Starting phenix.real_space_refine on Fri May 16 04:09:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gh2_40031/05_2025/8gh2_40031.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gh2_40031/05_2025/8gh2_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_40031/05_2025/8gh2_40031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gh2_40031/05_2025/8gh2_40031.map" model { file = "/net/cci-nas-00/data/ceres_data/8gh2_40031/05_2025/8gh2_40031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gh2_40031/05_2025/8gh2_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-5687/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: 9.11, per 1000 atoms: 0.65 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: 3.28 Conformation dependent library (CDL) restraints added in 1.8 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: 1.37 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: 3.61 Time building geometry restraints manager: 3.83 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: 4.180 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: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 31.990 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.190 ------------------------------------------------------------------------------- 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= 0.244 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 Details of bonding type rmsd hydrogen bonds : bond 0.20246 ( 624) hydrogen bonds : angle 6.74656 ( 1830) covalent geometry : bond 0.00375 (14201) covalent geometry : angle 0.78199 (19322) *********************** 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 : 1.559 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: 0.2518 time to fit residues: 87.6965 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 : 1.725 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.098742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.077941 restraints weight = 45705.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.080058 restraints weight = 23109.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.081435 restraints weight = 14402.843| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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= 0.139 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 Details of bonding type rmsd hydrogen bonds : bond 0.04376 ( 624) hydrogen bonds : angle 4.67371 ( 1830) covalent geometry : bond 0.00312 (14201) covalent geometry : angle 0.69432 (19322) *********************** 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 : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 ARG cc_start: 0.7441 (mmt180) cc_final: 0.7220 (mmp-170) REVERT: C 207 LEU cc_start: 0.8020 (tt) cc_final: 0.7314 (mp) REVERT: C 235 MET cc_start: 0.7133 (mtp) cc_final: 0.6640 (mtp) REVERT: C 261 TYR cc_start: 0.8779 (t80) cc_final: 0.8523 (t80) REVERT: C 320 ARG cc_start: 0.7954 (ptt-90) cc_final: 0.7558 (ptt-90) REVERT: D 190 ILE cc_start: 0.6717 (OUTLIER) cc_final: 0.6022 (mt) REVERT: D 244 MET cc_start: 0.7429 (mmm) cc_final: 0.7217 (mmm) REVERT: F 369 MET cc_start: 0.6544 (ttt) cc_final: 0.6232 (ttt) REVERT: F 629 ASP cc_start: 0.8172 (m-30) cc_final: 0.7921 (m-30) REVERT: F 638 MET cc_start: 0.8826 (mmm) cc_final: 0.8531 (mpp) outliers start: 21 outliers final: 13 residues processed: 189 average time/residue: 0.2348 time to fit residues: 68.0967 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 : 1.651 ------------------------------------------------------------------------------- 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 174 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 151 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.092717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.071551 restraints weight = 46849.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.073506 restraints weight = 24112.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.074770 restraints weight = 15356.323| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14201 Z= 0.219 Angle : 0.734 11.158 19322 Z= 0.370 Chirality : 0.046 0.259 2273 Planarity : 0.006 0.109 2522 Dihedral : 5.314 56.692 1991 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.55 % Allowed : 12.19 % Favored : 87.27 % Rotamer: Outliers : 2.47 % Allowed : 13.10 % Favored : 84.43 % 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: -1.23 (0.21), residues: 1830 helix: 0.56 (0.18), residues: 931 sheet: -1.84 (0.44), residues: 151 loop : -2.42 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 628 HIS 0.008 0.002 HIS D 48 PHE 0.023 0.002 PHE C 100 TYR 0.016 0.002 TYR F 348 ARG 0.005 0.001 ARG F 580 Details of bonding type rmsd hydrogen bonds : bond 0.04619 ( 624) hydrogen