraints excluded: chain F residue 877 THR Chi-restraints excluded: chain F residue 929 MET Chi-restraints excluded: chain G residue 431 HIS Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 570 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 338 optimal weight: 0.7980 chunk 343 optimal weight: 0.0000 chunk 42 optimal weight: 2.9990 chunk 299 optimal weight: 0.9980 chunk 284 optimal weight: 4.9990 chunk 231 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 164 optimal weight: 0.5980 chunk 165 optimal weight: 0.9990 chunk 252 optimal weight: 1.9990 chunk 324 optimal weight: 0.5980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.075115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.051925 restraints weight = 128856.138| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 4.30 r_work: 0.2918 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 30074 Z= 0.088 Angle : 0.467 11.620 40816 Z= 0.237 Chirality : 0.039 0.171 4540 Planarity : 0.003 0.056 5197 Dihedral : 7.490 84.711 4108 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.61 % Rotamer: Outliers : 0.83 % Allowed : 13.12 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.15), residues: 3604 helix: 2.64 (0.15), residues: 1213 sheet: 0.60 (0.21), residues: 665 loop : -0.31 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 447 TYR 0.015 0.001 TYR D 383 PHE 0.026 0.001 PHE A 22 TRP 0.012 0.001 TRP D 240 HIS 0.002 0.000 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.09 (30074) covalent geometry : angle 0.46702 / 0.24 (40816) hydrogen bonds : bond 0.02999 / 2.01 ( 1195) hydrogen bonds : angle 4.14339 / 2.90 ( 3426) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7625.05 seconds wall clock time: 131 minutes 25.90 seconds (7885.90 seconds total)