Starting phenix.real_space_refine on Mon Sep 14 14:35:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d0k_27107/09_2026/8d0k_27107.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d0k_27107/09_2026/8d0k_27107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d0k_27107/09_2026/8d0k_27107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d0k_27107/09_2026/8d0k_27107.map" model { file = "/net/cci-nas-00/data/ceres_data/8d0k_27107/09_2026/8d0k_27107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d0k_27107/09_2026/8d0k_27107.cif" } resolution = 4.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.040 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 20 5.49 5 S 162 5.16 5 C 19741 2.51 5 N 5333 2.21 5 O 5755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31011 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: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3535 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 20, 'TRANS': 410} Chain breaks: 1 Chain: "F" Number of atoms: 7388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7388 Classifications: {'peptide': 915} 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: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 422 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Time building chain proxies: 6.21, per 1000 atoms: 0.20 Number of scatterers: 31011 At special positions: 0 Unit cell: (121, 167.2, 240.9, 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 162 16.00 P 20 15.00 O 5755 8.00 N 5333 7.00 C 19741 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.4 seconds 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7246 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 41 sheets defined 39.2% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 9 through 27 removed outlier: 3.629A pdb=" N GLN A 13 " --> pdb=" O PRO A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 53 removed outlier: 4.052A 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 99 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 216 through 219 removed outlier: 3.866A pdb=" N LEU A 219 " --> pdb=" O ARG A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 265 through 274 removed outlier: 4.535A 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 458 removed outlier: 3.960A 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 removed outlier: 3.525A pdb=" N GLN A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) Proline residue: A 509 - end of helix removed outlier: 3.985A pdb=" N LEU A 513 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 551 through 566 removed outlier: 3.613A pdb=" N SER A 566 " --> pdb=" O LYS A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 573 removed outlier: 3.620A pdb=" N LEU A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 582 through 591 Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'A' and resid 672 through 676 removed outlier: 4.004A pdb=" N SER A 676 " --> pdb=" O LYS A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 811 removed outlier: 4.182A pdb=" N VAL A 805 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG A 806 " --> pdb=" O SER A 803 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU A 809 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 811 " --> pdb=" O PHE A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 873 Processing helix chain 'A' and resid 882 through 888 Processing helix chain 'A' and resid 1013 through 1017 Processing helix chain 'A' and resid 1090 through 1097 removed outlier: 4.262A 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 1147 removed outlier: 3.703A pdb=" N THR A1147 " --> pdb=" O TRP A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 20 removed outlier: 3.507A pdb=" N TRP B 17 " --> pdb=" O SER B 14 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLY B 18 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 19 " --> pdb=" O LEU B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 37 Processing helix chain 'B' and resid 103 through 125 Processing helix chain 'B' and resid 161 through 177 Proline residue: B 171 - end of helix Processing helix chain 'B' and resid 200 through 219 removed outlier: 3.710A pdb=" N GLU B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 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 277 Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 311 through 314 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 17 removed outlier: 3.696A pdb=" N VAL C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 120 removed outlier: 3.852A pdb=" N LEU C 105 " --> pdb=" O ASN C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 123 No H-bonds generated for 'chain 'C' and resid 121 through 123' Processing helix chain 'D' and resid 8 through 20 removed outlier: 4.076A pdb=" N LEU D 12 " --> pdb=" O GLU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 32 removed outlier: 3.606A pdb=" N TYR D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 35 No H-bonds generated for 'chain 'D' and resid 33 through 35' 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 94 removed outlier: 5.551A pdb=" N ASN D 92 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL D 94 " --> pdb=" O HIS D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 116 removed outlier: 3.578A pdb=" N ASP D 116 " --> pdb=" O THR D 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 113 through 116' Processing helix chain 'D' and resid 128 through 130 No H-bonds generated for 'chain 'D' and resid 128 through 130' Processing helix chain 'D' and resid 131 through 149 removed outlier: 4.215A pdb=" N MET D 135 " --> pdb=" O CYS D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 190 removed outlier: 3.645A pdb=" N ARG D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 230 removed outlier: 4.800A pdb=" N LYS D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TYR D 222 " --> pdb=" O ILE D 218 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU D 224 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLU D 225 " --> pdb=" O LYS D 221 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR D 226 " --> pdb=" O TYR D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 244 removed outlier: 3.539A 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 282 Processing helix chain 'D' and resid 291 through 302 Processing helix chain 'D' and resid 306 through 312 removed outlier: 4.164A pdb=" N SER D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY D 312 " --> pdb=" O ASN D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 342 Processing helix chain 'D' and resid 343 through 347 removed outlier: 3.621A pdb=" N VAL D 347 " --> pdb=" O PRO D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 368 removed outlier: 4.099A 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 169 Processing helix chain 'E' and resid 191 through 197 removed outlier: 3.759A pdb=" N GLY E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 235 Processing helix chain 'E' and resid 236 through 241 removed outlier: 4.031A pdb=" N ALA E 239 " --> pdb=" O SER E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 254 Processing helix chain 'E' and resid 275 through 284 removed outlier: 3.668A pdb=" N PHE E 284 " --> pdb=" O SER E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 299 removed outlier: 3.960A pdb=" N GLN E 290 " --> pdb=" O PRO E 286 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU E 291 " --> pdb=" O CYS E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 316 removed outlier: 3.670A pdb=" N GLN E 308 " --> pdb=" O GLY E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'E' and resid 337 through 344 Processing helix chain 'E' and resid 344 through 353 removed outlier: 3.874A pdb=" N HIS E 351 " --> pdb=" O TYR E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 372 Processing helix