Starting phenix.real_space_refine on Fri Jun 27 00:55:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d0k_27107/06_2025/8d0k_27107.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d0k_27107/06_2025/8d0k_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_27107/06_2025/8d0k_27107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d0k_27107/06_2025/8d0k_27107.map" model { file = "/net/cci-nas-00/data/ceres_data/8d0k_27107/06_2025/8d0k_27107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d0k_27107/06_2025/8d0k_27107.cif" } resolution = 4.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 18.32, per 1000 atoms: 0.59 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: 7.94 Conformation dependent library (CDL) restraints added in 4.0 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: 4.97 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: 13.29 Time building geometry restraints manager: 9.31 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=" 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=" N ASN F1030 " pdb=" CA ASN F1030 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.33e-02 5.65e+03 5.19e+00 bond pdb=" N GLN F 946 " pdb=" CA GLN F 946 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.19e-02 7.06e+03 4.25e+00 bond pdb=" N GLN A 432 " pdb=" CA GLN A 432 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.36e-02 5.41e+03 3.75e+00 bond pdb=" CE1 HIS A 494 " pdb=" NE2 HIS A 494 " ideal model delta sigma weight residual 1.321 1.337 -0.016 1.00e-02 1.00e+04 2.70e+00 ... (remaining 31767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 42406 1.69 - 3.37: 605 3.37 - 5.06: 89 5.06 - 6.74: 15 6.74 - 8.43: 5 Bond angle restraints: 43120 Sorted by residual: angle pdb=" C ASN A 890 " pdb=" N PHE A 891 " pdb=" CA PHE A 891 " ideal model delta sigma weight residual 121.54 128.62 -7.08 1.91e+00 2.74e-01 1.38e+01 angle pdb=" CA MET F 994 " pdb=" CB MET F 994 " pdb=" CG MET F 994 " ideal model delta sigma weight residual 114.10 121.26 -7.16 2.00e+00 2.50e-01 1.28e+01 angle pdb=" N GLN F 946 " pdb=" CA GLN F 946 " pdb=" C GLN F 946 " ideal model delta sigma weight residual 111.07 107.83 3.24 1.07e+00 8.73e-01 9.14e+00 angle pdb=" CA HIS A 494 " pdb=" C HIS A 494 " pdb=" O HIS A 494 " ideal model delta sigma weight residual 121.87 118.60 3.27 1.10e+00 8.26e-01 8.85e+00 angle pdb=" N GLU A 475 " pdb=" CA GLU A 475 " pdb=" CB GLU A 475 " ideal model delta sigma weight residual 110.12 114.47 -4.35 1.47e+00 4.63e-01 8.76e+00 ... (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: 3367 0.034 - 0.069: 954 0.069 - 0.103: 321 0.103 - 0.137: 129 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: 0.010 Normalize map: mean=0, sd=1: 3.570 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: 0.030 Extract box with map and model: 1.310 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 72.040 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 0.048 31772 Z= 0.104 Angle : 0.504 8.428 43120 Z= 0.258 Chirality : 0.039 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 : 9.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (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 TRP 0.015 0.001 TRP B 160 HIS 0.005 0.001 HIS E 351 PHE 0.040 0.001 PHE A 891 TYR 0.028 0.001 TYR B 174 ARG 0.005 0.000 ARG E 79 Details of bonding type rmsd hydrogen bonds : bond 0.19561 ( 1242) hydrogen bonds : angle 6.75820 ( 3522) covalent geometry : bond 0.00210 (31772) covalent geometry : angle 0.50393 (43120) *********************** 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 : 3.678 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: 0.7395 (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: 0.3732 time to fit residues: 102.7924 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 : 3.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 321 optimal weight: 0.9990 chunk 288 optimal weight: 0.7980 chunk 160 optimal weight: 0.7980 chunk 98 optimal weight: 0.4980 chunk 194 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 298 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 chunk 345 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN A 432 GLN A 505 GLN C 80 GLN E 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.082467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.060782 restraints weight = 169625.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.058847 restraints weight = 121594.