Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 14 00:45:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d0b_27104/07_2023/8d0b_27104.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d0b_27104/07_2023/8d0b_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_27104/07_2023/8d0b_27104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d0b_27104/07_2023/8d0b_27104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d0b_27104/07_2023/8d0b_27104.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d0b_27104/07_2023/8d0b_27104.pdb" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 13.72, per 1000 atoms: 0.47 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: 11.67 Conformation dependent library (CDL) restraints added in 4.2 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: 2.36 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: 13.77 Time building geometry restraints manager: 12.58 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: 16059 17.94 - 35.88: 1766 35.88 - 53.82: 377 53.82 - 71.75: 59 71.75 - 89.69: 26 Dihedral angle restraints: 18287 sinusoidal: 7640 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 18284 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: 3.420 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: 16.270 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 74.510 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.860 ------------------------------------------------------------------------------- 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 : 15.417 89.693 11387 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 % 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 *********************** 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 : 3.570 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 93 average time/residue: 0.4098 time to fit residues: 66.5060 Evaluate side-chains 87 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 3.864 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8732 ------------------------------------------------------------------------------- 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: 6.9990 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: 1.6046 ------------------------------------------------------------------------------- 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: 0.8057 moved from start: 0.0553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 30074 Z= 0.218 Angle : 0.494 8.714 40816 Z= 0.257 Chirality : 0.040 0.146 4540 Planarity : 0.004 0.057 5197 Dihedral : 7.436 87.892 4096 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.97 % Favored : 95.98 % Rotamer Outliers : 0.83 % 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: 2.50 (0.16), residues: 1209 sheet: 0.59 (0.21), residues: 677 loop : -0.36 (0.15), residues: 1718 *********************** 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 116 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 89 time to evaluate : 3.758 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 113 average time/residue: 0.4138 time to fit residues: 80.8746 Evaluate side-chains 98 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 3.556 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3707 time to fit residues: 12.1431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 272 optimal weight: 0.0470 chunk 223 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 328 optimal weight: 4.9990 chunk 354 optimal weight: 3.9990 chunk 292 optimal weight: 4.9990 chunk 325 optimal weight: 0.6980 chunk 111 optimal weight: 8.9990 chunk 263 optimal weight: 0.6980 overall best weight: 0.6680 ------------------------------------------------------------------------------- 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** C 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.0678 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= 0.128 Angle : 0.456 8.405 40816 Z= 0.236 Chirality : 0.039 0.148 4540 Planarity : 0.003 0.058 5197 Dihedral : 7.390 88.831 4096 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.25 % Favored : 96.73 % Rotamer Outliers : 0.58 % 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: 1.25 (0.15), residues: 3604 helix: 2.53 (0.16), residues: 1213 sheet: 0.64 (0.21), residues: 663 loop : -0.32 (0.15), residues: 1728 *********************** 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 108 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 3.776 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 107 average time/residue: 0.3910 time to fit residues: 73.6434 Evaluate side-chains 93 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 3.687 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2702 time to fit residues: 7.7386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 324 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 170 optimal weight: 0.0870 chunk 36 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 329 optimal weight: 7.9990 chunk 348 optimal weight: 6.9990 chunk 172 optimal weight: 0.6980 chunk 312 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 HIS ** 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** F 737 GLN G 404 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 30074 Z= 0.277 Angle : 0.510 8.498 40816 Z= 0.261 Chirality : 0.041 0.142 4540 Planarity : 0.004 0.058 5197 Dihedral : 7.487 87.547 4096 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.63 % Favored : 95.31 % Rotamer Outliers : 0.61 % 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: 1206 sheet: 0.47 (0.21), residues: 660 loop : -0.41 (0.15), residues: 1738 *********************** 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 108 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 4.508 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 105 average time/residue: 0.4119 time to fit residues: 76.7659 Evaluate side-chains 96 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 3.587 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2769 time to fit residues: 9.4594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 290 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 chunk 5 optimal weight: 30.0000 chunk 259 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 297 optimal weight: 8.9990 chunk 241 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 178 optimal weight: 0.0770 chunk 313 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 overall best weight: 2.5544 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 30074 Z= 0.324 Angle : 0.529 8.903 40816 Z= 0.271 Chirality : 0.041 0.143 4540 Planarity : 0.004 0.059 5197 Dihedral : 7.552 87.252 4096 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Rotamer Outliers : 0.95 % 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: 0.97 (0.15), residues: 3604 helix: 2.37 (0.16), residues: 1224 sheet: 0.35 (0.21), residues: 665 loop : -0.50 (0.15), residues: 1715 *********************** 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 122 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 91 time to evaluate : 3.616 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 17 residues processed: 122 average time/residue: 0.4053 time to fit residues: 86.3208 Evaluate side-chains 104 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 3.523 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2914 time to fit residues: 14.0550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 117 optimal weight: 0.8980 chunk 314 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 204 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 349 optimal weight: 10.0000 chunk 289 optimal weight: 50.0000 chunk 161 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 183 optimal weight: 9.