chain 'E' and resid 390 through 401 Processing helix chain 'E' and resid 404 through 417 Processing helix chain 'E' and resid 419 through 433 Processing helix chain 'E' and resid 443 through 455 Processing helix chain 'F' and resid 409 through 426 removed outlier: 4.137A pdb=" N ALA F 422 " --> pdb=" O ASP F 418 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N THR F 423 " --> pdb=" O GLU F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 490 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 Processing helix chain 'F' and resid 678 through 685 Processing helix chain 'F' and resid 693 through 701 Processing helix chain 'F' and resid 707 through 716 Processing helix chain 'F' and resid 724 through 732 removed outlier: 4.009A pdb=" N ASN F 730 " --> pdb=" O GLU F 726 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR F 732 " --> pdb=" O ILE F 728 " (cutoff:3.500A) Processing helix chain 'F' and resid 734 through 760 Processing helix chain 'F' and resid 760 through 773 Processing helix chain 'F' and resid 775 through 781 removed outlier: 3.643A pdb=" N THR F 779 " --> pdb=" O ILE F 775 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU F 780 " --> pdb=" O MET F 776 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET F 781 " --> pdb=" O SER F 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 775 through 781' Processing helix chain 'F' and resid 783 through 798 Processing helix chain 'F' and resid 863 through 873 Processing helix chain 'F' and resid 910 through 929 Processing helix chain 'F' and resid 935 through 962 removed outlier: 4.072A pdb=" N TYR F 957 " --> pdb=" O ALA F 953 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY F 958 " --> pdb=" O ASN F 954 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU F 960 " --> pdb=" O MET F 956 " (cutoff:3.500A) Processing helix chain 'F' and resid 969 through 993 Processing helix chain 'F' and resid 1014 through 1031 removed outlier: 3.522A pdb=" N VAL F1018 " --> pdb=" O ASN F1014 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS F1031 " --> pdb=" O SER F1027 " (cutoff:3.500A) Processing helix chain 'F' and resid 1268 through 1273 Processing helix chain 'F' and resid 1299 through 1303 Processing helix chain 'F' and resid 1318 through 1321 Processing helix chain 'F' and resid 1322 through 1342 removed outlier: 3.569A pdb=" N MET F1332 " --> pdb=" O ASN F1328 " (cutoff:3.500A) Processing helix chain 'F' and resid 1384 through 1398 removed outlier: 3.596A pdb=" N LEU F1388 " --> pdb=" O SER F1384 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE F1398 " --> pdb=" O PHE F1394 " (cutoff:3.500A) Processing helix chain 'F' and resid 1400 through 1408 Processing helix chain 'F' and resid 1410 through 1421 Processing helix chain 'F' and resid 1423 through 1443 removed outlier: 3.797A pdb=" N THR F1436 " --> pdb=" O LYS F1432 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA F1437 " --> pdb=" O LEU F1433 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE F1440 " --> pdb=" O THR F1436 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU F1441 " --> pdb=" O ALA F1437 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG F1443 " --> pdb=" O GLN F1439 " (cutoff:3.500A) Processing helix chain 'F' and resid 1444 through 1448 removed outlier: 3.938A pdb=" N SER F1447 " --> pdb=" O SER F1444 " (cutoff:3.500A) Processing helix chain 'F' and resid 1451 through 1455 removed outlier: 3.584A pdb=" N PHE F1455 " --> pdb=" O LEU F1451 " (cutoff:3.500A) No H-bonds generated for '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: 4.282A pdb=" N ASN G 162 " --> pdb=" O SER G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 236 Processing helix chain 'G' and resid 331 through 337 removed outlier: 3.659A pdb=" N ALA G 335 " --> pdb=" O THR G 331 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP G 336 " --> pdb=" O GLU G 332 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE G 337 " --> pdb=" O GLU G 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 331 through 337' 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 417 removed outlier: 4.270A pdb=" N SER G 415 " --> pdb=" O GLU G 411 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER G 416 " --> pdb=" O GLY G 412 " (cutoff:3.500A) Processing helix chain 'G' and resid 448 through 451 Processing helix chain 'G' and resid 475 through 483 removed outlier: 3.749A pdb=" N HIS G 479 " --> pdb=" O ASP G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 493 through 506 removed outlier: 3.712A pdb=" N ARG G 506 " --> pdb=" O ILE G 502 " (cutoff:3.500A) 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: 6.668A 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 81 through 84 removed outlier: 3.921A pdb=" N HIS A 178 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N LEU A 179 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER A 143 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY A 115 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 201 through 202 removed outlier: 7.043A pdb=" N ILE A 201 " --> pdb=" O GLN A 316 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 259 through 263 removed outlier: 3.669A pdb=" N LEU A 249 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE A 246 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU A 233 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N SER A 248 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 231 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 229 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A 226 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N THR A 284 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLY A 228 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL A 282 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A 230 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA A 280 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 263 removed outlier: 3.669A pdb=" N LEU A 249 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE A 246 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU A 233 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N SER A 248 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 231 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 229 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A 226 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N THR A 284 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLY A 228 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL A 282 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A 230 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA A 280 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 352 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 367 removed outlier: 4.551A pdb=" N GLY A 364 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 366 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU A 372 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLY A 380 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N CYS A 382 " --> pdb=" O PRO A 423 " (cutoff:3.500A) removed outlier: 9.475A pdb=" N LEU A 425 " --> pdb=" O CYS A 382 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS A 424 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP A 405 " --> pdb=" O CYS A 424 " (cutoff:3.500A) removed outlier: 11.943A pdb=" N ARG A 426 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 11.696A pdb=" N LEU A 403 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 11.792A pdb=" N ALA A 428 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N LEU A 401 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP A 405 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 356 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N HIS A 407 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG A 354 " --> pdb=" O HIS A 407 