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.059161 restraints weight = 123189.060| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0773 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= 0.118 Angle : 0.515 8.159 43120 Z= 0.268 Chirality : 0.040 0.154 4774 Planarity : 0.004 0.035 5478 Dihedral : 8.739 178.821 4366 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.03 % Favored : 95.89 % Rotamer: Outliers : 0.06 % Allowed : 3.82 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.14), residues: 3792 helix: 2.09 (0.15), residues: 1298 sheet: -0.04 (0.22), residues: 607 loop : -0.46 (0.15), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 160 HIS 0.015 0.001 HIS G 479 PHE 0.024 0.001 PHE A 891 TYR 0.015 0.001 TYR B 174 ARG 0.004 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.04224 ( 1242) hydrogen bonds : angle 5.20500 ( 3522) covalent geometry : bond 0.00253 (31772) covalent geometry : angle 0.51479 (43120) *********************** 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 151 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 3.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 PHE cc_start: 0.8221 (m-80) cc_final: 0.7744 (m-80) REVERT: A 742 MET cc_start: 0.8687 (pmm) cc_final: 0.8456 (pmm) REVERT: B 365 TYR cc_start: 0.8677 (m-80) cc_final: 0.8470 (m-80) REVERT: C 14 GLU cc_start: 0.9034 (mp0) cc_final: 0.8788 (mp0) REVERT: E 342 ASP cc_start: 0.8249 (t0) cc_final: 0.7952 (m-30) REVERT: F 560 MET cc_start: 0.8188 (mmp) cc_final: 0.7978 (mmm) REVERT: F 731 MET cc_start: 0.8345 (tpp) cc_final: 0.7991 (tpp) REVERT: F 781 MET cc_start: 0.8535 (mpp) cc_final: 0.7743 (mpp) REVERT: F 956 MET cc_start: 0.8741 (mmp) cc_final: 0.8541 (mmm) REVERT: F 1303 MET cc_start: 0.7033 (tpt) cc_final: 0.6619 (pmm) REVERT: G 402 PHE cc_start: 0.9054 (t80) cc_final: 0.8776 (t80) REVERT: G 574 LEU cc_start: 0.9653 (mm) cc_final: 0.9112 (pp) outliers start: 2 outliers final: 1 residues processed: 150 average time/residue: 0.3747 time to fit residues: 99.5422 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 : 3.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 92 optimal weight: 7.9990 chunk 212 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 241 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 298 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 320 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 HIS B 52 HIS ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN D 31 ASN E 24 HIS E 308 GLN ** E 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1009 ASN F1420 GLN ** G 515 GLN ** 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 = 0.3736 r_free = 0.3736 target = 0.079385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.058571 restraints weight = 174067.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.056537 restraints weight = 143873.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.057052 restraints weight = 142147.497| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 31772 Z= 0.311 Angle : 0.711 10.320 43120 Z= 0.362 Chirality : 0.044 0.172 4774 Planarity : 0.005 0.048 5478 Dihedral : 9.004 177.844 4366 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.59 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3792 helix: 1.62 (0.15), residues: 1299 sheet: -0.29 (0.21), residues: 592 loop : -0.74 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 160 HIS 0.012 0.002 HIS D 91 PHE 0.026 0.002 PHE E 143 TYR 0.035 0.002 TYR B 174 ARG 0.006 0.001 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.04926 ( 1242) hydrogen bonds : angle 5.43870 ( 3522) covalent geometry : bond 0.00685 (31772) covalent geometry : angle 0.71076 (43120) *********************** 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 135 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 3.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 742 MET cc_start: 0.8696 (pmm) cc_final: 0.8279 (pmm) REVERT: B 365 TYR cc_start: 0.8684 (m-80) cc_final: 0.8436 (m-80) REVERT: E 140 ILE cc_start: 0.8702 (pt) cc_final: 0.8491 (pt) REVERT: F 547 MET cc_start: 0.8085 (tmm) cc_final: 0.7867 (tmm) REVERT: F 560 MET cc_start: 0.8332 (mmp) cc_final: 0.8089 (mmm) REVERT: F 689 MET cc_start: 0.7698 (mmm) cc_final: 0.6319 (mmt) REVERT: F 731 MET cc_start: 0.8570 (tpp) cc_final: 0.8152 (tpp) REVERT: F 781 MET cc_start: 0.8753 (mpp) cc_final: 0.7915 (mpp) REVERT: F 956 MET cc_start: 0.8903 (mmp) cc_final: 0.8627 (mmm) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.3989 time to fit residues: 93.3434 Evaluate side-chains 106 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 3.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 273 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 297 optimal weight: 0.0470 chunk 24 optimal weight: 0.0050 chunk 153 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 256 optimal weight: 10.0000 chunk 286 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 302 optimal weight: 5.9990 overall best weight: 1.1896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 505 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 GLN F1420 GLN ** 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 = 0.3793 r_free = 0.3793 target = 0.081764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.060181 restraints weight = 170662.