bonds : angle 4.71326 ( 1830) covalent geometry : bond 0.00514 (14201) covalent geometry : angle 0.73436 (19322) *********************** 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 182 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.6620 (tpt) cc_final: 0.6265 (tpp) REVERT: C 172 HIS cc_start: 0.7685 (t70) cc_final: 0.7397 (t70) REVERT: C 235 MET cc_start: 0.7437 (mtp) cc_final: 0.7061 (mtp) REVERT: C 320 ARG cc_start: 0.8027 (ptt-90) cc_final: 0.7636 (ptt-90) REVERT: F 582 MET cc_start: 0.8700 (ttt) cc_final: 0.8486 (ttt) REVERT: F 585 MET cc_start: 0.9039 (mmm) cc_final: 0.8825 (mmm) REVERT: F 629 ASP cc_start: 0.8271 (m-30) cc_final: 0.7841 (m-30) REVERT: E 382 PHE cc_start: 0.7538 (m-10) cc_final: 0.7236 (m-80) REVERT: E 548 TRP cc_start: 0.7136 (p90) cc_final: 0.6010 (p90) outliers start: 37 outliers final: 25 residues processed: 172 average time/residue: 0.2168 time to fit residues: 57.6523 Evaluate side-chains 156 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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 22 LEU 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 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 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 233 LEU 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 F residue 645 GLU 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 139 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 546 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.095169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.073995 restraints weight = 46296.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.076029 restraints weight = 23513.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077342 restraints weight = 14825.488| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14201 Z= 0.123 Angle : 0.665 11.362 19322 Z= 0.327 Chirality : 0.044 0.256 2273 Planarity : 0.005 0.109 2522 Dihedral : 5.137 58.038 1991 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.87 % Favored : 88.58 % Rotamer: Outliers : 2.47 % Allowed : 14.84 % Favored : 82.69 % 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: -0.92 (0.21), residues: 1830 helix: 0.83 (0.18), residues: 932 sheet: -1.62 (0.43), residues: 168 loop : -2.32 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 648 HIS 0.011 0.001 HIS E 601 PHE 0.015 0.001 PHE E 527 TYR 0.015 0.002 TYR E 348 ARG 0.002 0.000 ARG F 632 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 624) hydrogen bonds : angle 4.24322 ( 1830) covalent geometry : bond 0.00285 (14201) covalent geometry : angle 0.66482 (19322) *********************** 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 186 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.6674 (tpt) cc_final: 0.6336 (tpp) REVERT: C 320 ARG cc_start: 0.8059 (ptt-90) cc_final: 0.7622 (ptt-90) REVERT: B 63 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6779 (mm) REVERT: B 96 ARG cc_start: 0.8268 (ptm160) cc_final: 0.7985 (ptm160) REVERT: D 51 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6794 (tpt-90) REVERT: F 582 MET cc_start: 0.8718 (ttt) cc_final: 0.8421 (ttt) REVERT: F 585 MET cc_start: 0.9084 (mmm) cc_final: 0.8752 (mmm) REVERT: F 629 ASP cc_start: 0.8235 (m-30) cc_final: 0.7865 (m-30) REVERT: E 356 TYR cc_start: 0.6393 (OUTLIER) cc_final: 0.5411 (m-80) REVERT: E 382 PHE cc_start: 0.7567 (m-10) cc_final: 0.7246 (m-80) REVERT: E 523 LEU cc_start: 0.7747 (mm) cc_final: 0.7528 (mm) REVERT: E 595 TYR cc_start: 0.6817 (m-80) cc_final: 0.6592 (m-80) REVERT: E 597 LEU cc_start: 0.9021 (pt) cc_final: 0.8625 (mm) outliers start: 37 outliers final: 24 residues processed: 174 average time/residue: 0.2466 time to fit residues: 64.2859 Evaluate side-chains 164 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 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 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 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 645 GLU Chi-restraints excluded: chain E residue 356 TYR 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 138 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 135 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 562 GLN E 546 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.095277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.074125 restraints weight = 46173.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.076161 restraints weight = 23465.