Starting phenix.real_space_refine on Mon Dec 30 20:58:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gh2_40031/12_2024/8gh2_40031.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gh2_40031/12_2024/8gh2_40031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gh2_40031/12_2024/8gh2_40031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gh2_40031/12_2024/8gh2_40031.map" model { file = "/net/cci-nas-00/data/ceres_data/8gh2_40031/12_2024/8gh2_40031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gh2_40031/12_2024/8gh2_40031.cif" } resolution = 3.66 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= -0.000 sd= 0.017 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: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 8812 2.51 5 N 2465 2.21 5 O 2583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13941 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2390 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 299} Chain: "C" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2390 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 299} Chain: "B" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2390 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 299} Chain: "D" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2390 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 299} Chain: "F" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2352 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 14, 'TRANS': 281} Chain breaks: 1 Chain: "E" Number of atoms: 2029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2029 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 12, 'TRANS': 245} Chain breaks: 1 Time building chain proxies: 9.20, per 1000 atoms: 0.66 Number of scatterers: 13941 At special positions: 0 Unit cell: (102.34, 119.54, 155.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 2583 8.00 N 2465 7.00 C 8812 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: 3.65 Conformation dependent library (CDL) restraints added in 2.0 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3404 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 12 sheets defined 55.1% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 39 through 47 Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 95 through 116 removed outlier: 3.834A pdb=" N LEU A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 145 Proline residue: A 135 - end of helix removed outlier: 3.622A pdb=" N ILE A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 removed outlier: 4.014A pdb=" N GLY A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 removed outlier: 3.996A pdb=" N ILE A 197 " --> pdb=" O TYR A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.549A pdb=" N LYS A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.729A pdb=" N GLY A 239 " --> pdb=" O MET A 235 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 316 removed outlier: 3.645A pdb=" N LYS A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 22 removed outlier: 3.970A pdb=" N SER C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU C 17 " --> pdb=" O ILE C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 69 through 76 removed outlier: 3.646A pdb=" N THR C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 116 removed outlier: 3.729A pdb=" N LEU C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN C 101 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA C 104 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY C 105 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE C 106 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N CYS C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 145 Proline residue: C 135 - end of helix removed outlier: 4.129A pdb=" N ILE C 144 " --> pdb=" O THR C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 171 removed outlier: 3.827A pdb=" N GLY C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 170 " --> pdb=" O PHE C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 190 Processing helix chain 'C' and resid 203 through 226 removed outlier: 4.042A pdb=" N GLU C 209 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 210 " --> pdb=" O THR C 206 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLY C 218 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N THR C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU C 220 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL C 222 " --> pdb=" O GLY C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 251 Processing helix chain 'C' and resid 294 through 319 removed outlier: 3.992A pdb=" N LYS C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU C 299 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 23 removed outlier: 3.668A pdb=" N ARG B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 46 Processing helix chain 'B' and resid 69 through 75 Processing helix chain 'B' and resid 97 through 116 removed outlier: 4.458A pdb=" N ASN B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 