Starting phenix.real_space_refine on Sat Aug 23 17:09:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gh3_40032/08_2025/8gh3_40032.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gh3_40032/08_2025/8gh3_40032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gh3_40032/08_2025/8gh3_40032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gh3_40032/08_2025/8gh3_40032.map" model { file = "/net/cci-nas-00/data/ceres_data/8gh3_40032/08_2025/8gh3_40032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gh3_40032/08_2025/8gh3_40032.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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 8551 2.51 5 N 2392 2.21 5 O 2491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13515 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: {'PCIS': 1, 'PTRANS': 22, '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': 3, 'PTRANS': 20, '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: {'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': 2, 'PTRANS': 21, 'TRANS': 299} Chain: "E" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1977 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 11, 'TRANS': 240} Chain breaks: 1 Chain: "F" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1978 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 12, 'TRANS': 241} Chain breaks: 1 Time building chain proxies: 2.80, per 1000 atoms: 0.21 Number of scatterers: 13515 At special positions: 0 Unit cell: (101.48, 116.1, 158.24, 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 2491 8.00 N 2392 7.00 C 8551 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: 1.03 Conformation dependent library (CDL) restraints added in 463.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3308 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 17 sheets defined 58.0% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 95 through 116 removed outlier: 3.831A pdb=" N LEU A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASN A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.824A 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 Processing helix chain 'A' and resid 156 through 171 removed outlier: 3.961A pdb=" N GLY A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 removed outlier: 3.660A 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 207 through 225 removed outlier: 3.662A pdb=" N GLN A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLY A 218 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N THR A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.508A pdb=" N GLY A 239 " --> pdb=" O MET A 235 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 317 removed outlier: 3.959A pdb=" N MET A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 23 removed outlier: 4.201A pdb=" N SER B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU B 17 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 removed outlier: 4.157A pdb=" N ASP B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 100 through 118 removed outlier: 4.303A pdb=" N LEU B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 145 Proline residue: B 135 - end of helix Processing helix chain 'B' and resid 156 through 169 removed outlier: 3.877A pdb=" N GLY B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 4.145A pdb=" N GLU B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.991A pdb=" N ALA B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 251 Processing helix chain 'B' and resid 294 through 322 removed outlier: 4.075A pdb=" N GLU B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N MET B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 322 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 25 removed outlier: 3.877A pdb=" N GLN C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.753A pdb=" N THR C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.762A pdb=" N MET C 94 " --> pdb=" O LYS C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 116 Processing helix chain 'C' and resid 129 through 144 Proline residue: C 135 - end of helix Processing helix chain 'C' and resid 157 through 171 Processing helix chain 'C' and resid 203 through 226 removed outlier: 3.796A pdb=" N GLU C 209 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLY C 218 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU C 220 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL C 222 " --> pdb=" O GLY C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.853A pdb=" N MET C 235 " --> pdb=" O ALA C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 319 removed outlier: 4.396A pdb=" N GLU C 302 " --> pdb=" O LYS C 298 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 removed outlier: 4.021A pdb=" N SER D 16 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU D 17 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 46 Processing helix chain 'D' and resid 95 through 118 removed outlier: 4.740A pdb=" N GLY D 105 " --> pdb=" O ASN D 101 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 110 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N CYS D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL D 117 " --> pdb=" O THR D 113 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER D 118 " --> pdb=" O CYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 143 removed outlier: 3.625A pdb=" N THR D 133 " --> pdb=" O PRO D 129 " (cutoff:3.500A) Proline residue: D 135 - end of helix Processing helix chain 'D' and resid 156 through 171 removed outlier: 4.564A pdb=" N GLY D 160 " --> pdb=" O SER D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.643A pdb=" N GLU D 209 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL D 214 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 225 removed outlier: 3.572A pdb=" N GLU D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 252 removed outlier: 4.455A pdb=" N HIS D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 317 removed outlier: 3.751A pdb=" N GLU D 299 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 373 removed outlier: 5.403A pdb=" N