Starting phenix.real_space_refine on Thu Jun 12 14:14:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gh2_40031/06_2025/8gh2_40031.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gh2_40031/06_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_40031/06_2025/8gh2_40031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gh2_40031/06_2025/8gh2_40031.map" model { file = "/net/cci-nas-00/data/ceres_data/8gh2_40031/06_2025/8gh2_40031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gh2_40031/06_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-5710/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: 9.39, per 1000 atoms: 0.67 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: 3.54 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: 1.43 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: 3.71 Time building geometry restraints manager: 4.16 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: 52.130 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: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 33.510 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.840 ------------------------------------------------------------------------------- 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 : 1.682 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: 0.2577 time to fit residues: 90.2198 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 : 1.751 ------------------------------------------------------------------------------- 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 = 0.098734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.077955 restraints weight = 45672.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.080070 restraints weight = 23063.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.081444 restraints weight = 14402.063| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 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 : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 ARG cc_start: 0.7442 (mmt180) cc_final: 0.7220 (mmp-170) REVERT: C 207 LEU cc_start: 0.8015 (tt) cc_final: 0.7311 (mp) REVERT: C 235 MET cc_start: 0.7135 (mtp) cc_final: 0.6641 (mtp) REVERT: C 261 TYR cc_start: 0.8780 (t80) cc_final: 0.8523 (t80) REVERT: C 320 ARG cc_start: 0.7957 (ptt-90) cc_final: 0.7560 (ptt-90) REVERT: D 190 ILE cc_start: 0.6720 (OUTLIER) cc_final: 0.6026 (mt) REVERT: D 244 MET cc_start: 0.7437 (mmm) cc_final: 0.7223 (mmm) REVERT: F 369 MET cc_start: 0.6544 (ttt) cc_final: 0.6231 (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: 0.2592 time to fit residues: 74.4914 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 : 1.699 ------------------------------------------------------------------------------- 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: 9.9990 chunk 91 optimal weight: 0.9980 chunk 176 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 151 optimal weight: 0.3980 chunk 41 optimal weight: 5.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.093908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.072754 restraints weight = 46574.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.074726 restraints weight = 23891.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.076033 restraints weight = 15132.927| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14201 Z= 0.179 Angle : 0.702 11.242 19322 Z= 0.351 Chirality : 0.045 0.255 2273 Planarity : 0.006 0.109 2522 Dihedral : 5.201 57.000 1991 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.55 % Allowed : 11.80 % Favored : 87.65 % Rotamer: Outliers : 2.27 % Allowed : 12.83 % Favored : 84.89 % 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: 0.66 (0.18), residues: 932 sheet: -1.74 (0.45), residues: 147 loop : -2.37 (0.24), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 648 HIS 0.008 0.001 HIS D 48 PHE 0.025 0.002 PHE C 100 TYR 0.014 0.002 TYR F 568 ARG 0.005 0.001 ARG F 580 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 624) hydrogen bonds : angle 4.53275 ( 1830) covalent geometry : bond 0.00419 (14201) covalent geometry : angle 0.70209 (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 181 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 1.548 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.6588 (tpt) cc_final: 0.6241 (tpp) REVERT: C 172 HIS cc_start: 0.7657 (t70) cc_final: 0.7429 (t70) REVERT: C 235 MET cc_start: 0.7359 (mtp) cc_final: 0.7093 (mtp) REVERT: C 261 TYR cc_start: 0.8861 (t80) cc_final: 0.8549 (t80) REVERT: C 320 ARG cc_start: 0.8041 (ptt-90) cc_final: 0.7647 (ptt-90) REVERT: B 96 ARG cc_start: 0.8329 (ptm160) cc_final: 0.8071 (ptm160) REVERT: D 191 VAL cc_start: 0.8486 (t) cc_final: 0.8278 (t) REVERT: F 585 MET cc_start: 0.9051 (mmm) cc_final: 0.8797 (mmm) REVERT: F 629 ASP cc_start: 0.8200 (m-30) cc_final: 0.7756 (m-30) REVERT: E 382 PHE cc_start: 0.7618 (m-10) cc_final: 0.7273 (m-80) REVERT: E 548 TRP cc_start: 0.7096 (p90) cc_final: 0.5996 (p90) REVERT: E 597 LEU cc_start: 0.9067 (pt) cc_final: 0.8660 (mm) outliers start: 34 outliers final: 22 residues processed: 171 average time/residue: 0.2265 time to fit residues: 58.9957 Evaluate side-chains 151 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.691 ------------------------------------------------------------------------------- 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 179 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain E residue 358 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 139 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 2 optimal weight: 0.0570 chunk 172 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 123 optimal weight: 0.0070 chunk 91 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.096531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075346 restraints weight = 46195.