145 removed outlier: 3.904A pdb=" N THR B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Proline residue: B 135 - end of helix Processing helix chain 'B' and resid 156 through 171 removed outlier: 4.001A pdb=" N GLY B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B 170 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG B 171 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 232 through 252 removed outlier: 3.744A pdb=" N ALA B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 323 removed outlier: 4.216A pdb=" N GLU B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N MET B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 302 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 23 Processing helix chain 'D' and resid 38 through 46 removed outlier: 3.618A pdb=" N VAL D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 71 through 76 removed outlier: 4.195A pdb=" N LEU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA D 76 " --> pdb=" O LEU D 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 71 through 76' Processing helix chain 'D' and resid 97 through 113 removed outlier: 4.392A pdb=" N GLY D 105 " --> pdb=" O ASN D 101 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 107 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 116 No H-bonds generated for 'chain 'D' and resid 114 through 116' Processing helix chain 'D' and resid 132 through 145 removed outlier: 3.590A pdb=" N ILE D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE D 144 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.650A pdb=" N GLY D 160 " --> pdb=" O SER D 156 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG D 171 " --> pdb=" O ILE D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 231 through 252 removed outlier: 3.783A pdb=" N GLY D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 316 removed outlier: 3.742A pdb=" N MET D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU D 303 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D 313 " --> pdb=" O LYS D 309 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 316 " --> pdb=" O ILE D 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 346 removed outlier: 4.617A pdb=" N ARG F 330 " --> pdb=" O GLU F 326 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLU F 331 " --> pdb=" O GLU F 327 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR F 332 " --> pdb=" O TRP F 328 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA F 335 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 369 Processing helix chain 'F' and resid 376 through 387 removed outlier: 3.726A pdb=" N LEU F 380 " --> pdb=" O ALA F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 406 removed outlier: 3.528A pdb=" N TRP F 396 " --> pdb=" O ASN F 392 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU F 399 " --> pdb=" O ALA F 395 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY F 400 " --> pdb=" O TRP F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 421 removed outlier: 4.355A pdb=" N ILE F 414 " --> pdb=" O CYS F 410 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET F 421 " --> pdb=" O ASN F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 440 removed outlier: 3.963A pdb=" N VAL F 435 " --> pdb=" O ALA F 431 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU F 440 " --> pdb=" O SER F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 456 removed outlier: 3.711A pdb=" N ALA F 446 " --> pdb=" O ASN F 442 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU F 447 " --> pdb=" O VAL F 443 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN F 448 " --> pdb=" O GLY F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 493 through 502 Processing helix chain 'F' and resid 510 through 524 removed outlier: 3.632A pdb=" N SER F 524 " --> pdb=" O LEU F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 526 through 539 removed outlier: 3.659A pdb=" N LYS F 532 " --> pdb=" O ASP F 528 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU F 539 " --> pdb=" O ARG F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 557 removed outlier: 4.024A pdb=" N TRP F 548 " --> pdb=" O ASP F 544 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR F 554 " --> pdb=" O LYS F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 575 removed outlier: 3.756A pdb=" N GLU F 566 " --> pdb=" O GLN F 562 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ARG F 570 " --> pdb=" O GLU F 566 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA F 571 " --> pdb=" O ALA F 567 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP F 573 " --> pdb=" O ASN F 569 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN F 575 " --> pdb=" O ALA F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 592 Processing helix chain 'F' and resid 594 through 610 Processing helix chain 'F' and resid 620 through 623 removed outlier: 4.319A pdb=" N ALA F 623 " --> pdb=" O SER F 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 620 through 