GLN E 371 " --> pdb=" O ILE E 367 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU E 372 " --> pdb=" O ALA E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 387 removed outlier: 3.640A pdb=" N ALA E 378 " --> pdb=" O ASN E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 406 removed outlier: 4.071A pdb=" N GLU E 405 " --> pdb=" O THR E 401 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN E 406 " --> pdb=" O THR E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 422 removed outlier: 3.547A pdb=" N ILE E 414 " --> pdb=" O CYS E 410 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU E 422 " --> pdb=" O HIS E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 441 removed outlier: 3.626A pdb=" N LEU E 433 " --> pdb=" O VAL E 429 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA E 434 " --> pdb=" O HIS E 430 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL E 435 " --> pdb=" O ALA E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 455 Processing helix chain 'E' and resid 512 through 524 removed outlier: 3.753A pdb=" N SER E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 541 removed outlier: 3.894A pdb=" N LEU E 540 " --> pdb=" O ARG E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 557 removed outlier: 3.993A pdb=" N TRP E 548 " --> pdb=" O ASP E 544 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS E 550 " --> pdb=" O HIS E 546 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU E 555 " --> pdb=" O LEU E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 575 removed outlier: 3.653A pdb=" N ALA E 564 " --> pdb=" O ARG E 560 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU E 566 " --> pdb=" O GLN E 562 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA E 567 " --> pdb=" O GLU E 563 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR E 568 " --> pdb=" O ALA E 564 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE E 574 " --> pdb=" O ARG E 570 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN E 575 " --> pdb=" O ALA E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 591 removed outlier: 4.248A pdb=" N MET E 582 " --> pdb=" O TYR E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 611 removed outlier: 3.702A pdb=" N ALA E 598 " --> pdb=" O GLN E 594 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HIS E 601 " --> pdb=" O LEU E 597 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 623 No H-bonds generated for 'chain 'E' and resid 621 through 623' Processing helix chain 'E' and resid 624 through 629 Processing helix chain 'E' and resid 630 through 632 No H-bonds generated for 'chain 'E' and resid 630 through 632' Processing helix chain 'E' and resid 633 through 638 removed outlier: 4.525A pdb=" N ASN E 636 " --> pdb=" O MET E 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 640 through 645 removed outlier: 3.776A pdb=" N GLU E 645 " --> pdb=" O SER E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 649 Processing helix chain 'F' and resid 354 through 359 removed outlier: 4.086A pdb=" N TYR F 358 " --> pdb=" O PRO F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 373 removed outlier: 4.374A pdb=" N GLU F 365 " --> pdb=" O LYS F 361 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 370 " --> pdb=" O GLY F 366 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN F 371 " --> pdb=" O ILE F 367 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU F 372 " --> pdb=" O ALA F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 389 removed outlier: 4.367A pdb=" N ALA F 378 " --> pdb=" O ASN F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 406 removed outlier: 3.753A pdb=" N TRP F 396 " --> pdb=" O ASN F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 423 removed outlier: 3.609A pdb=" N ILE F 414 " --> pdb=" O CYS F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 441 removed outlier: 3.806A pdb=" N HIS F 430 " --> pdb=" O ASP F 426 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL F 435 " --> pdb=" O ALA F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 457 removed outlier: 3.753A pdb=" N GLN F 457 " --> pdb=" O TRP F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 507 Processing helix chain 'F' and resid 510 through 524 Processing helix chain 'F' and resid 526 through 541 removed outlier: 3.694A pdb=" N ALA F 530 " --> pdb=" O ARG F 526 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG F 541 " --> pdb=" O ALA F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 558 removed outlier: 3.587A pdb=" N GLY F 558 " --> pdb=" O THR F 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 575 removed outlier: 4.082A pdb=" N ALA F 564 " --> pdb=" O ARG F 560 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU F 566 " --> pdb=" O GLN F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 592 removed outlier: 3.857A pdb=" N MET F 582 " --> pdb=" O TYR F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 610 Processing helix chain 'F' and resid 613 through 617 Processing helix chain 'F' and resid 619 through 638 removed outlier: 4.335A pdb=" N ALA F 623 " --> pdb=" O GLY F 619 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG F 625 " --> pdb=" O ARG F 621 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLY F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU F 627 " --> pdb=" O ALA F 623 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET F 638 " --> pdb=" O THR F 634 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 59 removed outlier: 6.075A pdb=" N LEU A 31 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA A 59 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 33 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR A 34 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 153 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 263 removed outlier: 3.672A pdb=" N ALA A 260 " --> pdb=" O MET A 275 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ARG A 287 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL A 278 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.529A