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.058310 restraints weight = 122467.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.058681 restraints weight = 122533.460| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31772 Z= 0.117 Angle : 0.535 8.625 43120 Z= 0.276 Chirality : 0.041 0.181 4774 Planarity : 0.004 0.042 5478 Dihedral : 8.861 179.430 4366 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 0.06 % Allowed : 2.91 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3792 helix: 1.88 (0.15), residues: 1293 sheet: -0.28 (0.21), residues: 603 loop : -0.62 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 160 HIS 0.005 0.001 HIS G 479 PHE 0.024 0.001 PHE E 222 TYR 0.023 0.001 TYR B 174 ARG 0.005 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 1242) hydrogen bonds : angle 4.93177 ( 3522) covalent geometry : bond 0.00256 (31772) covalent geometry : angle 0.53523 (43120) *********************** 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 143 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 141 time to evaluate : 3.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 PHE cc_start: 0.8270 (m-80) cc_final: 0.7748 (m-80) REVERT: A 742 MET cc_start: 0.8619 (pmm) cc_final: 0.8264 (pmm) REVERT: B 20 ASP cc_start: 0.8562 (m-30) cc_final: 0.7821 (t70) REVERT: B 210 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7864 (pm20) REVERT: F 379 MET cc_start: 0.8463 (tpp) cc_final: 0.8011 (tpp) REVERT: F 731 MET cc_start: 0.8560 (tpp) cc_final: 0.8048 (tpp) REVERT: F 781 MET cc_start: 0.8613 (mpp) cc_final: 0.8158 (mpp) REVERT: F 956 MET cc_start: 0.8832 (mmp) cc_final: 0.8602 (mmm) REVERT: F 1303 MET cc_start: 0.6894 (tpt) cc_final: 0.6409 (pmm) REVERT: G 574 LEU cc_start: 0.9608 (mm) cc_final: 0.9106 (pp) outliers start: 2 outliers final: 1 residues processed: 143 average time/residue: 0.3987 time to fit residues: 99.1687 Evaluate side-chains 114 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 3.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 257 optimal weight: 20.0000 chunk 306 optimal weight: 7.9990 chunk 336 optimal weight: 9.9990 chunk 219 optimal weight: 0.0870 chunk 323 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 217 optimal weight: 0.0040 chunk 66 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 overall best weight: 2.6176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 HIS ** E 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 GLN ** F 548 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.080728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.059196 restraints weight = 171400.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.057286 restraints weight = 126016.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.057574 restraints weight = 126153.149| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31772 Z= 0.182 Angle : 0.569 8.025 43120 Z= 0.292 Chirality : 0.041 0.150 4774 Planarity : 0.004 0.041 5478 Dihedral : 8.887 179.139 4366 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.04 % Favored : 93.93 % Rotamer: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3792 helix: 1.88 (0.15), residues: 1292 sheet: -0.24 (0.21), residues: 610 loop : -0.67 (0.15), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 160 HIS 0.007 0.001 HIS D 91 PHE 0.022 0.002 PHE E 222 TYR 0.023 0.001 TYR B 174 ARG 0.006 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 1242) hydrogen bonds : angle 4.91233 ( 3522) covalent geometry : bond 0.00405 (31772) covalent geometry : angle 0.56949 (43120) *********************** 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 136 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 3.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 PHE cc_start: 0.8251 (m-80) cc_final: 0.7864 (m-80) REVERT: A 283 LEU cc_start: 0.9230 (tp) cc_final: 0.8987 (tp) REVERT: A 742 MET cc_start: 0.8552 (pmm) cc_final: 0.8233 (pmm) REVERT: F 379 MET cc_start: 0.8385 (tpp) cc_final: 0.8114 (tpp) REVERT: F 689 MET cc_start: 0.8127 (mmm) cc_final: 0.7722 (mmm) REVERT: F 731 MET cc_start: 0.8746 (tpp) cc_final: 0.8196 (tpp) REVERT: F 781 MET cc_start: 0.8664 (mpp) cc_final: 0.7799 (mpp) REVERT: F 956 MET cc_start: 0.8836 (mmp) cc_final: 0.8569 (mmm) REVERT: F 1303 MET cc_start: 0.7062 (tpt) cc_final: 0.6538 (pmm) outliers start: 1 outliers final: 1 residues processed: 136 average time/residue: 0.3699 time to fit residues: 89.1360 Evaluate side-chains 109 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 3.