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 592 through 597 removed outlier: 3.645A pdb=" N ARG A 663 " --> pdb=" O SER A 593 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP A 664 " --> pdb=" O GLN A 685 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 683 " --> pdb=" O ARG A 666 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE A 692 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU A 635 " --> pdb=" O PHE A 692 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 621 through 624 removed outlier: 3.561A pdb=" N LEU A 608 " --> pdb=" O ALA A 654 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY A 610 " --> pdb=" O VAL A 652 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 742 through 744 removed outlier: 3.643A pdb=" N MET A 742 " --> pdb=" O SER A 762 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N TYR A 764 " --> pdb=" O LYS A 738 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS A 738 " --> pdb=" O TYR A 764 " (cutoff:3.500A) removed outlier: 7.417A 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: 7.417A pdb=" N LEU A 766 " --> pdb=" O CYS A 736 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS A 738 " --> pdb=" O TYR A 764 " (cutoff:3.500A) removed outlier: 7.719A 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 859 through 862 Processing sheet with id=AB3, first strand: chain 'A' and resid 991 through 994 removed outlier: 3.585A pdb=" N TYR A 983 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL A 982 " --> pdb=" O HIS A 945 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP A 947 " --> pdb=" O VAL A 982 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 904 " --> pdb=" O THR A 932 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA A 934 " --> pdb=" O ILE A 902 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE A 902 " --> pdb=" O ALA A 934 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N PHE A 898 " --> pdb=" O SER A 970 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER A 970 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA A 900 " --> pdb=" O HIS A 968 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N HIS A 968 " --> pdb=" O ALA A 900 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE A 902 " --> pdb=" O ARG A 966 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG A 966 " --> pdb=" O ILE A 902 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1117 through 1119 removed outlier: 3.778A pdb=" N VAL A1117 " --> pdb=" O LEU A1039 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A1037 " --> pdb=" O LEU A1119 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL A1156 " --> pdb=" O ILE A1201 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE A1201 " --> pdb=" O VAL A1156 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N SER A1158 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A1085 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N CYS A1198 " --> pdb=" O VAL A1085 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N THR A1087 " --> pdb=" O CYS A1198 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N SER A1200 " --> pdb=" O THR A1087 " (cutoff:3.500A) removed outlier: 10.296A pdb=" N ARG A1089 " --> pdb=" O SER A1200 " (cutoff:3.500A) removed outlier: 12.190A pdb=" N ARG A1202 " --> pdb=" O ARG A1089 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A1086 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS A1088 " --> pdb=" O ILE A1073 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A1073 " --> pdb=" O CYS A1088 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE A1068 " --> pdb=" O PHE A1040 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE A1040 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLN A1070 " --> pdb=" O GLN A1038 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLN A1038 " --> pdb=" O GLN A1070 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE A1072 " --> pdb=" O SER A1036 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER A1036 " --> pdb=" O ILE A1072 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ARG A1074 " --> pdb=" O VAL A1034 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL A1034 " --> pdb=" O ARG A1074 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU A1076 " --> pdb=" O VAL A1032 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1050 through 1051 Processing sheet with id=AB6, first strand: chain 'A' and resid 1175 through 1177 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 28 removed outlier: 6.485A pdb=" N ALA B 27 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N LEU B 60 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLY B 76 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL B 66 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER B 74 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 84 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ARG B 145 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN B 85 " --> pdb=" O ARG B 145 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 28 removed outlier: 6.485A pdb=" N ALA B 27 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N LEU B 60 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 151 " --> pdb=" O ARG B 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 49 removed outlier: 3.614A pdb=" N PHE B 47 " --> pdb=" O ILE B 54 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 224 through 225 removed outlier: 3.530A pdb=" N TYR B 291 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR B 292 " --> pdb=" O PHE B 281 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 322 through 323 removed outlier: 3.778A pdb=" N CYS B 322 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR B 365 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N TYR B 364 " --> pdb=" O THR B 360 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 8 through 9 removed outlier: 6.064A pdb=" N THR C 8 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N PHE C 29 " --> pdb=" O THR C 8 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE C 74 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU C 94 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU C 76 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 14.040A pdb=" N SER C 87 " --> pdb=" O GLN C 52 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N GLN C 54 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N VAL C 89 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU C 56 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ALA C 91 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N CYS C 58 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL C 93 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG C 41 " --> pdb=" O TYR C 35 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N TYR C 35 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR C 43 " --> pdb=" O CYS C 33 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLN C 47 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 10.528A pdb=" N PHE C 29 " --> pdb=" O GLN C 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.507A pdb=" N GLU D 44 " --> pdb=" O GLY D 81 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.507A pdb=" N GLU D 44 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 80 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU D 317 " --> pdb=" O ILE D 80 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 48 through 49 removed outlier: 3.935A pdb=" N ILE D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 106 through 111 removed outlier: 3.715A pdb=" N LEU D 106 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE D 108 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 110 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL D 165 " --> pdb=" O ILE D 110 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 36 through 37 Processing