623' Processing helix chain 'F' and resid 624 through 632 removed outlier: 3.704A pdb=" N LEU F 630 " --> pdb=" O GLY F 626 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU F 631 " --> pdb=" O LEU F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 639 removed outlier: 4.014A pdb=" N MET F 638 " --> pdb=" O THR F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 643 through 648 removed outlier: 3.911A pdb=" N SER F 647 " --> pdb=" O VAL F 644 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 346 Processing helix chain 'E' and resid 362 through 370 removed outlier: 3.813A pdb=" N LEU E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 387 removed outlier: 4.172A pdb=" N ALA E 378 " --> pdb=" O ASN E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 406 Processing helix chain 'E' and resid 410 through 423 removed outlier: 4.115A pdb=" N ILE E 414 " --> pdb=" O CYS E 410 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS E 418 " --> pdb=" O ILE E 414 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA E 419 " --> pdb=" O ALA E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 441 removed outlier: 3.825A pdb=" N VAL E 435 " --> pdb=" O ALA E 431 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU E 440 " --> pdb=" O SER E 436 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS E 441 " --> pdb=" O HIS E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 456 removed outlier: 3.741A pdb=" N SER E 456 " --> pdb=" O SER E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 524 removed outlier: 3.594A pdb=" N SER E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 541 removed outlier: 3.560A pdb=" N ALA E 531 " --> pdb=" O PHE E 527 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LYS E 532 " --> pdb=" O ASP E 528 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ASN E 533 " --> pdb=" O GLU E 529 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE E 534 " --> pdb=" O ALA E 530 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU E 539 " --> pdb=" O ARG E 535 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU E 540 " --> pdb=" O ARG E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 558 removed outlier: 4.031A pdb=" N TRP E 548 " --> pdb=" O ASP E 544 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU E 551 " --> pdb=" O MET E 547 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY E 558 " --> pdb=" O THR E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 566 Processing helix chain 'E' and resid 570 through 574 Processing helix chain 'E' and resid 578 through 593 Processing helix chain 'E' and resid 596 through 610 removed outlier: 3.856A pdb=" N LYS E 600 " --> pdb=" O PRO E 596 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 625 Processing helix chain 'E' and resid 626 through 638 removed outlier: 3.653A pdb=" N LEU E 630 " --> pdb=" O GLY E 626 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG E 632 " --> pdb=" O TRP E 628 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN E 636 " --> pdb=" O ARG E 632 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 59 removed outlier: 6.571A pdb=" N VAL A 4 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N TYR A 34 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 6 " --> pdb=" O TYR A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 263 removed outlier: 3.890A pdb=" N ALA A 260 " --> pdb=" O MET A 275 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET A 275 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 57 through 58 removed outlier: 6.636A pdb=" N LEU C 31 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL C 4 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N TYR C 34 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL C 6 " --> pdb=" O TYR C 34 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN C 3 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL C 83 " --> pdb=" O ASN C 3 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA C 5 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 257 through 263 removed outlier: 4.253A pdb=" N ALA C 260 " --> pdb=" O MET C 275 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET C 275 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG C 286 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY C 280 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ILE C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 60 removed outlier: 4.263A pdb=" N ASP B 35 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 32 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 82 " --> pdb=" O CYS B 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.781A pdb=" N VAL B 182 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL B 191 " --> pdb=" O VAL B 182 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 257 through 262 removed outlier: 5.544A pdb=" N ARG B 287 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL B 278 " --> pdb=" O GLU B 285 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B 