Starting phenix.real_space_refine on Thu Mar 21 05:47:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d0b_27104/03_2024/8d0b_27104.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d0b_27104/03_2024/8d0b_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d0b_27104/03_2024/8d0b_27104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d0b_27104/03_2024/8d0b_27104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d0b_27104/03_2024/8d0b_27104.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d0b_27104/03_2024/8d0b_27104.pdb" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.021 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 Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 51": "OD1" <-> "OD2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 244": "OE1" <-> "OE2" Residue "F PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 14.96, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.49 Conformation dependent library (CDL) restraints added in 5.3 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: 3.66 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: 12.00 Time building geometry restraints manager: 11.52 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=" CB GLU C 118 " pdb=" CG GLU C 118 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.24e+00 bond pdb=" C ASP A 952 " pdb=" N PRO A 953 " ideal model delta sigma weight residual 1.334 1.361 -0.027 1.51e-02 4.39e+03 3.18e+00 bond pdb=" C PRO A 956 " pdb=" N PRO A 957 " ideal model delta sigma weight residual 1.331 1.347 -0.016 1.27e-02 6.20e+03 1.50e+00 bond pdb=" CA SER E 170 " pdb=" CB SER E 170 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.24e+00 bond pdb=" CG GLU B 210 " pdb=" CD GLU B 210 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 1.01e+00 ... (remaining 30069 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.39: 787 105.39 - 112.55: 15623 112.55 - 119.70: 9846 119.70 - 126.86: 14078 126.86 - 134.02: 482 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=" CA GLU C 118 " pdb=" CB GLU C 118 " pdb=" CG GLU C 118 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CA MET A 828 " pdb=" CB MET A 828 " pdb=" CG MET A 828 " ideal model delta sigma weight residual 114.10 121.57 -7.47 2.00e+00 2.50e-01 1.40e+01 angle pdb=" CA LEU B 187 " pdb=" C LEU B 187 " pdb=" N GLU B 188 " ideal model delta sigma weight residual 119.52 116.67 2.85 7.90e-01 1.60e+00 1.30e+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: 3304 0.036 - 0.072: 855 0.072 - 0.108: 293 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 2.520 nonbonded pdb=" OH TYR D 279 " pdb=" OD2 ASP D 286 " model vdw 2.238 2.440 nonbonded pdb=" OH TYR D 26 " pdb=" OG SER D 319 " model vdw 2.243 2.440 nonbonded pdb=" OH TYR A 358 " pdb=" OD2 ASP A 376 " model vdw 2.256 2.440 nonbonded pdb=" NE2 GLN D 25 " pdb=" OE1 GLU D 396 " model vdw 2.268 2.520 ... (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 ========== 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: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.710 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 75.690 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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= 0.128 Angle : 0.483 10.763 40816 Z= 0.250 Chirality : 0.039 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 : 5.43 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (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 TRP 0.018 0.001 TRP A 50 HIS 0.003 0.000 HIS D 252 PHE 0.016 0.001 PHE B 215 TYR 0.018 0.001 TYR F1055 ARG 0.002 0.000 ARG B 139 *********************** 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 fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 3.506 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: 0.3921 time to fit residues: 63.1283 Evaluate side-chains 87 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 3.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 2.9990 chunk 273 optimal weight: 5.9990 chunk 151 optimal weight: 0.0270 chunk 93 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 chunk 282 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 327 optimal weight: 4.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN C 81 HIS F 475 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.0552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30074 Z= 0.199 Angle : 0.488 8.577 40816 Z= 0.254 Chirality : 0.040 0.143 4540 Planarity : 0.004 0.057 5197 Dihedral : 7.524 88.104 4108 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 0.80 % Allowed : 10.67 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.15), residues: 3604 helix: 2.50 (0.16), residues: 1210 sheet: 0.59 (0.21), residues: 676 loop : -0.34 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 50 HIS 0.003 0.000 HIS E 103 PHE 0.015 0.001 PHE E 42 TYR 0.015 0.001 TYR D 279 ARG 0.003 0.000 ARG C 85 *********************** 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 115 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 89 time to evaluate : 3.549 Fit side-chains revert: symmetry clash REVERT: F 731 MET cc_start: 0.8721 (mmm) cc_final: 0.8347 (mmm) REVERT: F 929 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7567 (mtp) REVERT: F 990 MET cc_start: 0.8817 (ttt) cc_final: 0.8471 (ttt) REVERT: F 994 MET cc_start: 0.8710 (ptt) cc_final: 0.8355 (ptp) outliers start: 26 outliers final: 9 residues processed: 112 average time/residue: 0.3838 time to fit residues: 73.9540 Evaluate side-chains 97 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 4.