sheet with id=AC9, first strand: chain 'E' and resid 184 through 187 removed outlier: 3.956A pdb=" N TYR E 184 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL E 209 " --> pdb=" O TYR E 184 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR E 208 " --> pdb=" O TYR E 201 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR E 201 " --> pdb=" O TYR E 208 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 332 through 333 removed outlier: 7.803A pdb=" N HIS F 342 " --> pdb=" O TRP F 366 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TRP F 366 " --> pdb=" O HIS F 342 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE F 362 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA F 348 " --> pdb=" O PHE F 360 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE F 360 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 9.480A pdb=" N VAL F 516 " --> pdb=" O HIS F 373 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER F 375 " --> pdb=" O VAL F 516 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ALA F 518 " --> pdb=" O SER F 375 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N CYS F 377 " --> pdb=" O ALA F 518 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA F 520 " --> pdb=" O CYS F 377 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N MET F 379 " --> pdb=" O ALA F 520 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 332 through 333 Processing sheet with id=AD3, first strand: chain 'F' and resid 431 through 438 removed outlier: 3.909A pdb=" N LYS F 437 " --> pdb=" O SER F 450 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER F 450 " --> pdb=" O LYS F 437 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N GLU F 451 " --> pdb=" O PRO F 391 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU F 453 " --> pdb=" O PHE F 389 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS F 475 " --> pdb=" O LEU F 390 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 609 through 611 removed outlier: 8.630A pdb=" N GLU F 610 " --> pdb=" O HIS F 582 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N CYS F 584 " --> pdb=" O GLU F 610 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL F 585 " --> pdb=" O MET F 560 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS F 545 " --> pdb=" O ILE F 558 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N MET F 560 " --> pdb=" O SER F 543 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N SER F 543 " --> pdb=" O MET F 560 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA F 562 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA F 541 " --> pdb=" O ALA F 562 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL F 564 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL F 539 " --> pdb=" O VAL F 564 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N HIS F 566 " --> pdb=" O LEU F 537 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N LEU F 537 " --> pdb=" O HIS F 566 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE F 542 " --> pdb=" O VAL F 635 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 998 through 1002 removed outlier: 6.108A pdb=" N VAL F 998 " --> pdb=" O ASN F1009 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASN F1009 " --> pdb=" O VAL F 998 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR F1000 " --> pdb=" O MET F1007 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU F 857 " --> pdb=" O ILE F1008 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP F 860 " --> pdb=" O ILE F1040 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ILE F1040 " --> pdb=" O ASP F 860 " (cutoff:3.500A) removed outlier: 12.903A pdb=" N ASP F1041 " --> pdb=" O PRO F1062 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL F1043 " --> pdb=" O VAL F1060 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 998 through 1002 removed outlier: 6.108A pdb=" N VAL F 998 " --> pdb=" O ASN F1009 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASN F1009 " --> pdb=" O VAL F 998 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR F1000 " --> pdb=" O MET F1007 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU F 857 " --> pdb=" O ILE F1008 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP F 860 " --> pdb=" O ILE F1040 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ILE F1040 " --> pdb=" O ASP F 860 " (cutoff:3.500A) removed outlier: 12.903A pdb=" N ASP F1041 " --> pdb=" O PRO F1062 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL F1043 " --> pdb=" O VAL F1060 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR F1055 " --> pdb=" O LYS F1075 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS F1075 " --> pdb=" O TYR F1055 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA F1057 " --> pdb=" O GLU F1073 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 1279 through 1282 removed outlier: 3.607A pdb=" N PHE F1279 " --> pdb=" O TYR F1292 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 1296 through 1297 Processing sheet with id=AD9, first strand: chain 'F' and resid 1356 through 1357 Processing sheet with id=AE1, first strand: chain 'G' and resid 170 through 175 removed outlier: 6.380A pdb=" N VAL G 170 " --> pdb=" O ARG G 597 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG G 597 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR G 172 " --> pdb=" O VAL G 595 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ALA G 592 " --> pdb=" O TYR G 575 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA G 572 " --> pdb=" O VAL G 344 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL G 342 " --> pdb=" O LEU G 574 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU G 576 " --> pdb=" O SER G 340 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER G 340 " --> pdb=" O LEU G 576 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N VAL G 374 " --> pdb=" O GLN G 339 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N MET G 341 " --> pdb=" O VAL G 374 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE G 376 " --> pdb=" O MET G 341 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU G 343 " --> pdb=" O ILE G 376 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N PHE G 378 " --> pdb=" O LEU G 343 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA G 345 " --> pdb=" O PHE G 378 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL G 423 " --> pdb=" O LEU G 377 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU G 420 " --> pdb=" O GLN G 454 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 194 through 196 removed outlier: 3.750A pdb=" N SER G 461 " --> pdb=" O LEU G 196 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU G 462 " --> pdb=" O PHE G 469 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE G 468 " --> pdb=" O VAL G 537 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE G 539 " --> pdb=" O ILE G 468 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY G 470 " --> pdb=" O ILE G 539 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE G 547 " --> pdb=" O ASN G 558 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 247 through 259 removed outlier: 5.162A pdb=" N VAL G 270 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N LEU G 314 " --> pdb=" O GLN G 283 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA G 316 " --> pdb=" O PRO G 285 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP G 287 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN G 300 " --> pdb=" O ILE G 257 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL G 302 " --> pdb=" O GLY G 255 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY G 255 " --> pdb=" O VAL G 302 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASN G 308 " --> pdb=" O GLU G 249 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU G 249 " --> pdb=" O ASN G 308 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 294 through 296 removed outlier: 3.787A pdb=" N TYR G 294 " --> pdb=" O SER G 487 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 563 through 564 1267 hydrogen bonds defined for protein. 