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.077500 restraints weight = 14752.830| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2593 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= 0.123 Angle : 0.669 11.295 19322 Z= 0.328 Chirality : 0.044 0.267 2273 Planarity : 0.005 0.113 2522 Dihedral : 4.992 58.980 1991 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.93 % Favored : 88.52 % Rotamer: Outliers : 2.54 % Allowed : 16.44 % Favored : 81.02 % 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: -0.81 (0.21), residues: 1830 helix: 0.91 (0.18), residues: 934 sheet: -1.65 (0.46), residues: 141 loop : -2.23 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 648 HIS 0.012 0.001 HIS E 601 PHE 0.012 0.001 PHE E 527 TYR 0.017 0.001 TYR E 356 ARG 0.003 0.000 ARG C 96 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 624) hydrogen bonds : angle 4.16041 ( 1830) covalent geometry : bond 0.00288 (14201) covalent geometry : angle 0.66856 (19322) *********************** 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 182 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 ARG cc_start: 0.7534 (mmp-170) cc_final: 0.6156 (mmt180) REVERT: C 235 MET cc_start: 0.7308 (mtp) cc_final: 0.6946 (mtp) REVERT: C 261 TYR cc_start: 0.8870 (t80) cc_final: 0.8611 (t80) REVERT: C 320 ARG cc_start: 0.8032 (ptt-90) cc_final: 0.7575 (ptt-90) REVERT: B 63 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6931 (mm) REVERT: B 96 ARG cc_start: 0.8135 (ptm160) cc_final: 0.7814 (ptm160) REVERT: D 51 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6686 (tpt-90) REVERT: D 235 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7550 (mpp) REVERT: F 582 MET cc_start: 0.8690 (ttt) cc_final: 0.8334 (ttt) REVERT: F 585 MET cc_start: 0.9077 (mmm) cc_final: 0.8691 (mmm) REVERT: F 629 ASP cc_start: 0.8259 (m-30) cc_final: 0.7903 (m-30) REVERT: E 382 PHE cc_start: 0.7651 (m-10) cc_final: 0.7320 (m-80) REVERT: E 523 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7502 (mm) REVERT: E 595 TYR cc_start: 0.6852 (m-80) cc_final: 0.6554 (m-80) REVERT: E 597 LEU cc_start: 0.9042 (pt) cc_final: 0.8622 (mm) outliers start: 38 outliers final: 25 residues processed: 170 average time/residue: 0.2269 time to fit residues: 58.8552 Evaluate side-chains 165 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 1.524 ------------------------------------------------------------------------------- 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 C residue 22 LEU Chi-restraints excluded: chain C residue 56 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 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 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 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 523 LEU 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 150 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 175 optimal weight: 0.0570 chunk 22 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 167 optimal weight: 9.9990 overall best weight: 1.7702 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.093869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.072676 restraints weight = 47120.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.074711 restraints weight = 23977.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.076038 restraints weight = 15049.700| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2798 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= 0.150 Angle : 0.688 11.248 19322 Z= 0.340 Chirality : 0.045 0.285 2273 Planarity : 0.005 0.113 2522 Dihedral : 5.046 59.352 1991 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.55 % Allowed : 11.53 % Favored : 87.92 % Rotamer: Outliers : 2.81 % Allowed : 16.84 % Favored : 80.35 % 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: -0.84 (0.21), residues: 1830 helix: 0.92 (0.18), residues: 935 sheet: -1.86 (0.44), residues: 147 loop : -2.25 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 648 HIS 0.013 0.001 HIS E 601 PHE 0.013 0.001 PHE A 27 TYR 0.017 0.002 TYR E 356 ARG 0.004 0.000 ARG F 536 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 624) hydrogen bonds : angle 4.25933 ( 1830) covalent geometry : bond 0.00357 (14201) covalent geometry : angle 0.68785 (19322) *********************** 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 178 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 1.584 Fit side-chains revert: symmetry clash REVERT: C 235 MET cc_start: 0.7291 (mtp) cc_final: 0.6864 (mtp) REVERT: C 261 TYR cc_start: 0.8884 (t80) cc_final: 0.8528 (t80) REVERT: C 320 ARG cc_start: 0.8035 (ptt-90) cc_final: 0.7589 (ptt-90) REVERT: B 63 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6861 (mm) REVERT: B 96 ARG cc_start: 0.8107 (ptm160) cc_final: 0.7858 (ptm160) REVERT: D 51 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.6938 (tpt-90) REVERT: D 235 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7642 (mpp) REVERT: F 582 MET cc_start: 0.8758 (ttt) cc_final: 0.8339 (ttt) REVERT: F 585 MET cc_start: 0.8972 (mmm) cc_final: 