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 1042 VAL 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 E residue 195 PHE Chi-restraints excluded: chain F residue 929 MET Chi-restraints excluded: chain G residue 166 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 182 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 272 optimal weight: 0.2980 chunk 223 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 328 optimal weight: 2.9990 chunk 354 optimal weight: 4.9990 chunk 292 optimal weight: 0.7980 chunk 325 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 263 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN C 81 HIS F 737 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.0714 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= 0.131 Angle : 0.452 8.446 40816 Z= 0.233 Chirality : 0.039 0.143 4540 Planarity : 0.003 0.058 5197 Dihedral : 7.478 89.344 4108 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.14 % Favored : 96.84 % Rotamer: Outliers : 0.86 % Allowed : 11.01 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.15), residues: 3604 helix: 2.54 (0.16), residues: 1213 sheet: 0.67 (0.21), residues: 674 loop : -0.33 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 50 HIS 0.002 0.000 HIS A 812 PHE 0.022 0.001 PHE A 22 TYR 0.016 0.001 TYR D 383 ARG 0.002 0.000 ARG C 85 *********************** 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 117 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 89 time to evaluate : 3.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8403 (m) REVERT: F 731 MET cc_start: 0.8672 (mmm) cc_final: 0.8316 (mmm) REVERT: F 929 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7596 (mtp) outliers start: 28 outliers final: 12 residues processed: 113 average time/residue: 0.3844 time to fit residues: 75.4522 Evaluate side-chains 101 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 3.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 457 VAL 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 1085 VAL 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 Chi-restraints excluded: chain G residue 472 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 324 optimal weight: 8.9990 chunk 246 optimal weight: 0.9990 chunk 170 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 220 optimal weight: 0.6980 chunk 329 optimal weight: 7.9990 chunk 348 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 312 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 HIS ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 30074 Z= 0.171 Angle : 0.459 7.661 40816 Z= 0.235 Chirality : 0.039 0.140 4540 Planarity : 0.003 0.057 5197 Dihedral : 7.481 89.362 4108 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 0.98 % Allowed : 11.28 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.15), residues: 3604 helix: 2.55 (0.16), residues: 1219 sheet: 0.59 (0.21), residues: 670 loop : -0.34 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 50 HIS 0.003 0.000 HIS A 533 PHE 0.018 0.001 PHE B 215 TYR 0.016 0.001 TYR D 383 ARG 0.002 0.000 ARG C 85 *********************** 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 121 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 89 time to evaluate : 3.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8424 (tt) REVERT: A 399 VAL cc_start: 0.8787 (OUTLIER) cc_final: 0.8415 (m) REVERT: C 106 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7712 (mt-10) REVERT: D 371 GLU cc_start: -0.1908 (OUTLIER) cc_final: -0.2260 (pt0) REVERT: F 394 MET cc_start: 0.7808 (tpt) cc_final: 0.7432 (tpp) REVERT: F 731 MET cc_start: 0.8691 (mmm) cc_final: 0.8076 (mmm) REVERT: F 929 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7622 (mtp) outliers start: 32 outliers final: 20 residues processed: 117 average time/residue: 0.3975 time to fit residues: 81.0110 Evaluate side-chains 110 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 3.743 ------------------------------------------------------------------------------- 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 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 1064 THR Chi-restraints excluded: chain A residue 1085 VAL 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 100 MET Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain F residue 326 SER 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 221 THR Chi-restraints excluded: chain G residue 472 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 290 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 5 optimal weight: 30.0000 chunk 259 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 297 optimal weight: 10.0000 chunk 241 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 178 optimal weight: 0.6980 