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** C 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 30074 Z= 0.318 Angle : 0.533 8.798 40816 Z= 0.273 Chirality : 0.041 0.175 4540 Planarity : 0.004 0.059 5197 Dihedral : 7.582 87.394 4096 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.02 % Favored : 94.92 % Rotamer Outliers : 0.46 % 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: 0.92 (0.15), residues: 3604 helix: 2.39 (0.16), residues: 1212 sheet: 0.28 (0.21), residues: 665 loop : -0.55 (0.15), residues: 1727 *********************** 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 101 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 3.454 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 98 average time/residue: 0.4001 time to fit residues: 68.7040 Evaluate side-chains 92 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 3.313 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2922 time to fit residues: 8.1934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 336 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 199 optimal weight: 0.9980 chunk 255 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 294 optimal weight: 10.0000 chunk 195 optimal weight: 3.9990 chunk 347 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 212 optimal weight: 0.9980 chunk 160 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8053 moved from start: 0.1075 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= 0.158 Angle : 0.480 9.826 40816 Z= 0.246 Chirality : 0.040 0.156 4540 Planarity : 0.004 0.059 5197 Dihedral : 7.490 88.396 4096 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer Outliers : 0.37 % 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: 1.06 (0.15), residues: 3604 helix: 2.45 (0.16), residues: 1224 sheet: 0.44 (0.21), residues: 651 loop : -0.47 (0.15), residues: 1729 *********************** 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 101 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 3.538 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 99 average time/residue: 0.4105 time to fit residues: 71.3669 Evaluate side-chains 90 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 3.679 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2856 time to fit residues: 6.7271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 215 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 chunk 68 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 221 optimal weight: 0.9980 chunk 237 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.8056 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 30074 Z= 0.186 Angle : 0.491 9.689 40816 Z= 0.249 Chirality : 0.040 0.158 4540 Planarity : 0.004 0.059 5197 Dihedral : 7.471 88.711 4096 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.22 % Favored : 95.75 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z (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: 1.05 (0.15), residues: 3604 helix: 2.44 (0.16), residues: 1225 sheet: 0.39 (0.21), residues: 649 loop : -0.45 (0.15), residues: 1730 *********************** 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 101 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 3.358 Fit side-chains outliers start: 13 outliers final: 3 residues processed: 98 average time/residue: 0.4151 time to fit residues: 70.6559 Evaluate side-chains 90 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 3.632 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3046 time to fit residues: 7.4890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 316 optimal weight: 6.9990 chunk 333 optimal weight: 0.0470 chunk 304 optimal weight: 0.0470 chunk 324 optimal weight: 7.9990 chunk 195 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 254 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 292 optimal weight: 30.0000 chunk 306 optimal weight: 0.1980 chunk 323 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 66 HIS F 505 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 30074 Z= 0.119 Angle : 0.476 11.421 40816 Z= 0.242 Chirality : 0.039 0.174 4540 Planarity : 0.003 0.058 5197 Dihedral : 7.403 89.556 4096 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.52 % Favored : 96.45 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z (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: 1.15 (0.15), residues: 3604 helix: 2.47 (0.15), residues: 1223 sheet: 0.54 (0.21), residues: 660 loop : -0.40 (0.16), residues: 1721 *********************** 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 91 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 3.558 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 89 average time/residue: 0.4386 time to fit residues: 68.4026 Evaluate side-chains 88 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 3.406 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 212 optimal weight: 0.7980 chunk 342 optimal weight: 10.0000 chunk 209 optimal weight: 0.9980 chunk 162 optimal weight: 0.5980 chunk 238 optimal weight: 0.0470 chunk 359 optimal weight: 0.0470 chunk 331 optimal weight: 7.9990 chunk 286 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 221 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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: 0.8020 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 30074 Z= 0.121 Angle : 0.471 10.938 40816 Z= 0.238 Chirality : 0.039 0.179 4540 Planarity : 0.003 0.057 5197 Dihedral : 7.343 89.856 4096 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z (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: 1.22 (0.15), residues: 3604 helix: 2.55 (0.15), residues: 1224 sheet: 0.60 (0.21), residues: 657 loop : -0.38 (0.15), residues: 1723 ********************** 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 92 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 3.565 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 92 average time/residue: 0.4322 time to fit residues: 69.9252 Evaluate side-chains 89 residues out of total 3261 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 3.541 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 87 optimal weight: 1.9990 chunk 264 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 286 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 294 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- 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** C 66 HIS F 727 ASN F 737 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.073547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.050258 restraints weight = 130673.926| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 4.62 r_work: 0.2846 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 30074 Z= 0.364 Angle : 0.555 14.305 40816 Z= 0.281 Chirality : 0.041 0.207 4540 Planarity : 0.004 0.059 5197 Dihedral : 7.486 88.220 4096 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.77 % Favored : 95.17 % Rotamer Outliers : 0.09 % 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: 1.08 (0.15), residues: 3604 helix: 2.48 (0.16), residues: 1220 sheet: 0.42 (0.21), residues: 663 loop : -0.45 (0.15), residues: 1721 =============================================================================== Job complete usr+sys time: 4550.96 seconds wall clock time: 85 minutes 14.91 seconds (5114.91 seconds total)