283 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 54 through 56 removed outlier: 3.569A pdb=" N THR D 55 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL D 4 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL D 81 " --> pdb=" O ASN D 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 124 through 125 Processing sheet with id=AB2, first strand: chain 'D' and resid 182 through 183 Processing sheet with id=AB3, first strand: chain 'D' and resid 257 through 260 removed outlier: 3.634A pdb=" N ALA D 260 " --> pdb=" O MET D 275 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET D 275 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG D 286 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY D 280 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ILE D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1830 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: 3.80 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3886 1.33 - 1.46: 2154 1.46 - 1.58: 8020 1.58 - 1.70: 1 1.70 - 1.82: 140 Bond restraints: 14201 Sorted by residual: bond pdb=" CA LEU D 157 " pdb=" C LEU D 157 " ideal model delta sigma weight residual 1.522 1.480 0.043 1.40e-02 5.10e+03 9.36e+00 bond pdb=" CA VAL D 179 " pdb=" C VAL D 179 " ideal model delta sigma weight residual 1.522 1.501 0.021 7.10e-03 1.98e+04 8.56e+00 bond pdb=" CA TYR D 259 " pdb=" C TYR D 259 " ideal model delta sigma weight residual 1.530 1.499 0.031 1.08e-02 8.57e+03 8.47e+00 bond pdb=" N VAL D 262 " pdb=" CA VAL D 262 " ideal model delta sigma weight residual 1.458 1.425 0.033 1.17e-02 7.31e+03 8.04e+00 bond pdb=" CA TYR D 261 " pdb=" C TYR D 261 " ideal model delta sigma weight residual 1.526 1.484 0.042 1.51e-02 4.39e+03 7.88e+00 ... (remaining 14196 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 18814 2.21 - 4.43: 425 4.43 - 6.64: 63 6.64 - 8.85: 16 8.85 - 11.07: 4 Bond angle restraints: 19322 Sorted by residual: angle pdb=" N LEU D 158 " pdb=" CA LEU D 158 " pdb=" C LEU D 158 " ideal model delta sigma weight residual 111.75 104.40 7.35 1.28e+00 6.10e-01 3.30e+01 angle pdb=" C THR D 127 " pdb=" N ASN D 128 " pdb=" CA ASN D 128 " ideal model delta sigma weight residual 121.61 128.44 -6.83 1.39e+00 5.18e-01 2.41e+01 angle pdb=" N GLN D 196 " pdb=" CA GLN D 196 " pdb=" C GLN D 196 " ideal model delta sigma weight residual 112.41 106.34 6.07 1.30e+00 5.92e-01 2.18e+01 angle pdb=" C HIS C 172 " pdb=" CA HIS C 172 " pdb=" CB HIS C 172 " ideal model delta sigma weight residual 110.17 119.26 -9.09 1.97e+00 2.58e-01 2.13e+01 angle pdb=" C GLY A 38 " pdb=" N ALA A 39 " pdb=" CA ALA A 39 " ideal model delta sigma weight residual 121.80 132.87 -11.07 2.44e+00 1.68e-01 2.06e+01 ... (remaining 19317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 7782 17.88 - 35.77: 700 35.77 - 53.65: 148 53.65 - 71.54: 31 71.54 - 89.42: 15 Dihedral angle restraints: 8676 sinusoidal: 3390 harmonic: 5286 Sorted by residual: dihedral pdb=" CA HIS C 172 " pdb=" C HIS C 172 " pdb=" N PRO C 173 " pdb=" CA PRO C 173 " ideal model delta harmonic sigma weight residual 180.00 -128.08 -51.92 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CA ASN F 354 " pdb=" C ASN F 354 " pdb=" N PRO F 355 " pdb=" CA PRO F 355 " ideal model delta harmonic sigma weight residual 180.00 -150.05 -29.95 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ARG B 96 " pdb=" C ARG B 96 " pdb=" N ASP B 97 " pdb=" CA ASP B 97 " ideal model delta harmonic sigma weight residual -180.00 -151.01 -28.99 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 8673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1717 0.045 - 0.091: 412 0.091 - 0.136: 128 0.136 - 0.181: 12 0.181 - 0.227: 4 Chirality restraints: 2273 Sorted by residual: chirality pdb=" CB ILE F 622 " pdb=" CA ILE F 622 " pdb=" CG1 ILE F 622 " pdb=" CG2 ILE F 622 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA HIS D 172 " pdb=" N HIS D 172 " pdb=" C HIS D 172 " pdb=" CB HIS D 172 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA HIS A 172 " pdb=" N HIS A 172 " pdb=" C HIS A 172 " pdb=" CB HIS A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2270 not shown) Planarity restraints: 2522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 172 " -0.078 5.00e-02 4.00e+02 1.17e-01 2.17e+01 pdb=" N PRO C 173 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO C 173 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO C 173 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 354 " 0.069 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO F 355 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO F 355 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO F 355 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER D 156 " -0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C SER D 156 " 0.065 2.00e-02 2.50e+03 pdb=" O SER D 156 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU D 157 " -0.022 2.00e-02 2.50e+03 ... (remaining 2519 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2305 