0.8695 (mmm) REVERT: F 629 ASP cc_start: 0.8319 (m-30) cc_final: 0.7969 (m-30) REVERT: E 382 PHE cc_start: 0.7779 (m-10) cc_final: 0.7523 (m-10) REVERT: E 425 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8493 (mmmt) REVERT: E 548 TRP cc_start: 0.6878 (p90) cc_final: 0.5783 (p90) REVERT: E 595 TYR cc_start: 0.6955 (m-80) cc_final: 0.6570 (m-80) REVERT: E 597 LEU cc_start: 0.9072 (pt) cc_final: 0.8629 (mm) outliers start: 42 outliers final: 30 residues processed: 167 average time/residue: 0.2415 time to fit residues: 60.2693 Evaluate side-chains 165 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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 22 LEU 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 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 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 232 THR Chi-restraints excluded: chain D residue 235 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 175 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 136 optimal weight: 0.0070 chunk 141 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 overall best weight: 1.3802 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.094292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.073183 restraints weight = 46723.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.075208 restraints weight = 23750.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.076538 restraints weight = 14881.156| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14201 Z= 0.135 Angle : 0.691 13.546 19322 Z= 0.337 Chirality : 0.044 0.302 2273 Planarity : 0.005 0.115 2522 Dihedral : 5.012 59.849 1991 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.55 % Allowed : 11.04 % Favored : 88.42 % Rotamer: Outliers : 2.61 % Allowed : 17.78 % Favored : 79.61 % 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: -0.77 (0.21), residues: 1830 helix: 0.93 (0.18), residues: 935 sheet: -1.67 (0.42), residues: 167 loop : -2.19 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 648 HIS 0.015 0.001 HIS E 601 PHE 0.011 0.001 PHE A 27 TYR 0.016 0.001 TYR E 356 ARG 0.005 0.000 ARG C 96 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 624) hydrogen bonds : angle 4.18217 ( 1830) covalent geometry : bond 0.00323 (14201) covalent geometry : angle 0.69079 (19322) *********************** 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: 39 poor density : 138 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 235 MET cc_start: 0.7362 (mtp) cc_final: 0.6935 (mtp) REVERT: C 261 TYR cc_start: 0.8864 (t80) cc_final: 0.8519 (t80) REVERT: C 320 ARG cc_start: 0.8026 (ptt-90) cc_final: 0.7549 (ptt-90) REVERT: B 63 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6973 (mm) REVERT: D 51 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6865 (tpt-90) REVERT: F 582 MET cc_start: 0.8728 (ttt) cc_final: 0.8294 (ttt) REVERT: F 585 MET cc_start: 0.8822 (mmm) cc_final: 0.8605 (mmm) REVERT: F 629 ASP cc_start: 0.8307 (m-30) cc_final: 0.7947 (m-30) REVERT: E 382 PHE cc_start: 0.7800 (m-10) cc_final: 0.7521 (m-10) REVERT: E 425 LYS cc_start: 0.8832 (mmtt) cc_final: 0.8495 (mmmt) REVERT: E 595 TYR cc_start: 0.7048 (m-80) cc_final: 0.6643 (m-80) REVERT: E 597 LEU cc_start: 0.9074 (pt) cc_final: 0.8630 (mm) outliers start: 39 outliers final: 29 residues processed: 168 average time/residue: 0.2320 time to fit residues: 59.6550 Evaluate side-chains 161 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 1.529 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 0.0060 chunk 45 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 179 optimal weight: 0.0470 chunk 103 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 51 optimal weight: 0.0470 chunk 65 optimal weight: 0.7980 chunk 134 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 139 GLN F 403 GLN E 546 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.096728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.075694 restraints weight = 46408.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.077791 restraints weight = 23446.