chunk 313 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 404 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 30074 Z= 0.298 Angle : 0.512 8.710 40816 Z= 0.262 Chirality : 0.041 0.141 4540 Planarity : 0.004 0.057 5197 Dihedral : 7.585 88.200 4108 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.55 % Favored : 95.39 % Rotamer: Outliers : 1.17 % Allowed : 12.05 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.15), residues: 3604 helix: 2.49 (0.16), residues: 1220 sheet: 0.44 (0.21), residues: 664 loop : -0.43 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 13 HIS 0.005 0.001 HIS E 103 PHE 0.016 0.001 PHE E 42 TYR 0.016 0.001 TYR D 383 ARG 0.003 0.000 ARG E 245 *********************** 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 126 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 88 time to evaluate : 3.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8535 (tt) REVERT: B 20 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8177 (m-30) REVERT: C 106 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7729 (mt-10) REVERT: F 394 MET cc_start: 0.7779 (tpt) cc_final: 0.7483 (tpp) REVERT: F 756 MET cc_start: 0.9026 (tmm) cc_final: 0.8805 (tmm) REVERT: F 929 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7625 (mtp) outliers start: 38 outliers final: 24 residues processed: 122 average time/residue: 0.3877 time to fit residues: 81.3040 Evaluate side-chains 114 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 3.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 457 VAL 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 1064 THR Chi-restraints excluded: chain A residue 1085 VAL Chi-restraints excluded: chain B residue 20 ASP 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 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 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 326 SER 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 166 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 117 optimal weight: 1.9990 chunk 314 optimal weight: 0.8980 chunk 68 optimal weight: 0.0870 chunk 204 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 349 optimal weight: 8.9990 chunk 289 optimal weight: 30.0000 chunk 161 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN C 81 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.0984 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= 0.152 Angle : 0.463 8.937 40816 Z= 0.237 Chirality : 0.039 0.147 4540 Planarity : 0.003 0.057 5197 Dihedral : 7.508 89.154 4108 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.23 % Rotamer: Outliers : 1.07 % Allowed : 12.39 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.15), residues: 3604 helix: 2.55 (0.16), residues: 1218 sheet: 0.54 (0.21), residues: 669 loop : -0.39 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 50 HIS 0.003 0.000 HIS E 103 PHE 0.018 0.001 PHE B 215 TYR 0.015 0.001 TYR D 383 ARG 0.002 0.000 ARG C 85 *********************** 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 124 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 89 time to evaluate : 3.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8535 (tt) REVERT: A 399 VAL cc_start: 0.8762 (OUTLIER) cc_final: 0.8398 (m) REVERT: B 20 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8170 (m-30) REVERT: C 106 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7645 (mt-10) REVERT: F 394 MET cc_start: 0.7679 (tpt) cc_final: 0.7429 (tpp) REVERT: F 756 MET cc_start: 0.9015 (tmm) cc_final: 0.8810 (tmm) REVERT: F 929 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7746 (ttm) REVERT: F 985 MET cc_start: 0.8882 (mmm) cc_final: 0.8405 (mpp) outliers start: 35 outliers final: 27 residues processed: 120 average time/residue: 0.3891 time to fit residues: 80.7144 Evaluate side-chains 118 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 87 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR 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 854 VAL Chi-restraints excluded: chain A residue 856 ASP 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 1064 THR Chi-restraints excluded: chain A residue 1085 VAL Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 60 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 100 MET Chi-restraints excluded: chain C residue 110 ARG 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 326 SER 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 166 ASN Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 567 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 336 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 chunk 255 optimal weight: 8.9990 chunk 197 optimal weight: 8.9990 chunk 294 optimal weight: 10.0000 chunk 195 optimal weight: 20.0000 chunk 347 optimal weight: 1.9990 chunk 217 optimal weight: 0.0870 chunk 212 optimal weight: 0.0870 chunk 160 optimal weight: 3.