3522 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: 6.99 Time building geometry restraints manager: 3.38 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: 9360 1.34 - 1.45: 4726 1.45 - 1.57: 17426 1.57 - 1.69: 39 1.69 - 1.81: 221 Bond restraints: 31772 Sorted by residual: bond pdb=" C1' DT H 12 " pdb=" N1 DT H 12 " ideal model delta sigma weight residual 1.468 1.522 -0.054 1.40e-02 5.10e+03 1.46e+01 bond pdb=" N GLN G 515 " pdb=" CA GLN G 515 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.25e-02 6.40e+03 1.13e+01 bond pdb=" C3' DT H 6 " pdb=" C2' DT H 6 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DG H 9 " pdb=" C2' DG H 9 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.17e+00 bond pdb=" C3' DG H 17 " pdb=" C2' DG H 17 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.58e+00 ... (remaining 31767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 42346 1.69 - 3.37: 664 3.37 - 5.06: 90 5.06 - 6.74: 15 6.74 - 8.43: 5 Bond angle restraints: 43120 Sorted by residual: angle pdb=" O4' DG H 4 " pdb=" C4' DG H 4 " pdb=" C3' DG H 4 " ideal model delta sigma weight residual 106.00 103.31 2.69 6.00e-01 2.78e+00 2.00e+01 angle pdb=" O4' DT H 12 " pdb=" C1' DT H 12 " pdb=" N1 DT H 12 " ideal model delta sigma weight residual 108.00 110.99 -2.99 7.00e-01 2.04e+00 1.82e+01 angle pdb=" N3 DT H 18 " pdb=" C4 DT H 18 " pdb=" O4 DT H 18 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT H 12 " pdb=" C4 DT H 12 " pdb=" O4 DT H 12 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT H 7 " pdb=" C4 DT H 7 " pdb=" O4 DT H 7 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 ... (remaining 43115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 18885 35.66 - 71.32: 380 71.32 - 106.98: 33 106.98 - 142.64: 0 142.64 - 178.30: 1 Dihedral angle restraints: 19299 sinusoidal: 8109 harmonic: 11190 Sorted by residual: dihedral pdb=" CA ASN A 35 " pdb=" C ASN A 35 " pdb=" N VAL A 36 " pdb=" CA VAL A 36 " ideal model delta harmonic sigma weight residual -180.00 -159.27 -20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LEU E 211 " pdb=" C LEU E 211 " pdb=" N LYS E 212 " pdb=" CA LYS E 212 " ideal model delta harmonic sigma weight residual -180.00 -159.32 -20.68 0 5.00e+00 4.00e-02 1.71e+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 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 19296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3353 0.034 - 0.069: 954 0.069 - 0.103: 333 0.103 - 0.137: 131 0.137 - 0.172: 3 Chirality restraints: 4774 Sorted by residual: chirality pdb=" CB ILE A 868 " pdb=" CA ILE A 868 " pdb=" CG1 ILE A 868 " pdb=" CG2 ILE A 868 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CB ILE E 214 " pdb=" CA ILE E 214 " pdb=" CG1 ILE E 214 " pdb=" CG2 ILE E 214 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA VAL F 889 " pdb=" N VAL F 889 " pdb=" C VAL F 889 " pdb=" CB VAL F 889 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 4771 not shown) Planarity restraints: 5478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 891 " 0.019 2.00e-02 2.50e+03 1.75e-02 5.38e+00 pdb=" CG PHE A 891 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 891 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 891 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 891 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 891 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 891 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 515 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C GLN G 515 " -0.035 2.00e-02 2.50e+03 pdb=" O GLN G 515 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU G 516 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 493 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C GLN A 493 " -0.031 2.00e-02 2.50e+03 pdb=" O GLN A 493 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS A 494 " 0.010 2.00e-02 2.50e+03 ... (remaining 5475 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1715 2.73 - 3.27: 31247 3.27 - 3.82: 51660 3.82 - 4.36: 56584 4.36 - 4.90: 96209 Nonbonded interactions: 237415 Sorted by model distance: nonbonded pdb=" O ASN D 236 " pdb=" OG SER D 239 " model vdw 2.188 3.040 nonbonded pdb=" O LYS A 795 " pdb=" OG SER A 850 " model vdw 2.189 3.040 nonbonded pdb=" OG SER E 155 " pdb=" OE1 GLU E 158 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP D 232 " pdb=" OG SER D 265 " model vdw 2.213 3.040 nonbonded pdb=" O LEU G 325 " pdb=" OG1 THR G 534 " model vdw 2.221 3.040 ... (remaining 237410 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.510 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: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.480 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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 31772 Z= 0.133 Angle : 0.513 8.428 43120 Z= 0.285 Chirality : 0.040 0.172 4774 Planarity : 0.003 0.039 5478 Dihedral : 14.910 178.304 12053 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.74 % Favored : 96.15 % Rotamer: Outliers : 0.06 % Allowed : 0.26 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.14), residues: 3792 helix: 1.99 (0.15), residues: 1304 sheet: 0.10 (0.22), residues: 603 loop : -0.49 (0.15), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 79 TYR 0.028 0.001 TYR B 174 PHE 0.040 0.001 PHE A 891 TRP 0.015 0.001 TRP B 160 HIS 0.005 0.001 HIS E 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.13 (31772) covalent geometry : angle 0.51270 / 0.28 (43120) hydrogen bonds : bond 0.19561 / 13.24 ( 1242) hydrogen bonds : angle 6.75820 / 4.73 ( 3522) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 742 MET cc_start: 0.8375 (pmm) cc_final: 0.7981 (pmm) REVERT: B 37 MET cc_start: 0.7665 (ptm) cc_final: 0.7396 (ppp) REVERT: B 365 TYR cc_start: 0.8876 (m-80) cc_final: 0.8590 (m-80) REVERT: C 14 GLU cc_start: 0.9287 (mp0) cc_final: 0.8830 (mp0) REVERT: E 342 ASP cc_start: 0.8500 (t0) cc_final: 0.8082 (m-30) REVERT: F 731 MET cc_start: 0.8261 (tpp) cc_final: 0.7768 (tpp) REVERT: F 781 MET cc_start: 0.8804 (mpp) cc_final: 0.8046 (mpp) REVERT: G 402 PHE cc_start: 0.9200 (t80) cc_final: 0.8878 (t80) outliers start: 2 outliers final: 1 residues processed: 158 average time/residue: 0.1839 time to fit residues: 50.6117 Evaluate side-chains 117 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.0070 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.0070 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 8.9990 overall best weight: 1.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN A 505 GLN D 31 ASN ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.082032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.060559 restraints weight = 170569.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.059154 restraints weight = 125542.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.059444 restraints weight = 121530.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.059492 restraints weight = 92006.