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.079135 restraints weight = 14619.153| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2878 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= 0.119 Angle : 0.701 16.777 19322 Z= 0.342 Chirality : 0.045 0.319 2273 Planarity : 0.005 0.116 2522 Dihedral : 4.884 59.547 1991 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.27 % Favored : 89.18 % Rotamer: Outliers : 2.21 % Allowed : 18.32 % Favored : 79.48 % 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: -0.64 (0.21), residues: 1830 helix: 1.08 (0.18), residues: 932 sheet: -1.62 (0.45), residues: 141 loop : -2.18 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 648 HIS 0.017 0.001 HIS E 601 PHE 0.010 0.001 PHE E 527 TYR 0.015 0.001 TYR E 358 ARG 0.005 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.02981 ( 624) hydrogen bonds : angle 3.99499 ( 1830) covalent geometry : bond 0.00271 (14201) covalent geometry : angle 0.70111 (19322) *********************** 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 190 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 235 MET cc_start: 0.7240 (mtp) cc_final: 0.6915 (mtp) REVERT: C 261 TYR cc_start: 0.8831 (t80) cc_final: 0.8615 (t80) REVERT: C 320 ARG cc_start: 0.8020 (ptt-90) cc_final: 0.7571 (ptt-90) REVERT: B 24 GLU cc_start: 0.8693 (tp30) cc_final: 0.8431 (tp30) REVERT: B 96 ARG cc_start: 0.8518 (ptm-80) cc_final: 0.8317 (ptm160) REVERT: D 51 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6274 (tpt-90) REVERT: D 235 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7519 (mpp) REVERT: F 375 MET cc_start: 0.8162 (ppp) cc_final: 0.7936 (ppp) REVERT: F 582 MET cc_start: 0.8724 (ttt) cc_final: 0.8295 (ttt) REVERT: F 629 ASP cc_start: 0.8180 (m-30) cc_final: 0.7895 (m-30) REVERT: E 382 PHE cc_start: 0.7846 (m-10) cc_final: 0.7559 (m-10) REVERT: E 595 TYR cc_start: 0.6986 (m-80) cc_final: 0.6560 (m-80) REVERT: E 597 LEU cc_start: 0.9101 (pt) cc_final: 0.8671 (mm) REVERT: E 633 MET cc_start: 0.7977 (ttt) cc_final: 0.7375 (ppp) outliers start: 33 outliers final: 27 residues processed: 177 average time/residue: 0.2466 time to fit residues: 65.0648 Evaluate side-chains 172 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 250 LEU Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 56 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 B residue 42 VAL 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 51 ARG Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 139 GLN 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 F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 173 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 46 optimal weight: 0.0370 chunk 128 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 HIS B 139 GLN D 139 GLN E 546 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.095909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.074841 restraints weight = 46070.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.076896 restraints weight = 23523.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.078235 restraints weight = 14744.899| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2960 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= 0.123 Angle : 0.700 16.329 19322 Z= 0.339 Chirality : 0.044 0.316 2273 Planarity : 0.005 0.117 2522 Dihedral : 4.702 52.290 1989 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.49 % Favored : 89.02 % Rotamer: Outliers : 2.27 % Allowed : 18.78 % Favored : 78.94 % 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: 1.07 (0.18), residues: 932 sheet: -1.67 (0.45), residues: 141 loop : -2.18 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 648 HIS 0.021 0.001 HIS E 601 PHE 0.010 0.001 PHE E 527 TYR 0.017 0.001 TYR E 356 ARG 0.007 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.03157 ( 624) hydrogen bonds : angle 4.02887 ( 1830) covalent geometry : bond 0.00292 (14201) covalent geometry : angle 0.69968 (19322) *********************** 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 178 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 235 MET cc_start: 0.7296 (mtp) cc_final: 0.6927 (mtp) REVERT: C 320 ARG cc_start: 0.8028 (ptt-90) cc_final: 0.7591 (ptt-90) REVERT: B 24 GLU cc_start: 0.8710 (tp30) cc_final: 0.8421 (tp30) REVERT: B 96 ARG cc_start: 0.8567 (ptm-80) cc_final: 0.8281 (ptm160) REVERT: D 51 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.6328 (tpt-90) REVERT: D 235 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7555 (mpp) REVERT: F 582 MET cc_start: 0.8710 (ttt) cc_final: 0.8330 (ttt) REVERT: F 585 MET cc_start: 0.9193 (mmm) cc_final: 0.8790 (mmm) REVERT: F 629 ASP cc_start: 0.8231 (m-30) cc_final: 0.7671 (m-30) REVERT: E 382 PHE cc_start: 0.7875 (m-10) cc_final: 0.7589 (m-10) REVERT: E 425 LYS cc_start: 0.8825 (mmtt) cc_final: 0.8457 (mmmt) REVERT: E 597 LEU cc_start: 0.9108 (pt) cc_final: 0.8718 (mm) outliers start: 34 outliers final: 28 residues processed: 165 average time/residue: 0.2300 time to fit residues: 57.3906 Evaluate side-chains 171 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 1.483 ------------------------------------------------------------------------------- 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 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 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 316 GLU Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 139 GLN 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 293 ILE Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU 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 46 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 81 optimal weight: 0.0770 chunk 11 optimal weight: 0.0040 chunk 162 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 overall best weight: 0.4950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 521 HIS E 546 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.096882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.075781 restraints weight = 46247.