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 147 optimal weight: 6.9990 chunk 159 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 315 optimal weight: 4.9990 chunk 369 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 329 optimal weight: 8.9990 chunk 330 optimal weight: 5.9990 chunk 346 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 691 GLN A 875 ASN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN D 31 ASN F 946 GLN F1420 GLN G 211 GLN ** G 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.081726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.060123 restraints weight = 171292.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.058197 restraints weight = 122538.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.058623 restraints weight = 118969.934| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31772 Z= 0.126 Angle : 0.529 8.147 43120 Z= 0.271 Chirality : 0.041 0.165 4774 Planarity : 0.004 0.039 5478 Dihedral : 8.793 179.899 4366 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.56 % Favored : 95.39 % Rotamer: Outliers : 0.06 % Allowed : 1.34 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 3792 helix: 1.97 (0.15), residues: 1296 sheet: -0.33 (0.21), residues: 603 loop : -0.60 (0.15), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 160 HIS 0.004 0.001 HIS G 479 PHE 0.022 0.001 PHE A 891 TYR 0.028 0.001 TYR B 174 ARG 0.006 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 1242) hydrogen bonds : angle 4.71578 ( 3522) covalent geometry : bond 0.00279 (31772) covalent geometry : angle 0.52915 (43120) *********************** 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 144 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 3.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 PHE cc_start: 0.8298 (m-80) cc_final: 0.7764 (m-80) REVERT: A 283 LEU cc_start: 0.9192 (tp) cc_final: 0.8963 (tp) REVERT: A 742 MET cc_start: 0.8410 (pmm) cc_final: 0.8070 (pmm) REVERT: F 379 MET cc_start: 0.8319 (tpp) cc_final: 0.8099 (tpp) REVERT: F 560 MET cc_start: 0.8263 (mmp) cc_final: 0.8004 (mmm) REVERT: F 689 MET cc_start: 0.8026 (mmm) cc_final: 0.7232 (mmm) REVERT: F 731 MET cc_start: 0.8831 (tpp) cc_final: 0.8382 (tpp) REVERT: F 781 MET cc_start: 0.8674 (mpp) cc_final: 0.7929 (mpp) REVERT: F 956 MET cc_start: 0.8816 (mmp) cc_final: 0.8551 (mmm) REVERT: F 1303 MET cc_start: 0.6979 (tpt) cc_final: 0.6457 (pmm) outliers start: 2 outliers final: 1 residues processed: 144 average time/residue: 0.3843 time to fit residues: 97.7553 Evaluate side-chains 109 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 4.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 52 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 316 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 289 optimal weight: 2.9990 chunk 379 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 191 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 125 optimal weight: 0.3980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN F 946 GLN F1420 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 = 0.3789 r_free = 0.3789 target = 0.081938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.060042 restraints weight = 169995.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.058576 restraints weight = 122386.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.059158 restraints weight = 110624.223| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 31772 Z= 0.099 Angle : 0.517 8.851 43120 Z= 0.261 Chirality : 0.041 0.173 4774 Planarity : 0.004 0.038 5478 Dihedral : 8.668 179.539 4366 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.70 % Rotamer: Outliers : 0.06 % Allowed : 1.25 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.14), residues: 3792 helix: 2.03 (0.15), residues: 1296 sheet: -0.22 (0.21), residues: 607 loop : -0.56 (0.15), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 160 HIS 0.005 0.001 HIS A 84 PHE 0.022 0.001 PHE A 891 TYR 0.019 0.001 TYR B 174 ARG 0.006 0.000 ARG A 436 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 1242) hydrogen bonds : angle 4.53798 ( 3522) covalent geometry : bond 0.00218 (31772) covalent geometry : angle 0.51668 (43120) *********************** 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 145 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 3.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 PHE cc_start: 0.8181 (m-80) cc_final: 0.7661 (m-80) REVERT: A 283 LEU cc_start: 0.9179 (tp) cc_final: 0.8970 (tp) REVERT: A 742 MET cc_start: 0.8459 (pmm) cc_final: 0.8162 (pmm) REVERT: B 231 MET cc_start: 0.8218 (ppp) cc_final: 0.8014 (ppp) REVERT: F 560 MET cc_start: 0.8243 (mmp) cc_final: 0.7999 (mmm) REVERT: F 731 MET cc_start: 0.8839 (tpp) cc_final: 0.8409 (tpp) REVERT: F 781 MET cc_start: 0.8710 (mpp) cc_final: 0.8508 (mpp) REVERT: F 956 MET cc_start: 0.8783 (mmp) cc_final: 0.8521 (mmm) REVERT: F 1303 MET cc_start: 0.6918 (tpt) cc_final: 0.6568 (pmm) outliers start: 2 outliers final: 2 residues processed: 145 average time/residue: 0.3875 time to fit residues: 99.4136 Evaluate side-chains 111 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 3.