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.077398 restraints weight = 23536.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.078736 restraints weight = 14817.895| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14201 Z= 0.117 Angle : 0.659 11.349 19322 Z= 0.323 Chirality : 0.044 0.252 2273 Planarity : 0.005 0.110 2522 Dihedral : 5.002 58.398 1991 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.49 % Favored : 88.96 % Rotamer: Outliers : 2.21 % Allowed : 15.04 % Favored : 82.75 % 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: 0.88 (0.18), residues: 932 sheet: -1.56 (0.47), residues: 141 loop : -2.25 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 648 HIS 0.010 0.001 HIS E 601 PHE 0.009 0.001 PHE C 318 TYR 0.013 0.001 TYR F 568 ARG 0.003 0.000 ARG C 96 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 624) hydrogen bonds : angle 4.12369 ( 1830) covalent geometry : bond 0.00267 (14201) covalent geometry : angle 0.65903 (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 183 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.8874 (t) cc_final: 0.8658 (p) REVERT: C 1 MET cc_start: 0.6613 (tpt) cc_final: 0.6299 (tpp) REVERT: C 261 TYR cc_start: 0.8815 (t80) cc_final: 0.8561 (t80) REVERT: C 320 ARG cc_start: 0.8016 (ptt-90) cc_final: 0.7589 (ptt-90) REVERT: B 63 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6856 (mm) REVERT: B 96 ARG cc_start: 0.8159 (ptm160) cc_final: 0.7856 (ptm160) REVERT: B 316 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: D 51 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6606 (tpt-90) REVERT: F 585 MET cc_start: 0.9071 (mmm) cc_final: 0.8704 (mmm) REVERT: F 629 ASP cc_start: 0.8208 (m-30) cc_final: 0.7711 (m-30) REVERT: E 382 PHE cc_start: 0.7711 (m-10) cc_final: 0.7336 (m-80) REVERT: E 597 LEU cc_start: 0.9019 (pt) cc_final: 0.8659 (mm) outliers start: 33 outliers final: 20 residues processed: 172 average time/residue: 0.2431 time to fit residues: 63.7336 Evaluate side-chains 163 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain 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 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 441 HIS 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: 9.9990 chunk 28 optimal weight: 4.9990 chunk 135 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 181 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 HIS ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 562 GLN ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.095410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.074241 restraints weight = 46333.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.076279 restraints weight = 23644.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.077605 restraints weight = 14939.279| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2565 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= 0.130 Angle : 0.670 11.673 19322 Z= 0.328 Chirality : 0.044 0.270 2273 Planarity : 0.005 0.113 2522 Dihedral : 4.926 59.243 1991 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.87 % Favored : 88.58 % Rotamer: Outliers : 2.34 % Allowed : 16.58 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.21), residues: 1830 helix: 0.94 (0.18), residues: 936 sheet: -1.59 (0.47), residues: 141 loop : -2.24 (0.24), residues: 753 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 0.010 0.001 PHE A 27 TYR 0.012 0.001 TYR E 358 ARG 0.003 0.000 ARG C 96 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 624) hydrogen bonds : angle 4.14536 ( 1830) covalent geometry : bond 0.00306 (14201) covalent geometry : angle 0.67011 (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 178 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 235 MET cc_start: 0.7257 (mtp) cc_final: 0.6902 (mtp) REVERT: C 261 TYR cc_start: 0.8867 (t80) cc_final: 0.8631 (t80) REVERT: C 320 ARG cc_start: 0.8019 (ptt-90) cc_final: 0.7599 (ptt-90) REVERT: B 63 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6889 (mm) REVERT: D 51 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6685 (tpt-90) REVERT: F 585 MET cc_start: 0.9007 (mmm) cc_final: 0.8603 (mmm) REVERT: F 629 ASP cc_start: 0.8261 (m-30) cc_final: 0.7899 (m-30) REVERT: E 382 PHE cc_start: 0.7707 (m-10) cc_final: 0.7407 (m-80) REVERT: E 597 LEU cc_start: 0.9038 (pt) cc_final: 0.8668 (mm) outliers start: 35 outliers final: 25 residues processed: 166 average time/residue: 0.2273 time to fit residues: 57.7804 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 : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain 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 275 MET Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 441 HIS Chi-restraints excluded: chain E residue 358 TYR Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 608 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 150 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 175 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 135 optimal weight: 0.5980 chunk 167 optimal weight: 8.