2.76 - 3.30: 14370 3.30 - 3.83: 22394 3.83 - 4.37: 24736 4.37 - 4.90: 42172 Nonbonded interactions: 105977 Sorted by model distance: nonbonded pdb=" O GLU A 316 " pdb=" OG1 THR A 317 " model vdw 2.227 3.040 nonbonded pdb=" O VAL E 342 " pdb=" OG1 THR E 346 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASN D 3 " pdb=" OG1 THR D 30 " model vdw 2.266 3.040 nonbonded pdb=" O ILE F 367 " pdb=" NE2 GLN F 371 " model vdw 2.283 3.120 nonbonded pdb=" OD1 ASP D 50 " pdb=" N ARG D 51 " model vdw 2.288 3.120 ... (remaining 105972 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 336 through 459 or resid 515 through 648)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.360 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: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.330 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 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 : 0.004 0.064 14201 Z= 0.245 Angle : 0.782 11.066 19322 Z= 0.435 Chirality : 0.044 0.227 2273 Planarity : 0.006 0.117 2522 Dihedral : 14.741 89.425 5272 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.93 % Allowed : 12.13 % Favored : 86.94 % Rotamer: Outliers : 2.14 % Allowed : 1.20 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.21), residues: 1830 helix: 0.27 (0.19), residues: 889 sheet: -1.60 (0.48), residues: 135 loop : -2.33 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 648 HIS 0.010 0.001 HIS C 172 PHE 0.012 0.001 PHE F 534 TYR 0.034 0.002 TYR E 358 ARG 0.005 0.000 ARG E 535 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 219 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 207 LEU cc_start: 0.7939 (tt) cc_final: 0.7315 (mp) REVERT: C 235 MET cc_start: 0.6879 (mtp) cc_final: 0.6651 (mtp) REVERT: C 261 TYR cc_start: 0.8782 (t80) cc_final: 0.8391 (t80) REVERT: D 46 LEU cc_start: 0.7948 (mm) cc_final: 0.7197 (pp) REVERT: E 382 PHE cc_start: 0.7361 (m-80) cc_final: 0.7121 (m-80) outliers start: 32 outliers final: 4 residues processed: 238 average time/residue: 0.2659 time to fit residues: 92.9747 Evaluate side-chains 166 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 162 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 197 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 9.9990 chunk 137 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 93 optimal weight: 0.0370 chunk 73 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 169 ASN ** C 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS F 344 ASN F 371 GLN F 549 ASN F 584 ASN E 614 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14201 Z= 0.211 Angle : 0.694 11.247 19322 Z= 0.344 Chirality : 0.044 0.220 2273 Planarity : 0.006 0.108 2522 Dihedral : 5.108 58.610 1992 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.60 % Favored : 88.85 % Rotamer: Outliers : 1.40 % Allowed : 9.76 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.21), residues: 1830 helix: 0.58 (0.18), residues: 934 sheet: -1.59 (0.48), residues: 135 loop : -2.30 (0.24), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 648 HIS 0.009 0.001 HIS E 601 PHE 0.022 0.002 PHE E 382 TYR 0.020 0.002 TYR E 568 ARG 0.004 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 ARG cc_start: 0.7457 (mmt180) cc_final: 0.7235 (mmp-170) REVERT: C 207 LEU cc_start: 0.8042 (tt) cc_final: 0.7336 (mp) REVERT: C 235 MET cc_start: 0.7132 (mtp) cc_final: 0.6638 (mtp) REVERT: C 261 TYR cc_start: 0.8796 (t80) cc_final: 0.8549 (t80) REVERT: C 320 ARG cc_start: 0.8009 (ptt-90) cc_final: 0.7602 (ptt-90) REVERT: D 190 ILE cc_start: 0.6667 (OUTLIER) cc_final: 0.5957 (mt) REVERT: F 369 MET cc_start: 0.6517 (ttt) cc_final: 0.6198 (ttt) REVERT: F 629 ASP cc_start: 0.8169 (m-30) cc_final: 0.7916 (m-30) REVERT: F 638 MET cc_start: 0.8812 (mmm) cc_final: 0.8539 (mpp) outliers start: 21 outliers final: 13 residues processed: 189 average time/residue: 0.2443 time to fit residues: 70.8388 Evaluate side-chains 166 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain D residue 178 TYR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 441 HIS Chi-restraints excluded: chain E residue 358 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN C 268 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14201 Z= 0.195 Angle : 0.654 11.316 19322 Z= 0.323 Chirality : 0.044 0.237 2273 Planarity : 0.005 0.109 2522 Dihedral : 4.962 55.970 1991 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.55 % Favored : 88.91 % Rotamer: Outliers : 2.14 % Allowed : 12.23 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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: -0.90 (0.21), residues: 1830 helix: 0.80 (0.18), residues: 933 sheet: -1.59 (0.48), residues: 135 loop : -2.24 (0.24), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 648 HIS 0.008 0.001 HIS E 601 PHE 0.025 0.002 PHE C 100 TYR 0.014 0.001 TYR F 568 ARG 0.003 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 HIS cc_start: 0.7594 (t-90) cc_final: 0.7314 (t-90) REVERT: C 207 LEU cc_start: 