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.059800 restraints weight = 89206.569| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31772 Z= 0.144 Angle : 0.541 7.666 43120 Z= 0.285 Chirality : 0.041 0.175 4774 Planarity : 0.004 0.038 5478 Dihedral : 8.755 176.993 4366 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.40 % Favored : 95.52 % Rotamer: Outliers : 0.06 % Allowed : 3.67 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.14), residues: 3792 helix: 2.04 (0.15), residues: 1303 sheet: -0.09 (0.21), residues: 612 loop : -0.51 (0.15), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 32 TYR 0.015 0.001 TYR B 174 PHE 0.025 0.001 PHE A 891 TRP 0.011 0.001 TRP B 160 HIS 0.018 0.001 HIS G 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (31772) covalent geometry : angle 0.54053 / 0.28 (43120) hydrogen bonds : bond 0.04663 / 3.15 ( 1242) hydrogen bonds : angle 5.45764 / 3.86 ( 3522) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 PHE cc_start: 0.8156 (m-80) cc_final: 0.7745 (m-80) REVERT: A 742 MET cc_start: 0.8666 (pmm) cc_final: 0.8352 (pmm) REVERT: B 365 TYR cc_start: 0.8597 (m-80) cc_final: 0.8397 (m-80) REVERT: C 14 GLU cc_start: 0.9087 (mp0) cc_final: 0.8755 (mp0) REVERT: E 135 LEU cc_start: 0.8612 (tp) cc_final: 0.8368 (tt) REVERT: E 140 ILE cc_start: 0.8458 (pt) cc_final: 0.7895 (pt) REVERT: E 342 ASP cc_start: 0.8121 (t0) cc_final: 0.7885 (m-30) REVERT: F 781 MET cc_start: 0.8700 (mpp) cc_final: 0.7878 (mpp) REVERT: F 956 MET cc_start: 0.8755 (mmp) cc_final: 0.8434 (mmm) REVERT: F 1303 MET cc_start: 0.6717 (tpt) cc_final: 0.6335 (pmm) REVERT: G 402 PHE cc_start: 0.8981 (t80) cc_final: 0.8707 (t80) outliers start: 2 outliers final: 1 residues processed: 147 average time/residue: 0.1728 time to fit residues: 44.6419 Evaluate side-chains 116 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 213 optimal weight: 1.9990 chunk 292 optimal weight: 0.1980 chunk 243 optimal weight: 0.3980 chunk 331 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 22 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 402 GLN A 432 GLN ** G 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.082820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.061245 restraints weight = 171597.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.060109 restraints weight = 121537.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.060440 restraints weight = 113879.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.060483 restraints weight = 87346.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.060765 restraints weight = 84599.125| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 31772 Z= 0.107 Angle : 0.511 9.143 43120 Z= 0.266 Chirality : 0.041 0.189 4774 Planarity : 0.004 0.039 5478 Dihedral : 8.737 176.771 4366 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.86 % Rotamer: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.14), residues: 3792 helix: 2.05 (0.15), residues: 1301 sheet: 0.03 (0.22), residues: 595 loop : -0.51 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 98 TYR 0.019 0.001 TYR D 23 PHE 0.021 0.001 PHE A 891 TRP 0.021 0.001 TRP B 160 HIS 0.004 0.001 HIS E 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (31772) covalent geometry : angle 0.51105 / 0.27 (43120) hydrogen bonds : bond 0.04116 / 2.77 ( 1242) hydrogen bonds : angle 5.09792 / 3.60 ( 3522) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 PHE cc_start: 0.8105 (m-80) cc_final: 0.7653 (m-80) REVERT: A 742 MET cc_start: 0.8661 (pmm) cc_final: 0.8369 (pmm) REVERT: F 689 MET cc_start: 0.7634 (mmm) cc_final: 0.6697 (mmt) REVERT: F 781 MET cc_start: 0.8665 (mpp) cc_final: 0.7823 (mpp) REVERT: F 1303 MET cc_start: 0.6884 (tpt) cc_final: 0.6617 (pmm) REVERT: G 402 PHE cc_start: 0.8988 (t80) cc_final: 0.8730 (t80) REVERT: G 574 LEU cc_start: 0.9607 (mm) cc_final: 0.9073 (pp) outliers start: 1 outliers final: 1 residues processed: 153 average time/residue: 0.1776 time to fit residues: 47.6188 Evaluate side-chains 117 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 192 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 307 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 303 optimal weight: 4.9990 chunk 256 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 chunk 122 optimal weight: 0.9990 chunk 305 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 GLN ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 GLN ** A1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 HIS ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN F 463 GLN F1009 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.081033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.059993 restraints weight = 171965.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.058413 restraints weight = 134653.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.058698 restraints weight = 131024.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.058746 restraints weight = 97937.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.059053 restraints weight = 94680.962| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31772 Z= 0.205 Angle : 0.581 8.398 43120 Z= 0.300 Chirality : 0.042 0.193 4774 Planarity : 0.004 0.039 5478 Dihedral : 8.819 176.518 4366 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.46 % Favored : 94.49 % Rotamer: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.14), residues: 3792 helix: 2.00 (0.15), residues: 1297 sheet: -0.27 (0.21), residues: 610 loop : -0.56 (0.15), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 650 TYR 0.030 0.001 TYR B 174 PHE 0.026 0.002 PHE E 222 TRP 0.021 0.001 TRP B 160 HIS 0.009 0.001 HIS D 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (31772) covalent geometry : angle 0.58106 / 0.30 (43120) hydrogen bonds : bond 0.04152 / 2.80 ( 1242) hydrogen bonds : angle 5.06220 / 3.58 ( 3522) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 PHE cc_start: 0.8052 (m-80) cc_final: 0.7534 (m-80) REVERT: A 742 MET cc_start: 0.8649 (pmm) cc_final: 0.8268 (pmm) REVERT: B 231 MET cc_start: 0.8045 (ppp) cc_final: 0.7839 (ppp) REVERT: F 689 MET cc_start: 0.7666 (mmm) cc_final: 0.7204 (mmm) REVERT: F 781 MET cc_start: 0.8568 (mpp) cc_final: 0.7752 (mpp) REVERT: F 956 MET cc_start: 0.8823 (mmp) cc_final: 0.8485 (mmm) REVERT: G 209 MET cc_start: 0.9203 (mtm) cc_final: 0.8599 (mtm) REVERT: G 402 PHE cc_start: 0.8995 (t80) cc_final: 0.8733 (t80) outliers start: 1 outliers final: 1 residues processed: 140 average time/residue: 0.1731 time to fit residues: 42.6862 Evaluate side-chains 107 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 260 optimal weight: 4.9990 chunk 266 optimal weight: 9.9990 chunk 368 optimal weight: 0.4980 chunk 223 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 257 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 197 optimal weight: 4.9990 chunk 283 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 343 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 GLN F 553 HIS F 737 GLN ** G 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.082692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.060779 restraints weight = 169324.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.058860 restraints weight = 116123.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.059505 restraints weight = 108080.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.059482 restraints weight = 88762.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.059677 restraints weight = 85317.759| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 31772 Z= 0.103 Angle : 0.519 9.839 43120 Z= 0.266 Chirality : 0.041 0.202 4774 Planarity : 0.004 0.039 5478 Dihedral : 8.749 176.716 4366 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 0.03 % Allowed : 2.10 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3792 helix: 2.05 (0.15), residues: 1292 sheet: -0.20 (0.21), residues: 613 loop : -0.53 (0.15), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 98 TYR 0.015 0.001 TYR E 22 PHE 0.022 0.001 PHE F1364 TRP 0.010 0.001 TRP B 160 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (31772) covalent geometry : angle 0.51934 / 0.27 (43120) hydrogen bonds : bond 0.03727 / 2.51 ( 1242) hydrogen bonds : angle 4.78328 / 3.38 ( 3522) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 PHE cc_start: 0.8223 (m-80) cc_final: 0.7699 (m-80) REVERT: A 742 MET cc_start: 0.8657 (pmm) cc_final: 0.8323 (pmm) REVERT: F 560 MET cc_start: 0.8277 (mmp) cc_final: 0.8014 (mmm) REVERT: F 689 MET cc_start: 0.7559 (mmm) cc_final: 0.7184 (mmm) REVERT: F 781 MET cc_start: 0.8767 (mpp) cc_final: 0.8260 (mpp) REVERT: F 956 MET cc_start: 0.8818 (mmp) cc_final: 0.8592 (mmm) REVERT: G 209 MET cc_start: 0.9232 (mtm) cc_final: 0.8582 (mtm) REVERT: G 402 PHE cc_start: 0.9066 (t80) cc_final: 0.8777 (t80) REVERT: G 574 LEU cc_start: 0.9623 (mm) cc_final: 0.9120 (pp) outliers start: 1 outliers final: 1 residues processed: 148 average time/residue: 0.1774 time to fit residues: 45.8863 Evaluate side-chains 111 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 340 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 137 optimal weight: 8.9990 chunk 275 optimal weight: 0.9990 chunk 225 optimal weight: 6.9990 chunk 316 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 GLN A 505 GLN A 525 HIS ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** F 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1420 GLN ** G 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.081410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.059737 restraints weight = 171525.