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.077882 restraints weight = 23492.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.079228 restraints weight = 14742.809| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2981 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= 0.119 Angle : 0.713 16.530 19322 Z= 0.344 Chirality : 0.044 0.313 2273 Planarity : 0.005 0.117 2522 Dihedral : 4.671 52.496 1989 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.73 % Favored : 89.78 % Rotamer: Outliers : 2.01 % Allowed : 19.12 % 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: -0.61 (0.21), residues: 1830 helix: 1.10 (0.18), residues: 930 sheet: -1.60 (0.45), residues: 141 loop : -2.14 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 648 HIS 0.023 0.001 HIS E 601 PHE 0.010 0.001 PHE E 527 TYR 0.015 0.001 TYR E 356 ARG 0.006 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.02989 ( 624) hydrogen bonds : angle 3.96220 ( 1830) covalent geometry : bond 0.00276 (14201) covalent geometry : angle 0.71275 (19322) ********************** 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 178 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 235 MET cc_start: 0.7204 (mtp) cc_final: 0.6871 (mtp) REVERT: C 320 ARG cc_start: 0.7998 (ptt-90) cc_final: 0.7573 (ptt-90) REVERT: B 24 GLU cc_start: 0.8689 (tp30) cc_final: 0.8430 (tp30) REVERT: B 63 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6577 (mm) REVERT: D 51 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6181 (tpt-90) REVERT: D 235 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7437 (mpp) REVERT: F 582 MET cc_start: 0.8718 (ttt) cc_final: 0.8280 (ttt) REVERT: F 585 MET cc_start: 0.9176 (mmm) cc_final: 0.8764 (mmm) REVERT: F 625 ARG cc_start: 0.5551 (tpt170) cc_final: 0.4943 (tpt170) REVERT: F 629 ASP cc_start: 0.8251 (m-30) cc_final: 0.7668 (m-30) REVERT: E 382 PHE cc_start: 0.7843 (m-10) cc_final: 0.7580 (m-10) REVERT: E 595 TYR cc_start: 0.7204 (m-80) cc_final: 0.6907 (m-80) REVERT: E 597 LEU cc_start: 0.9095 (pt) cc_final: 0.8683 (mm) REVERT: E 633 MET cc_start: 0.8002 (ttt) cc_final: 0.7397 (ppp) outliers start: 30 outliers final: 27 residues processed: 166 average time/residue: 0.2361 time to fit residues: 59.9581 Evaluate side-chains 174 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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 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 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 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 293 ILE Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU 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 155 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 0.0370 chunk 15 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- 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** E 546 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.096573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.075562 restraints weight = 46561.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.077673 restraints weight = 23740.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.079041 restraints weight = 14833.201| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14201 Z= 0.119 Angle : 0.694 16.116 19322 Z= 0.337 Chirality : 0.044 0.319 2273 Planarity : 0.006 0.118 2522 Dihedral : 4.636 51.930 1989 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.22 % Favored : 89.29 % Rotamer: Outliers : 2.14 % Allowed : 19.18 % 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: -0.61 (0.21), residues: 1830 helix: 1.12 (0.18), residues: 935 sheet: -1.63 (0.45), residues: 141 loop : -2.20 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 648 HIS 0.021 0.001 HIS E 601 PHE 0.010 0.001 PHE E 527 TYR 0.016 0.001 TYR E 356 ARG 0.006 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.03046 ( 624) hydrogen bonds : angle 3.99110 ( 1830) covalent geometry : bond 0.00281 (14201) covalent geometry : angle 0.69419 (19322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4314.96 seconds wall clock time: 76 minutes 35.01 seconds (4595.01 seconds total)