0.8009 (tt) cc_final: 0.7351 (mp) REVERT: C 235 MET cc_start: 0.7211 (mtp) cc_final: 0.6881 (mtp) REVERT: C 261 TYR cc_start: 0.8796 (t80) cc_final: 0.8575 (t80) REVERT: C 320 ARG cc_start: 0.8019 (ptt-90) cc_final: 0.7644 (ptt-90) REVERT: B 63 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6528 (mm) REVERT: F 585 MET cc_start: 0.8999 (mmm) cc_final: 0.8798 (mmm) REVERT: F 629 ASP cc_start: 0.8170 (m-30) cc_final: 0.7838 (m-30) REVERT: E 548 TRP cc_start: 0.6970 (p90) cc_final: 0.5887 (p90) REVERT: E 597 LEU cc_start: 0.9006 (pt) cc_final: 0.8620 (mm) outliers start: 32 outliers final: 20 residues processed: 183 average time/residue: 0.2297 time to fit residues: 65.3244 Evaluate side-chains 167 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 441 HIS Chi-restraints excluded: chain F residue 648 TRP Chi-restraints excluded: chain E residue 358 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 79 optimal weight: 0.0470 chunk 111 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 175 optimal weight: 0.3980 chunk 86 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 546 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14201 Z= 0.198 Angle : 0.659 11.310 19322 Z= 0.324 Chirality : 0.043 0.251 2273 Planarity : 0.005 0.110 2522 Dihedral : 4.901 56.672 1991 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.44 % Favored : 89.02 % Rotamer: Outliers : 2.41 % Allowed : 13.77 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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: -0.82 (0.21), residues: 1830 helix: 0.90 (0.18), residues: 935 sheet: -1.52 (0.47), residues: 141 loop : -2.26 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 648 HIS 0.010 0.001 HIS E 601 PHE 0.018 0.001 PHE E 382 TYR 0.013 0.001 TYR F 568 ARG 0.002 0.000 ARG F 536 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8653 (p) REVERT: A 268 HIS cc_start: 0.7657 (t-90) cc_final: 0.7339 (t-90) REVERT: C 261 TYR cc_start: 0.8794 (t80) cc_final: 0.8581 (t80) REVERT: C 320 ARG cc_start: 0.8054 (ptt-90) cc_final: 0.7662 (ptt-90) REVERT: B 63 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6729 (mm) REVERT: B 96 ARG cc_start: 0.8224 (ptm160) cc_final: 0.7939 (ptm160) REVERT: D 51 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.6417 (tpt-90) REVERT: D 230 SER cc_start: 0.8108 (m) cc_final: 0.7566 (t) REVERT: F 585 MET cc_start: 0.9020 (mmm) cc_final: 0.8708 (mmm) REVERT: F 629 ASP cc_start: 0.8187 (m-30) cc_final: 0.7824 (m-30) REVERT: E 382 PHE cc_start: 0.7728 (m-10) cc_final: 0.7461 (m-80) REVERT: E 597 LEU cc_start: 0.8999 (pt) cc_final: 0.8655 (mm) outliers start: 36 outliers final: 24 residues processed: 177 average time/residue: 0.2569 time to fit residues: 68.3037 Evaluate side-chains 173 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 441 HIS Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain E residue 358 TYR Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 608 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 0.0670 chunk 150 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 403 GLN ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14201 Z= 0.283 Angle : 0.711 11.365 19322 Z= 0.352 Chirality : 0.045 0.280 2273 Planarity : 0.006 0.112 2522 Dihedral : 5.095 58.283 1991 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.55 % Allowed : 11.86 % Favored : 87.60 % Rotamer: Outliers : 2.74 % Allowed : 15.64 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 1.69 % 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: -0.98 (0.21), residues: 1830 helix: 0.75 (0.18), residues: 935 sheet: -1.76 (0.44), residues: 151 loop : -2.29 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 628 HIS 0.009 0.001 HIS E 601 PHE 0.017 0.002 PHE A 27 TYR 0.014 0.002 TYR D 261 ARG 0.005 0.000 ARG F 536 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.6662 (tpt) cc_final: 0.6392 (tpp) REVERT: C 235 MET cc_start: 0.7371 (mtp) cc_final: 0.6962 (mtp) REVERT: C 261 TYR cc_start: 0.8892 (t80) cc_final: 0.8579 (t80) REVERT: C 320 ARG cc_start: 0.8118 (ptt-90) cc_final: 0.7670 (ptt-90) REVERT: B 63 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6679 (mm) REVERT: B 96 ARG cc_start: 0.8094 (ptm160) cc_final: 0.7883 (ptm160) REVERT: F 375 MET cc_start: 0.8156 (ppp) cc_final: 0.7896 (ppp) REVERT: F 585 MET cc_start: 0.9045 (mmm) cc_final: 0.8765 (mmm) REVERT: F 629 ASP cc_start: 0.8258 (m-30) cc_final: 0.7701 (m-30) REVERT: E 382 PHE cc_start: 0.7838 (m-10) cc_final: 0.7559 (m-10) REVERT: E 425 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8519 (mmmt) REVERT: E 548 TRP cc_start: 0.6959 (p90) cc_final: 0.5747 (p90) outliers start: 41 outliers final: 28 residues processed: 166 average time/residue: 0.2461 time to fit residues: 61.9296 Evaluate side-chains 160 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 194 TYR Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain E residue 358 TYR Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 608 