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 367 optimal weight: 0.7980 chunk 349 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 787 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 HIS ** 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 = 0.3749 r_free = 0.3749 target = 0.080092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.058308 restraints weight = 173403.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.056756 restraints weight = 131880.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.057290 restraints weight = 122664.265| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 31772 Z= 0.212 Angle : 0.598 9.358 43120 Z= 0.306 Chirality : 0.042 0.159 4774 Planarity : 0.004 0.036 5478 Dihedral : 8.739 179.271 4366 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.99 % Favored : 93.96 % Rotamer: Outliers : 0.03 % Allowed : 1.14 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.14), residues: 3792 helix: 1.89 (0.15), residues: 1301 sheet: -0.33 (0.21), residues: 595 loop : -0.68 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 160 HIS 0.009 0.001 HIS D 91 PHE 0.031 0.002 PHE B 182 TYR 0.024 0.001 TYR B 174 ARG 0.006 0.000 ARG F 922 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 1242) hydrogen bonds : angle 4.80045 ( 3522) covalent geometry : bond 0.00472 (31772) covalent geometry : angle 0.59840 (43120) *********************** 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 135 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 3.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 PHE cc_start: 0.8276 (m-80) cc_final: 0.7666 (m-80) REVERT: A 283 LEU cc_start: 0.9184 (tp) cc_final: 0.8961 (tp) REVERT: A 742 MET cc_start: 0.8503 (pmm) cc_final: 0.8074 (pmm) REVERT: B 167 MET cc_start: 0.9124 (ppp) cc_final: 0.8699 (ppp) REVERT: F 379 MET cc_start: 0.8796 (tpt) cc_final: 0.8561 (tpp) REVERT: F 560 MET cc_start: 0.8363 (mmp) cc_final: 0.8069 (mmm) REVERT: F 689 MET cc_start: 0.8009 (mmm) cc_final: 0.7550 (mmm) REVERT: F 731 MET cc_start: 0.8882 (tpp) cc_final: 0.8446 (tpp) REVERT: F 781 MET cc_start: 0.8708 (mpp) cc_final: 0.8488 (mpp) REVERT: F 956 MET cc_start: 0.8865 (mmp) cc_final: 0.8554 (mmm) REVERT: F 1303 MET cc_start: 0.6938 (tpt) cc_final: 0.6504 (pmm) outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 0.3926 time to fit residues: 93.2701 Evaluate side-chains 109 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 5.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 161 optimal weight: 0.9990 chunk 351 optimal weight: 0.5980 chunk 340 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 345 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 203 optimal weight: 0.8980 chunk 285 optimal weight: 3.9990 chunk 320 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN 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 = 0.3782 r_free = 0.3782 target = 0.081575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.059554 restraints weight = 170544.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.057756 restraints weight = 118891.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.058151 restraints weight = 112728.337| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 31772 Z= 0.105 Angle : 0.533 10.296 43120 Z= 0.269 Chirality : 0.041 0.158 4774 Planarity : 0.004 0.038 5478 Dihedral : 8.644 179.949 4366 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.32 % Favored : 95.62 % Rotamer: Outliers : 0.03 % Allowed : 0.41 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.14), residues: 3792 helix: 2.01 (0.15), residues: 1294 sheet: -0.23 (0.21), residues: 611 loop : -0.63 (0.15), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP D 240 HIS 0.005 0.001 HIS B 183 PHE 0.033 0.001 PHE F1364 TYR 0.028 0.001 TYR B 174 ARG 0.004 0.000 ARG F 392 Details of bonding type rmsd hydrogen bonds : bond 0.03501 ( 1242) hydrogen bonds : angle 4.58498 ( 3522) covalent geometry : bond 0.00231 (31772) covalent geometry : angle 0.53345 (43120) *********************** 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 142 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 5.