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.058022 restraints weight = 122317.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.058467 restraints weight = 119975.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.058491 restraints weight = 92318.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.058750 restraints weight = 89430.741| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31772 Z= 0.179 Angle : 0.570 15.334 43120 Z= 0.292 Chirality : 0.041 0.199 4774 Planarity : 0.004 0.038 5478 Dihedral : 8.767 177.002 4366 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.38 % Favored : 94.57 % Rotamer: Outliers : 0.03 % Allowed : 1.78 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.14), residues: 3792 helix: 2.04 (0.15), residues: 1288 sheet: -0.27 (0.21), residues: 629 loop : -0.60 (0.15), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 436 TYR 0.023 0.001 TYR B 174 PHE 0.022 0.001 PHE B 182 TRP 0.046 0.001 TRP B 160 HIS 0.008 0.001 HIS D 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (31772) covalent geometry : angle 0.57036 / 0.29 (43120) hydrogen bonds : bond 0.03879 / 2.62 ( 1242) hydrogen bonds : angle 4.85579 / 3.43 ( 3522) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 PHE cc_start: 0.8166 (m-80) cc_final: 0.7665 (m-80) REVERT: A 742 MET cc_start: 0.8632 (pmm) cc_final: 0.8237 (pmm) REVERT: F 781 MET cc_start: 0.8639 (mpp) cc_final: 0.8175 (mpp) REVERT: F 956 MET cc_start: 0.8786 (mmp) cc_final: 0.8541 (mmm) REVERT: G 574 LEU cc_start: 0.9604 (mm) cc_final: 0.9106 (pp) outliers start: 1 outliers final: 1 residues processed: 137 average time/residue: 0.1751 time to fit residues: 42.4635 Evaluate side-chains 108 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 18 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 285 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 27 optimal weight: 10.0000 chunk 346 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN A 432 GLN A 505 GLN A 875 ASN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN D 31 ASN E 24 HIS E 303 HIS ** F 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1420 GLN ** G 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.080712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.059610 restraints weight = 172149.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.057992 restraints weight = 138208.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.058313 restraints weight = 138951.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.058609 restraints weight = 101753.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.058737 restraints weight = 97594.323| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31772 Z= 0.203 Angle : 0.595 7.987 43120 Z= 0.306 Chirality : 0.042 0.205 4774 Planarity : 0.004 0.038 5478 Dihedral : 8.817 176.620 4366 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.35 % Favored : 94.59 % Rotamer: Outliers : 0.03 % Allowed : 1.72 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.14), residues: 3792 helix: 1.91 (0.15), residues: 1288 sheet: -0.34 (0.21), residues: 612 loop : -0.68 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 379 TYR 0.034 0.002 TYR B 174 PHE 0.031 0.002 PHE B 182 TRP 0.053 0.002 TRP B 160 HIS 0.008 0.001 HIS D 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (31772) covalent geometry : angle 0.59528 / 0.31 (43120) hydrogen bonds : bond 0.04039 / 2.73 ( 1242) hydrogen bonds : angle 4.89971 / 3.47 ( 3522) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 PHE cc_start: 0.8149 (m-80) cc_final: 0.7598 (m-80) REVERT: A 283 LEU cc_start: 0.9137 (tp) cc_final: 0.8905 (tp) REVERT: A 742 MET cc_start: 0.8557 (pmm) cc_final: 0.8166 (pmm) REVERT: B 167 MET cc_start: 0.9139 (ppp) cc_final: 0.8637 (ppp) REVERT: F 379 MET cc_start: 0.8468 (tpp) cc_final: 0.7907 (tpp) REVERT: F 689 MET cc_start: 0.8041 (mmm) cc_final: 0.7568 (mmm) REVERT: F 781 MET cc_start: 0.8653 (mpp) cc_final: 0.8220 (mpp) REVERT: F 956 MET cc_start: 0.8755 (mmp) cc_final: 0.8537 (mmm) REVERT: G 209 MET cc_start: 0.9313 (mtm) cc_final: 0.8773 (mtm) outliers start: 1 outliers final: 1 residues processed: 138 average time/residue: 0.1793 time to fit residues: 43.6406 Evaluate side-chains 112 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 241 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 271 optimal weight: 3.9990 chunk 87 optimal weight: 0.0020 chunk 315 optimal weight: 4.9990 chunk 86 optimal weight: 0.4980 chunk 308 optimal weight: 7.9990 chunk 47 optimal weight: 0.0970 chunk 53 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 GLN A 505 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** F 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1420 GLN ** G 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.081369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.055440 restraints weight = 170044.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.055530 restraints weight = 115698.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.056126 restraints weight = 81762.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.056263 restraints weight = 74713.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.056275 restraints weight = 68877.633| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31772 Z= 0.144 Angle : 0.555 9.915 43120 Z= 0.285 Chirality : 0.041 0.209 4774 Planarity : 0.004 0.040 5478 Dihedral : 8.776 177.188 4366 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.09 % Favored : 94.86 % Rotamer: Outliers : 0.03 % Allowed : 0.90 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3792 helix: 1.97 (0.15), residues: 1294 sheet: -0.28 (0.21), residues: 612 loop : -0.67 (0.15), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 98 TYR 0.017 0.001 TYR E 22 PHE 0.025 0.001 PHE B 182 TRP 0.034 0.001 TRP B 160 HIS 0.005 0.001 HIS F 794 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (31772) covalent geometry : angle 0.55535 / 0.28 (43120) hydrogen bonds : bond 0.03832 / 2.58 ( 1242) hydrogen bonds : angle 4.79116 / 3.39 ( 3522) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 PHE cc_start: 0.8431 (m-80) cc_final: 0.7923 (m-80) REVERT: A 283 LEU cc_start: 0.9197 (tp) cc_final: 0.8964 (tp) REVERT: A 742 MET cc_start: 0.8513 (pmm) cc_final: 0.8133 (pmm) REVERT: B 37 MET cc_start: 0.7865 (ptm) cc_final: 0.7375 (ppp) REVERT: B 167 MET cc_start: 0.9183 (ppp) cc_final: 0.8714 (ppp) REVERT: F 379 MET cc_start: 0.8521 (tpp) cc_final: 0.8188 (tpp) REVERT: F 560 MET cc_start: 0.8587 (mmp) cc_final: 0.8170 (mmm) REVERT: F 689 MET cc_start: 0.8060 (mmm) cc_final: 0.7205 (mmm) REVERT: F 781 MET cc_start: 0.8752 (mpp) cc_final: 0.7926 (mpp) REVERT: F 956 MET cc_start: 0.8875 (mmp) cc_final: 0.8611 (mmm) REVERT: G 209 MET cc_start: 0.9381 (mtm) cc_final: 0.8830 (mtm) REVERT: G 304 MET cc_start: 0.7329 (tmm) cc_final: 0.7062 (tmm) outliers start: 1 outliers final: 1 residues processed: 140 average time/residue: 0.1657 time to fit residues: 40.7873 Evaluate side-chains 111 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 364 optimal weight: 10.0000 chunk 339 optimal weight: 0.0070 chunk 178 optimal weight: 0.9980 chunk 137 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 365 optimal weight: 0.9980 chunk 286 optimal weight: 5.9990 chunk 353 optimal weight: 7.9990 chunk 198 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 GLN A 505 GLN D 31 ASN ** F 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1420 GLN ** G 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.081843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.060354 restraints weight = 169964.