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 562 GLN ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14201 Z= 0.252 Angle : 0.704 12.792 19322 Z= 0.345 Chirality : 0.045 0.288 2273 Planarity : 0.006 0.112 2522 Dihedral : 5.097 58.947 1991 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.55 % Favored : 88.91 % Rotamer: Outliers : 3.07 % Allowed : 16.84 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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: -0.99 (0.21), residues: 1830 helix: 0.73 (0.18), residues: 940 sheet: -1.84 (0.44), residues: 146 loop : -2.27 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 648 HIS 0.012 0.001 HIS E 601 PHE 0.015 0.002 PHE E 527 TYR 0.023 0.002 TYR E 348 ARG 0.003 0.000 ARG F 536 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.6645 (tpt) cc_final: 0.6400 (tpp) REVERT: C 320 ARG cc_start: 0.8114 (ptt-90) cc_final: 0.7650 (ptt-90) REVERT: B 63 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6782 (mm) REVERT: B 96 ARG cc_start: 0.8074 (ptm160) cc_final: 0.7806 (ptm160) REVERT: D 51 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6998 (tpt-90) REVERT: D 235 MET cc_start: 0.7781 (mpp) cc_final: 0.7569 (mtm) REVERT: F 375 MET cc_start: 0.8162 (ppp) cc_final: 0.7901 (ppp) REVERT: F 585 MET cc_start: 0.8914 (mmm) cc_final: 0.8619 (mmm) REVERT: F 629 ASP cc_start: 0.8261 (m-30) cc_final: 0.7914 (m-30) REVERT: E 382 PHE cc_start: 0.7706 (m-10) cc_final: 0.7471 (m-10) REVERT: E 425 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8505 (mmmt) outliers start: 46 outliers final: 31 residues processed: 171 average time/residue: 0.2440 time to fit residues: 63.7516 Evaluate side-chains 166 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 194 TYR Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain E residue 358 TYR Chi-restraints excluded: chain E residue 551 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14201 Z= 0.204 Angle : 0.697 15.683 19322 Z= 0.341 Chirality : 0.045 0.295 2273 Planarity : 0.005 0.113 2522 Dihedral : 5.007 59.368 1991 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.98 % Favored : 88.47 % Rotamer: Outliers : 2.34 % Allowed : 18.58 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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: -0.78 (0.21), residues: 1830 helix: 0.91 (0.18), residues: 934 sheet: -1.64 (0.43), residues: 167 loop : -2.18 (0.25), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 648 HIS 0.016 0.001 HIS E 601 PHE 0.013 0.001 PHE E 527 TYR 0.018 0.001 TYR E 356 ARG 0.004 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.6666 (tpt) cc_final: 0.6429 (tpp) REVERT: C 235 MET cc_start: 0.7339 (mtp) cc_final: 0.6998 (mtp) REVERT: C 261 TYR cc_start: 0.8773 (t80) cc_final: 0.8501 (t80) REVERT: C 320 ARG cc_start: 0.8079 (ptt-90) cc_final: 0.7621 (ptt-90) REVERT: B 63 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6853 (mm) REVERT: D 51 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6746 (tpt-90) REVERT: D 235 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7439 (mtm) REVERT: F 375 MET cc_start: 0.8097 (ppp) cc_final: 0.7886 (ppp) REVERT: F 585 MET cc_start: 0.8800 (mmm) cc_final: 0.8525 (mmm) REVERT: F 629 ASP cc_start: 0.8268 (m-30) cc_final: 0.7928 (m-30) REVERT: E 382 PHE cc_start: 0.7821 (m-10) cc_final: 0.7533 (m-10) REVERT: E 425 LYS cc_start: 0.8828 (mmtt) cc_final: 0.8497 (mmmt) REVERT: E 595 TYR cc_start: 0.7119 (m-80) cc_final: 0.6849 (m-80) outliers start: 35 outliers final: 27 residues processed: 167 average time/residue: 0.2515 time to fit residues: 63.4453 Evaluate side-chains 163 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain E residue 358 TYR Chi-restraints excluded: chain E residue 551 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14201 Z= 0.207 Angle : 0.709 15.600 19322 Z= 0.346 Chirality : 0.045 0.308 2273 Planarity : 0.005 0.113 2522 Dihedral : 4.977 59.452 1991 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.55 % Favored : 88.91 % Rotamer: Outliers : 2.47 % Allowed : 18.85 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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: -0.75 (0.21), residues: 1830 helix: 0.93 (0.18), residues: 931 sheet: -1.63 (0.42), residues: 167 loop : -2.15 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 648 HIS 0.017 0.001 HIS E 601 PHE 0.013 0.001 PHE E 527 TYR 0.015 0.001 TYR E 356 ARG 0.005 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 235 MET cc_start: 0.7325 (mtp) cc_final: 0.6931 (mtp) REVERT: C 261 TYR cc_start: 0.8820 (t80) cc_final: 0.8542 (t80) REVERT: C 320 ARG cc_start: 0.8066 (ptt-90) cc_final: 0.7611 (ptt-90) REVERT: B 63 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6947 (mm) REVERT: D 51 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6598 (tpt-90) REVERT: D 235 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7427 (mtm) REVERT: F 629 ASP cc_start: 0.8224 (m-30) cc_final: 0.7889 (m-30) REVERT: E 382 PHE cc_start: 0.7772 (m-10) cc_final: 0.7485 (m-10) outliers