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.094549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.073279 restraints weight = 46963.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.075305 restraints weight = 23892.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.076622 restraints weight = 15089.478| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2752 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= 0.143 Angle : 0.681 11.242 19322 Z= 0.335 Chirality : 0.045 0.290 2273 Planarity : 0.005 0.113 2522 Dihedral : 4.995 59.802 1991 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.77 % Favored : 88.69 % Rotamer: Outliers : 2.81 % Allowed : 16.91 % Favored : 80.28 % 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: 0.96 (0.18), residues: 935 sheet: -1.76 (0.44), residues: 149 loop : -2.22 (0.24), residues: 746 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 0.012 0.001 PHE A 27 TYR 0.015 0.001 TYR E 358 ARG 0.003 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 624) hydrogen bonds : angle 4.20130 ( 1830) covalent geometry : bond 0.00340 (14201) covalent geometry : angle 0.68135 (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 185 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 235 MET cc_start: 0.7314 (mtp) cc_final: 0.6861 (mtp) REVERT: C 320 ARG cc_start: 0.8045 (ptt-90) cc_final: 0.7607 (ptt-90) REVERT: B 63 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6842 (mm) REVERT: D 51 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.6806 (tpt-90) REVERT: F 585 MET cc_start: 0.8889 (mmm) cc_final: 0.8607 (mmm) REVERT: F 629 ASP cc_start: 0.8263 (m-30) cc_final: 0.7907 (m-30) REVERT: E 382 PHE cc_start: 0.7750 (m-10) cc_final: 0.7402 (m-10) REVERT: E 425 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8494 (mmmt) REVERT: E 595 TYR cc_start: 0.7000 (m-80) cc_final: 0.6700 (m-80) REVERT: E 597 LEU cc_start: 0.9072 (pt) cc_final: 0.8630 (mm) outliers start: 42 outliers final: 28 residues processed: 170 average time/residue: 0.2451 time to fit residues: 63.0858 Evaluate side-chains 163 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 1.797 ------------------------------------------------------------------------------- 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 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 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: 0.4980 chunk 61 optimal weight: 0.4980 chunk 134 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 136 optimal weight: 0.2980 chunk 141 optimal weight: 0.0570 chunk 162 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.095276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.074096 restraints weight = 46595.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.076126 restraints weight = 23699.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.077458 restraints weight = 14921.460| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2818 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= 0.125 Angle : 0.688 15.410 19322 Z= 0.335 Chirality : 0.044 0.302 2273 Planarity : 0.005 0.114 2522 Dihedral : 4.930 59.655 1991 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.82 % Favored : 88.63 % Rotamer: Outliers : 2.34 % Allowed : 18.05 % 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: -0.70 (0.21), residues: 1830 helix: 1.03 (0.18), residues: 936 sheet: -1.65 (0.45), residues: 146 loop : -2.21 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 648 HIS 0.016 0.001 HIS E 601 PHE 0.015 0.001 PHE E 527 TYR 0.015 0.001 TYR E 356 ARG 0.004 0.000 ARG C 96 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 624) hydrogen bonds : angle 4.10529 ( 1830) covalent geometry : bond 0.00296 (14201) covalent geometry : angle 0.68754 (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 182 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: C 235 MET cc_start: 0.7263 (mtp) cc_final: 0.6885 (mtp) REVERT: C 320 ARG cc_start: 0.8001 (ptt-90) cc_final: 0.7568 (ptt-90) REVERT: B 63 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6922 (mm) REVERT: D 51 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6680 (tpt-90) REVERT: F 375 MET cc_start: 0.8168 (ppp) cc_final: 0.7881 (ppp) REVERT: F 629 ASP cc_start: 0.8228 (m-30) cc_final: 0.7872 (m-30) REVERT: E 382 PHE cc_start: 0.7794 (m-10) cc_final: 0.7440 (m-10) REVERT: E 425 LYS cc_start: 0.8833 (mmtt) cc_final: 0.8490 (mmmt) REVERT: E 595 TYR cc_start: 0.6903 (m-80) cc_final: 0.6559 (m-80) REVERT: E 597 LEU cc_start: 0.9098 (pt) cc_final: 0.8670 (mm) outliers start: 35 outliers final: 27 residues processed: 171 average time/residue: 0.2330 time to fit residues: 60.1313 Evaluate side-chains 166 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 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 C residue 13 ILE Chi-restraints excluded: chain C residue 24 GLU 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 268 HIS Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 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: 0.9980 chunk 66 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 179 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.095732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.074610 restraints weight = 46477.