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 PHE cc_start: 0.8357 (m-80) cc_final: 0.7823 (m-80) REVERT: A 262 ILE cc_start: 0.8423 (mt) cc_final: 0.8105 (mm) REVERT: A 283 LEU cc_start: 0.9235 (tp) cc_final: 0.9004 (tp) REVERT: A 742 MET cc_start: 0.8532 (pmm) cc_final: 0.8233 (pmm) REVERT: F 379 MET cc_start: 0.8642 (tpt) cc_final: 0.8406 (tpp) REVERT: F 731 MET cc_start: 0.8844 (tpp) cc_final: 0.8387 (tpp) REVERT: F 956 MET cc_start: 0.8856 (mmp) cc_final: 0.8557 (mmm) REVERT: F 1303 MET cc_start: 0.6977 (tpt) cc_final: 0.6535 (pmm) outliers start: 1 outliers final: 1 residues processed: 142 average time/residue: 0.6138 time to fit residues: 157.4628 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 : 5.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 274 optimal weight: 0.6980 chunk 224 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 243 optimal weight: 0.6980 chunk 249 optimal weight: 7.9990 chunk 298 optimal weight: 6.9990 chunk 349 optimal weight: 5.9990 chunk 296 optimal weight: 6.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN A 432 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 HIS ** 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 = 0.3736 r_free = 0.3736 target = 0.079529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.053643 restraints weight = 173287.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.053355 restraints weight = 118876.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.053460 restraints weight = 96189.736| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 31772 Z= 0.237 Angle : 0.644 9.713 43120 Z= 0.328 Chirality : 0.043 0.161 4774 Planarity : 0.004 0.060 5478 Dihedral : 8.801 179.340 4366 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.86 % Favored : 93.09 % Rotamer: Outliers : 0.03 % Allowed : 0.17 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.14), residues: 3792 helix: 1.73 (0.15), residues: 1300 sheet: -0.32 (0.21), residues: 603 loop : -0.77 (0.15), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 240 HIS 0.010 0.001 HIS D 91 PHE 0.036 0.002 PHE F1364 TYR 0.038 0.002 TYR B 174 ARG 0.007 0.001 ARG E 235 Details of bonding type rmsd hydrogen bonds : bond 0.04180 ( 1242) hydrogen bonds : angle 4.93149 ( 3522) covalent geometry : bond 0.00524 (31772) covalent geometry : angle 0.64394 (43120) ********************** 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 130 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 3.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ILE cc_start: 0.8526 (mt) cc_final: 0.8196 (mm) REVERT: A 283 LEU cc_start: 0.9212 (tp) cc_final: 0.8984 (tp) REVERT: A 742 MET cc_start: 0.8506 (pmm) cc_final: 0.8080 (pmm) REVERT: B 167 MET cc_start: 0.9037 (ppp) cc_final: 0.8578 (ppp) REVERT: F 379 MET cc_start: 0.8888 (tpt) cc_final: 0.8677 (tpp) REVERT: F 731 MET cc_start: 0.8870 (tpp) cc_final: 0.8568 (tpp) REVERT: F 781 MET cc_start: 0.8646 (mpp) cc_final: 0.8027 (mpp) REVERT: F 956 MET cc_start: 0.8975 (mmp) cc_final: 0.8654 (mmm) REVERT: F 1303 MET cc_start: 0.7097 (tpt) cc_final: 0.6667 (pmm) outliers start: 1 outliers final: 1 residues processed: 130 average time/residue: 0.3757 time to fit residues: 85.9489 Evaluate side-chains 98 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 4.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 51 optimal weight: 0.0020 chunk 215 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 260 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 322 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 259 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 250 optimal weight: 4.9990 chunk 359 optimal weight: 7.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.081281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.059497 restraints weight = 169603.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.057909 restraints weight = 121478.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.058250 restraints weight = 119184.413| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1920 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= 0.111 Angle : 0.538 9.858 43120 Z= 0.273 Chirality : 0.041 0.158 4774 Planarity : 0.004 0.038 5478 Dihedral : 8.649 178.987 4366 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.61 % Favored : 95.33 % Rotamer: Outliers : 0.03 % Allowed : 0.41 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3792 helix: 2.02 (0.15), residues: 1289 sheet: -0.29 (0.22), residues: 590 loop : -0.67 (0.15), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP D 240 HIS 0.005 0.001 HIS B 183 PHE 0.027 0.001 PHE F1364 TYR 0.033 0.001 TYR B 174 ARG 0.002 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 1242) hydrogen bonds : angle 4.61287 ( 3522) covalent geometry : bond 0.00248 (31772) covalent geometry : angle 0.53777 (43120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8590.18 seconds wall clock time: 153 minutes 47.16 seconds (9227.16 seconds total)