start: 37 outliers final: 29 residues processed: 170 average time/residue: 0.2658 time to fit residues: 67.6954 Evaluate side-chains 166 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain E residue 358 TYR Chi-restraints excluded: chain E residue 551 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 162 optimal weight: 0.0980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 GLN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14201 Z= 0.198 Angle : 0.706 16.316 19322 Z= 0.344 Chirality : 0.045 0.313 2273 Planarity : 0.005 0.114 2522 Dihedral : 4.974 58.895 1991 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.60 % Favored : 88.91 % Rotamer: Outliers : 2.54 % Allowed : 18.58 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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 (0.21), residues: 1830 helix: 0.99 (0.18), residues: 931 sheet: -1.57 (0.43), residues: 166 loop : -2.17 (0.25), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 648 HIS 0.021 0.001 HIS E 601 PHE 0.012 0.001 PHE E 527 TYR 0.013 0.001 TYR E 358 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 235 MET cc_start: 0.7286 (mtp) cc_final: 0.6990 (mtp) REVERT: C 320 ARG cc_start: 0.8058 (ptt-90) cc_final: 0.7623 (ptt-90) REVERT: B 24 GLU cc_start: 0.8756 (tp30) cc_final: 0.8479 (tp30) REVERT: B 63 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6951 (mm) REVERT: D 51 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6542 (tpt-90) REVERT: F 585 MET cc_start: 0.8984 (mmm) cc_final: 0.8542 (mmm) REVERT: F 629 ASP cc_start: 0.8197 (m-30) cc_final: 0.7944 (m-30) REVERT: E 382 PHE cc_start: 0.7803 (m-10) cc_final: 0.7580 (m-10) REVERT: E 425 LYS cc_start: 0.8823 (mmtt) cc_final: 0.8497 (mmmt) REVERT: E 595 TYR cc_start: 0.7041 (m-80) cc_final: 0.6803 (m-80) outliers start: 38 outliers final: 30 residues processed: 171 average time/residue: 0.2433 time to fit residues: 63.6150 Evaluate side-chains 171 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 194 TYR Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 633 MET Chi-restraints excluded: chain E residue 358 TYR Chi-restraints excluded: chain E residue 551 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 GLN ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14201 Z= 0.200 Angle : 0.703 15.569 19322 Z= 0.342 Chirality : 0.045 0.323 2273 Planarity : 0.006 0.118 2522 Dihedral : 4.932 58.552 1991 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.33 % Favored : 89.18 % Rotamer: Outliers : 2.54 % Allowed : 18.58 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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: -0.71 (0.21), residues: 1830 helix: 1.02 (0.18), residues: 932 sheet: -1.76 (0.44), residues: 145 loop : -2.19 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 648 HIS 0.022 0.001 HIS E 601 PHE 0.012 0.001 PHE E 527 TYR 0.013 0.001 TYR E 358 ARG 0.005 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 235 MET cc_start: 0.7310 (mtp) cc_final: 0.6979 (mtp) REVERT: C 320 ARG cc_start: 0.8055 (ptt-90) cc_final: 0.7613 (ptt-90) REVERT: B 24 GLU cc_start: 0.8755 (tp30) cc_final: 0.8472 (tp30) REVERT: B 63 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6920 (mm) REVERT: D 51 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6487 (tpt-90) REVERT: F 585 MET cc_start: 0.9001 (mmm) cc_final: 0.8531 (mmm) REVERT: F 629 ASP cc_start: 0.8221 (m-30) cc_final: 0.7955 (m-30) outliers start: 38 outliers final: 32 residues processed: 168 average time/residue: 0.2473 time to fit residues: 63.4681 Evaluate side-chains 174 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 194 TYR Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 633 MET Chi-restraints excluded: chain E residue 358 TYR Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 608 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 HIS ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.095818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.074700 restraints weight = 46133.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.076749 restraints weight = 23629.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.078088 restraints weight = 14903.544| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14201 Z= 0.194 Angle : 0.707 16.760 19322 Z= 0.343 Chirality : 0.045 0.319 2273 Planarity : 0.006 0.116 2522 Dihedral : 4.909 57.992 1991 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.49 % Favored : 89.02 % Rotamer: Outliers : 2.27 % Allowed : 19.25 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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: -0.66 (0.21), residues: 1830 helix: 1.09 (0.18), residues: 930 sheet: -1.63 (0.45), residues: 141 loop : -2.22 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 648 HIS 0.023 0.001 HIS E 601 PHE 0.012 0.001 PHE E 527 TYR 0.013 0.001 TYR E 358 ARG 0.005 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2804.21 seconds wall clock time: 52 minutes 52.33 seconds (3172.33 seconds total)