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.076674 restraints weight = 23580.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.078006 restraints weight = 14795.393| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2874 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= 0.121 Angle : 0.694 16.149 19322 Z= 0.339 Chirality : 0.044 0.303 2273 Planarity : 0.005 0.114 2522 Dihedral : 4.932 59.493 1991 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.87 % Favored : 88.63 % Rotamer: Outliers : 2.41 % Allowed : 18.45 % Favored : 79.14 % 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: 1.09 (0.18), residues: 930 sheet: -1.59 (0.46), residues: 141 loop : -2.18 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 648 HIS 0.018 0.001 HIS E 601 PHE 0.013 0.001 PHE E 527 TYR 0.014 0.001 TYR E 358 ARG 0.006 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.03212 ( 624) hydrogen bonds : angle 4.06644 ( 1830) covalent geometry : bond 0.00284 (14201) covalent geometry : angle 0.69416 (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 183 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: C 235 MET cc_start: 0.7263 (mtp) cc_final: 0.6907 (mtp) REVERT: C 320 ARG cc_start: 0.7990 (ptt-90) cc_final: 0.7575 (ptt-90) REVERT: B 24 GLU cc_start: 0.8747 (tp30) cc_final: 0.8473 (tp30) REVERT: B 63 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.7005 (mm) REVERT: D 51 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6404 (tpt-90) REVERT: F 375 MET cc_start: 0.8126 (ppp) cc_final: 0.7914 (ppp) REVERT: F 585 MET cc_start: 0.9058 (mmm) cc_final: 0.8612 (mmm) REVERT: F 629 ASP cc_start: 0.8229 (m-30) cc_final: 0.7956 (m-30) REVERT: E 382 PHE cc_start: 0.7850 (m-10) cc_final: 0.7468 (m-10) REVERT: E 425 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8458 (mmmt) REVERT: E 595 TYR cc_start: 0.6870 (m-80) cc_final: 0.6503 (m-80) REVERT: E 597 LEU cc_start: 0.9084 (pt) cc_final: 0.8661 (mm) outliers start: 36 outliers final: 29 residues processed: 171 average time/residue: 0.2541 time to fit residues: 67.1086 Evaluate side-chains 172 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 1.745 ------------------------------------------------------------------------------- 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 C residue 13 ILE Chi-restraints excluded: chain C residue 24 GLU 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 268 HIS Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 173 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 27 optimal weight: 0.0980 chunk 35 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.095460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.074387 restraints weight = 46108.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.076415 restraints weight = 23519.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.077736 restraints weight = 14845.634| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2953 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= 0.128 Angle : 0.695 11.149 19322 Z= 0.337 Chirality : 0.044 0.324 2273 Planarity : 0.005 0.114 2522 Dihedral : 4.907 59.321 1991 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.60 % Favored : 88.91 % Rotamer: Outliers : 2.21 % Allowed : 18.92 % 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: -0.64 (0.21), residues: 1830 helix: 1.10 (0.18), residues: 931 sheet: -1.71 (0.44), residues: 148 loop : -2.17 (0.24), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 648 HIS 0.020 0.001 HIS E 601 PHE 0.014 0.001 PHE E 527 TYR 0.018 0.001 TYR E 583 ARG 0.006 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 624) hydrogen bonds : angle 4.07934 ( 1830) covalent geometry : bond 0.00304 (14201) covalent geometry : angle 0.69457 (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 177 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: C 235 MET cc_start: 0.7295 (mtp) cc_final: 0.6903 (mtp) REVERT: C 320 ARG cc_start: 0.7991 (ptt-90) cc_final: 0.7563 (ptt-90) REVERT: B 24 GLU cc_start: 0.8750 (tp30) cc_final: 0.8444 (tp30) REVERT: B 63 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6995 (mm) REVERT: D 51 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6450 (tpt-90) REVERT: F 585 MET cc_start: 0.9035 (mmm) cc_final: 0.8572 (mmm) REVERT: F 629 ASP cc_start: 0.8231 (m-30) cc_final: 0.7667 (m-30) REVERT: E 382 PHE cc_start: 0.7794 (m-10) cc_final: 0.7423 (m-10) REVERT: E 425 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8455 (mmmt) REVERT: E 595 TYR cc_start: 0.6894 (m-80) cc_final: 0.6520 (m-80) REVERT: E 597 LEU cc_start: 0.9094 (pt) cc_final: 0.8661 (mm) outliers start: 33 outliers final: 28 residues processed: 167 average time/residue: 0.2417 time to fit residues: 61.3298 Evaluate side-chains 171 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.539 ------------------------------------------------------------------------------- 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 C residue 13 ILE Chi-restraints excluded: chain C residue 24 GLU 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 F residue 372 LEU Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 633 MET Chi-restraints excluded: chain E residue 358 TYR Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 608 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 46 optimal weight: 8.9990 chunk 161 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 71 optimal weight: 0.0870 chunk 36 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 162 optimal weight: 0.0870 chunk 69 optimal weight: 0.8980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 GLN D 139 GLN F 403 GLN F 521 HIS E 546 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.097324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.076258 restraints weight = 46242.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.078337 restraints weight = 23467.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.079703 restraints weight = 14737.350| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2997 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= 0.118 Angle : 0.698 18.434 19322 Z= 0.335 Chirality : 0.044 0.316 2273 Planarity : 0.005 0.118 2522 Dihedral : 4.821 58.880 1991 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.16 % Favored : 89.34 % Rotamer: Outliers : 2.07 % Allowed : 19.25 % 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: -0.52 (0.21), residues: 1830 helix: 1.17 (0.18), residues: 932 sheet: -1.52 (0.46), residues: 141 loop : -2.13 (0.25), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 648 HIS 0.023 0.001 HIS E 601 PHE 0.013 0.001 PHE E 527 TYR 0.016 0.001 TYR E 583 ARG 0.006 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.02957 ( 624) hydrogen bonds : angle 3.96326 ( 1830) covalent geometry : bond 0.00273 (14201) covalent geometry : angle 0.69766 (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 187 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 235 MET cc_start: 0.7178 (mtp) cc_final: 0.6858 (mtp) REVERT: C 320 ARG cc_start: 0.7971 (ptt-90) cc_final: 0.7574 (ptt-90) REVERT: B 24 GLU cc_start: 0.8655 (tp30) cc_final: 0.8428 (tp30) REVERT: B 63 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6979 (mm) REVERT: D 51 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.5999 (tpt-90) REVERT: D 225 LYS cc_start: 0.7749 (tttt) cc_final: 0.7265 (ttmt) REVERT: F 585 MET cc_start: 0.8971 (mmm) cc_final: 0.8526 (mmm) REVERT: F 629 ASP cc_start: 0.8214 (m-30) cc_final: 0.7645 (m-30) REVERT: E 382 PHE cc_start: 0.7783 (m-10) cc_final: 0.7486 (m-10) REVERT: E 595 TYR cc_start: 0.6773 (m-80) cc_final: 0.6379 (m-80) REVERT: E 597 LEU cc_start: 0.9065 (pt) cc_final: 0.8650 (mm) REVERT: E 633 MET cc_start: 0.8061 (ttt) cc_final: 0.7608 (ppp) outliers start: 31 outliers final: 24 residues processed: 177 average time/residue: 0.2329 time to fit residues: 63.3739 Evaluate side-chains 174 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.652 ------------------------------------------------------------------------------- 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 13 ILE 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 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 194 TYR Chi-restraints excluded: chain D residue 197 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: 2.9990 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 54 optimal weight: 0.0470 chunk 103 optimal weight: 2.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.097125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.076023 restraints weight = 46518.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.078106 restraints weight = 23658.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.079438 restraints weight = 14907.232| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3043 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 : 0.711 17.418 19322 Z= 0.341 Chirality : 0.044 0.316 2273 Planarity : 0.006 0.115 2522 Dihedral : 4.804 58.948 1991 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.16 % Favored : 89.34 % Rotamer: Outliers : 1.74 % Allowed : 19.92 % Favored : 78.34 % 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: -0.62 (0.21), residues: 1830 helix: 1.08 (0.18), residues: 943 sheet: -1.65 (0.45), residues: 145 loop : -2.19 (0.25), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 648 HIS 0.022 0.001 HIS E 601 PHE 0.014 0.001 PHE E 527 TYR 0.015 0.001 TYR E 583 ARG 0.006 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.03005 ( 624) hydrogen bonds : angle 3.94448 ( 1830) covalent geometry : bond 0.00280 (14201) covalent geometry : angle 0.71146 (19322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5192.61 seconds wall clock time: 92 minutes 34.09 seconds (5554.09 seconds total)