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1024 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= 0.159 Angle : 0.461 8.320 40816 Z= 0.235 Chirality : 0.039 0.156 4540 Planarity : 0.003 0.057 5197 Dihedral : 7.486 89.759 4108 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.94 % Favored : 96.03 % Rotamer: Outliers : 1.29 % Allowed : 12.45 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.15), residues: 3604 helix: 2.59 (0.16), residues: 1218 sheet: 0.52 (0.21), residues: 671 loop : -0.38 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 50 HIS 0.003 0.000 HIS E 103 PHE 0.024 0.001 PHE A 22 TYR 0.015 0.001 TYR D 383 ARG 0.002 0.000 ARG C 85 *********************** 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 133 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 91 time to evaluate : 4.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8484 (tt) REVERT: A 399 VAL cc_start: 0.8750 (OUTLIER) cc_final: 0.8378 (m) REVERT: B 20 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8164 (m-30) REVERT: F 394 MET cc_start: 0.7642 (tpt) cc_final: 0.7389 (tpp) REVERT: F 756 MET cc_start: 0.9019 (tmm) cc_final: 0.8810 (tmm) REVERT: F 929 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7729 (ttm) REVERT: F 985 MET cc_start: 0.8936 (mmm) cc_final: 0.8459 (mpp) outliers start: 42 outliers final: 31 residues processed: 129 average time/residue: 0.3676 time to fit residues: 82.0275 Evaluate side-chains 123 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 88 time to evaluate : 3.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR 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 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 1046 CYS Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1085 VAL Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 160 TRP Chi-restraints excluded: chain B residue 210 GLU 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 E residue 50 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 560 MET Chi-restraints excluded: chain F residue 571 ASP 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 166 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 215 optimal weight: 0.0170 chunk 138 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 104 optimal weight: 0.0060 chunk 68 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 237 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1076 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= 0.155 Angle : 0.463 10.108 40816 Z= 0.236 Chirality : 0.039 0.162 4540 Planarity : 0.003 0.057 5197 Dihedral : 7.473 89.925 4108 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.34 % Rotamer: Outliers : 1.17 % Allowed : 12.66 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.15), residues: 3604 helix: 2.62 (0.16), residues: 1212 sheet: 0.52 (0.21), residues: 669 loop : -0.36 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 50 HIS 0.002 0.000 HIS E 103 PHE 0.032 0.001 PHE A 22 TYR 0.015 0.001 TYR D 383 ARG 0.003 0.000 ARG C 85 *********************** 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 130 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 92 time to evaluate : 3.451 Fit side-chains revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8461 (tt) REVERT: A 399 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8276 (m) REVERT: B 20 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8155 (m-30) REVERT: F 394 MET cc_start: 0.7637 (tpt) cc_final: 0.7435 (tpp) REVERT: F 756 MET cc_start: 0.9012 (tmm) cc_final: 0.8798 (tmm) REVERT: F 929 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7717 (ttm) REVERT: F 985 MET cc_start: 0.8940 (mmm) cc_final: 0.8451 (mpp) outliers start: 38 outliers final: 30 residues processed: 125 average time/residue: 0.3915 time to fit residues: 83.8094 Evaluate side-chains 123 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 89 time to evaluate : 3.646 ------------------------------------------------------------------------------- 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 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 1046 CYS Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1085 VAL Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 160 TRP 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 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 326 SER Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 560 MET Chi-restraints excluded: chain F residue 571 ASP 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 316 optimal weight: 8.9990 chunk 333 optimal weight: 3.9990 chunk 304 optimal weight: 0.3980 chunk 324 optimal weight: 6.9990 chunk 195 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 254 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 306 optimal weight: 0.0270 chunk 323 optimal weight: 1.9990 overall best weight: 1.4844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30074 Z= 0.202 Angle : 0.481 9.939 40816 Z= 0.244 Chirality : 0.039 0.156 4540 Planarity : 0.003 0.057 5197 Dihedral : 7.499 89.640 4108 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.89 % Rotamer: Outliers : 1.20 % Allowed : 13.00 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.15), residues: 3604 helix: 2.61 (0.16), residues: 1212 sheet: 0.47 (0.21), residues: 670 loop : -0.37 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 50 HIS 0.003 0.000 HIS E 103 PHE 0.031 0.001 PHE A 22 TYR 0.015 0.001 TYR D 383 ARG 0.003 