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.058680 restraints weight = 125823.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.059140 restraints weight = 119461.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.059206 restraints weight = 91604.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.059364 restraints weight = 87986.415| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31772 Z= 0.119 Angle : 0.540 9.483 43120 Z= 0.275 Chirality : 0.041 0.207 4774 Planarity : 0.004 0.040 5478 Dihedral : 8.722 177.754 4366 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.43 % Favored : 95.52 % Rotamer: Outliers : 0.03 % Allowed : 0.47 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.14), residues: 3792 helix: 2.01 (0.15), residues: 1298 sheet: -0.22 (0.21), residues: 598 loop : -0.63 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 392 TYR 0.034 0.001 TYR B 174 PHE 0.027 0.001 PHE E 222 TRP 0.031 0.001 TRP B 160 HIS 0.005 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (31772) covalent geometry : angle 0.54014 / 0.28 (43120) hydrogen bonds : bond 0.03624 / 2.45 ( 1242) hydrogen bonds : angle 4.67892 / 3.32 ( 3522) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 PHE cc_start: 0.8190 (m-80) cc_final: 0.7694 (m-80) REVERT: A 283 LEU cc_start: 0.9173 (tp) cc_final: 0.8949 (tp) REVERT: A 742 MET cc_start: 0.8347 (pmm) cc_final: 0.8010 (pmm) REVERT: A 1083 GLU cc_start: 0.8215 (pm20) cc_final: 0.7596 (pm20) REVERT: B 37 MET cc_start: 0.7625 (ptm) cc_final: 0.7413 (ppp) REVERT: B 167 MET cc_start: 0.9134 (ppp) cc_final: 0.8712 (ppp) REVERT: F 379 MET cc_start: 0.8197 (tpp) cc_final: 0.7832 (tpp) REVERT: F 544 MET cc_start: 0.8040 (pmm) cc_final: 0.7828 (pmm) REVERT: F 560 MET cc_start: 0.8100 (mmp) cc_final: 0.7864 (mmm) REVERT: F 689 MET cc_start: 0.7933 (mmm) cc_final: 0.7015 (mmm) REVERT: F 781 MET cc_start: 0.8698 (mpp) cc_final: 0.7888 (mpp) REVERT: F 956 MET cc_start: 0.8698 (mmp) cc_final: 0.8473 (mmm) REVERT: G 209 MET cc_start: 0.9212 (mtm) cc_final: 0.8682 (mtm) REVERT: G 304 MET cc_start: 0.7363 (tmm) cc_final: 0.7148 (tmm) outliers start: 1 outliers final: 1 residues processed: 143 average time/residue: 0.1703 time to fit residues: 43.3366 Evaluate side-chains 112 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 72 optimal weight: 8.9990 chunk 316 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 chunk 254 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 308 optimal weight: 9.9990 chunk 288 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 152 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN F 553 HIS ** F 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1420 GLN ** G 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.081602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.060365 restraints weight = 169489.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.058833 restraints weight = 128288.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.059160 restraints weight = 124606.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.059380 restraints weight = 93908.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.059464 restraints weight = 87224.371| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31772 Z= 0.133 Angle : 0.544 9.428 43120 Z= 0.276 Chirality : 0.041 0.207 4774 Planarity : 0.004 0.039 5478 Dihedral : 8.702 177.711 4366 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.83 % Favored : 95.12 % Rotamer: Outliers : 0.03 % Allowed : 0.23 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.14), residues: 3792 helix: 2.04 (0.15), residues: 1297 sheet: -0.24 (0.21), residues: 604 loop : -0.63 (0.15), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 392 TYR 0.032 0.001 TYR B 174 PHE 0.024 0.001 PHE B 182 TRP 0.030 0.001 TRP B 160 HIS 0.005 0.001 HIS E 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (31772) covalent geometry : angle 0.54365 / 0.28 (43120) hydrogen bonds : bond 0.03612 / 2.44 ( 1242) hydrogen bonds : angle 4.64931 / 3.29 ( 3522) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 PHE cc_start: 0.8123 (m-80) cc_final: 0.7641 (m-80) REVERT: A 283 LEU cc_start: 0.9152 (tp) cc_final: 0.8935 (tp) REVERT: A 742 MET cc_start: 0.8357 (pmm) cc_final: 0.8018 (pmm) REVERT: A 1083 GLU cc_start: 0.8298 (pm20) cc_final: 0.7713 (pm20) REVERT: B 167 MET cc_start: 0.9129 (ppp) cc_final: 0.8693 (ppp) REVERT: B 231 MET cc_start: 0.8166 (ppp) cc_final: 0.7955 (ppp) REVERT: F 379 MET cc_start: 0.8106 (tpp) cc_final: 0.7895 (tpp) REVERT: F 544 MET cc_start: 0.8017 (pmm) cc_final: 0.7805 (pmm) REVERT: F 560 MET cc_start: 0.8000 (mmp) cc_final: 0.7763 (mmm) REVERT: F 689 MET cc_start: 0.7983 (mmm) cc_final: 0.7475 (mmm) REVERT: F 731 MET cc_start: 0.8460 (tpt) cc_final: 0.7774 (tpp) REVERT: F 781 MET cc_start: 0.8665 (mpp) cc_final: 0.7925 (mpp) REVERT: F 956 MET cc_start: 0.8669 (mmp) cc_final: 0.8462 (mmm) REVERT: G 209 MET cc_start: 0.9212 (mtm) cc_final: 0.8677 (mtm) REVERT: G 304 MET cc_start: 0.7379 (tmm) cc_final: 0.7160 (tmm) outliers start: 1 outliers final: 1 residues processed: 141 average time/residue: 0.1752 time to fit residues: 43.8926 Evaluate side-chains 110 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 83 optimal weight: 0.0980 chunk 290 optimal weight: 6.9990 chunk 279 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 chunk 363 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 352 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 225 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 167 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 GLN ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1420 GLN ** G 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.082583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.060987 restraints weight = 170062.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.059703 restraints weight = 119258.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.060159 restraints weight = 111037.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.060265 restraints weight = 85863.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.060358 restraints weight = 81512.557| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 31772 Z= 0.097 Angle : 0.527 9.690 43120 Z= 0.266 Chirality : 0.041 0.198 4774 Planarity : 0.003 0.038 5478 Dihedral : 8.635 178.220 4366 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 0.03 % Allowed : 0.20 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3792 helix: 2.09 (0.15), residues: 1296 sheet: -0.12 (0.22), residues: 598 loop : -0.59 (0.15), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 392 TYR 0.030 0.001 TYR B 174 PHE 0.021 0.001 PHE A 891 TRP 0.024 0.001 TRP B 160 HIS 0.005 0.001 HIS F 794 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (31772) covalent geometry : angle 0.52749 / 0.27 (43120) hydrogen bonds : bond 0.03329 / 2.25 ( 1242) hydrogen bonds : angle 4.50432 / 3.19 ( 3522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4221.97 seconds wall clock time: 75 minutes 7.17 seconds (4507.17 seconds total)