0.000 ARG C 85 *********************** 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 128 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 89 time to evaluate : 3.531 Fit side-chains revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8498 (tt) REVERT: A 399 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8328 (m) REVERT: B 20 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8179 (m-30) REVERT: F 756 MET cc_start: 0.9033 (tmm) cc_final: 0.8808 (tmm) REVERT: F 929 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7718 (ttm) REVERT: F 985 MET cc_start: 0.8942 (mmm) cc_final: 0.8446 (mpp) outliers start: 39 outliers final: 30 residues processed: 123 average time/residue: 0.3830 time to fit residues: 81.2503 Evaluate side-chains 123 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 89 time to evaluate : 3.433 ------------------------------------------------------------------------------- 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 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 1046 CYS Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1085 VAL Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 160 TRP 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 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 326 SER Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 560 MET Chi-restraints excluded: chain F residue 571 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 212 optimal weight: 0.4980 chunk 342 optimal weight: 8.9990 chunk 209 optimal weight: 0.8980 chunk 162 optimal weight: 0.0030 chunk 238 optimal weight: 0.2980 chunk 359 optimal weight: 2.9990 chunk 331 optimal weight: 7.9990 chunk 286 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 221 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1153 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= 0.123 Angle : 0.465 10.487 40816 Z= 0.234 Chirality : 0.039 0.177 4540 Planarity : 0.003 0.056 5197 Dihedral : 7.421 89.336 4108 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.70 % Rotamer: Outliers : 0.86 % Allowed : 13.16 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.15), residues: 3604 helix: 2.64 (0.15), residues: 1215 sheet: 0.60 (0.21), residues: 671 loop : -0.31 (0.16), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 240 HIS 0.002 0.000 HIS A 407 PHE 0.030 0.001 PHE A 22 TYR 0.015 0.001 TYR D 383 ARG 0.003 0.000 ARG G 447 ********************** 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 118 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 3.689 Fit side-chains REVERT: A 142 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8484 (tt) REVERT: A 399 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8245 (m) REVERT: B 20 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8183 (m-30) REVERT: D 244 LEU cc_start: 0.9052 (mt) cc_final: 0.8814 (mp) REVERT: F 756 MET cc_start: 0.8998 (tmm) cc_final: 0.8741 (tmm) REVERT: F 929 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7682 (ttm) REVERT: F 985 MET cc_start: 0.8917 (mmm) cc_final: 0.8410 (mpp) outliers start: 28 outliers final: 21 residues processed: 114 average time/residue: 0.4041 time to fit residues: 80.7842 Evaluate side-chains 114 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 3.479 ------------------------------------------------------------------------------- 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 868 ILE Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1005 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 20 ASP Chi-restraints excluded: chain B residue 160 TRP 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 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 326 SER Chi-restraints excluded: chain F residue 529 ILE Chi-restraints excluded: chain F residue 560 MET Chi-restraints excluded: chain F residue 571 ASP 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 472 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 227 optimal weight: 4.9990 chunk 305 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 chunk 42 optimal weight: 0.1980 chunk 79 optimal weight: 3.9990 chunk 286 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 294 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.073865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.050500 restraints weight = 129889.087| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 4.28 r_work: 0.2872 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30074 Z= 0.263 Angle : 0.513 12.169 40816 Z= 0.259 Chirality : 0.040 0.152 4540 Planarity : 0.004 0.057 5197 Dihedral : 7.519 89.291 4108 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.34 % Rotamer: Outliers : 0.95 % Allowed : 13.03 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.15), residues: 3604 helix: 2.59 (0.16), residues: 1220 sheet: 0.45 (0.21), residues: 676 loop : -0.38 (0.16), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 132 HIS 0.004 0.001 HIS A1030 PHE 0.032 0.001 PHE A 22 TYR 0.015 0.001 TYR D 383 ARG 0.003 0.000 ARG B 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4990.25 seconds wall clock time: 92 minutes 12.38 seconds (5532.38 seconds total)