pdb=" N VAL B 83 " --> pdb=" O ALA B 5 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 30 removed outlier: 6.968A pdb=" N SER B 29 " --> pdb=" O THR B 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.688A pdb=" N LEU B 33 " --> pdb=" O ALA B 59 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 123 through 125 Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA9, first strand: chain 'B' and resid 257 through 263 removed outlier: 4.027A pdb=" N ALA B 260 " --> pdb=" O MET B 275 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET B 275 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG B 286 " --> pdb=" O VAL B 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 2 through 4 removed outlier: 8.014A pdb=" N LYS C 57 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU C 31 " --> pdb=" O LYS C 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 81 through 84 removed outlier: 3.751A pdb=" N CYS C 124 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB4, first strand: chain 'C' and resid 257 through 263 removed outlier: 4.059A pdb=" N ALA C 260 " --> pdb=" O MET C 275 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET C 275 " --> pdb=" O ALA C 260 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 55 through 57 removed outlier: 6.183A pdb=" N VAL D 4 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N TYR D 34 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL D 6 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AB7, first strand: chain 'D' and resid 257 through 258 removed outlier: 4.084A pdb=" N ARG D 286 " --> pdb=" O VAL D 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 261 through 263 691 hydrogen bonds defined for protein. 2034 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: 2.13 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4434 1.34 - 1.46: 1341 1.46 - 1.57: 7848 1.57 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 13763 Sorted by residual: bond pdb=" C LEU D 63 " pdb=" N PRO D 64 " ideal model delta sigma weight residual 1.329 1.352 -0.022 1.18e-02 7.18e+03 3.63e+00 bond pdb=" C LYS D 91 " pdb=" N PRO D 92 " ideal model delta sigma weight residual 1.331 1.352 -0.021 1.27e-02 6.20e+03 2.69e+00 bond pdb=" N VAL A 126 " pdb=" CA VAL A 126 " ideal model delta sigma weight residual 1.459 1.439 0.020 1.25e-02 6.40e+03 2.58e+00 bond pdb=" CA ASN D 169 " pdb=" C ASN D 169 " ideal model delta sigma weight residual 1.522 1.501 0.022 1.38e-02 5.25e+03 2.47e+00 bond pdb=" CA HIS D 172 " pdb=" C HIS D 172 " ideal model delta sigma weight residual 1.528 1.511 0.017 1.11e-02 8.12e+03 2.38e+00 ... (remaining 13758 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 18289 1.98 - 3.96: 363 3.96 - 5.93: 57 5.93 - 7.91: 10 7.91 - 9.89: 3 Bond angle restraints: 18722 Sorted by residual: angle pdb=" N VAL B 85 " pdb=" CA VAL B 85 " pdb=" C VAL B 85 " ideal model delta sigma weight residual 113.20 108.26 4.94 9.60e-01 1.09e+00 2.64e+01 angle pdb=" N VAL D 85 " pdb=" CA VAL D 85 " pdb=" C VAL D 85 " ideal model delta sigma weight residual 113.47 108.99 4.48 1.01e+00 9.80e-01 1.97e+01 angle pdb=" N ASN D 169 " pdb=" CA ASN D 169 " pdb=" C ASN D 169 " ideal model delta sigma weight residual 113.01 107.93 5.08 1.20e+00 6.94e-01 1.79e+01 angle pdb=" C ASN D 128 " pdb=" N PRO D 129 " pdb=" CA PRO D 129 " ideal model delta sigma weight residual 127.00 136.89 -9.89 2.40e+00 1.74e-01 1.70e+01 angle pdb=" N VAL A 130 " pdb=" CA VAL A 130 " pdb=" C VAL A 130 " ideal model delta sigma weight residual 109.34 117.56 -8.22 2.08e+00 2.31e-01 1.56e+01 ... (remaining 18717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 7502 16.63 - 33.26: 715 33.26 - 49.89: 150 49.89 - 66.52: 28 66.52 - 83.15: 17 Dihedral angle restraints: 8412 sinusoidal: 3274 harmonic: 5138 Sorted by residual: dihedral pdb=" CA LEU B 63 " pdb=" C LEU B 63 " pdb=" N PRO B 64 " pdb=" CA PRO B 64 " ideal model delta harmonic sigma weight residual 0.00 -44.54 44.54 0 5.00e+00 4.00e-02 7.93e+01 dihedral pdb=" CA ASN B 128 " pdb=" C ASN B 128 " pdb=" N PRO B 129 " pdb=" CA PRO B 129 " ideal model delta harmonic sigma weight residual 0.00 -32.48 32.48 0 5.00e+00 4.00e-02 4.22e+01 dihedral pdb=" CA GLU A 267 " pdb=" C GLU A 267 " pdb=" N HIS A 268 " pdb=" CA HIS A 268 " ideal model delta harmonic sigma weight residual -180.00 -153.60 -26.40 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 8409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1520 0.038 - 0.077: 501 0.077 - 0.115: 181 0.115 - 0.154: 15 0.154 - 0.192: 2 Chirality restraints: 2219 Sorted by residual: chirality pdb=" CG LEU E 637 " pdb=" CB LEU E 637 " pdb=" CD1 LEU E 637 " pdb=" CD2 LEU E 637 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.23e-01 chirality pdb=" CB VAL C 85 " pdb=" CA VAL C 85 " pdb=" CG1 VAL C 85 " pdb=" CG2 VAL C 85 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CB THR C 232 " pdb=" CA THR C 232 " pdb=" OG1 THR C 232 " pdb=" CG2 THR C 232 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 2216 not shown) Planarity restraints: 2434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 63 " -0.069 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO D 64 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 389 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO E 390 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 390 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 390 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 124 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C CYS C 124 " -0.030 2.00e-02 2.50e+03 pdb=" O CYS C 124 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE C 125 " 0.010 2.00e-02 2.50e+03 ... (remaining 2431 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1504 2.75 - 3.28: 14123 3.28 - 3.82: 21878 3.82 - 4.36: 24521 4.36 - 4.90: 42105 Nonbonded interactions: 104131 Sorted by model distance: nonbonded pdb=" O LEU D 25 " pdb=" NH2 ARG D 51 " model vdw 2.208 3.120 nonbonded pdb=" O LEU F 551 " pdb=" OG1 THR F 554 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR A 264 " pdb=" O CYS A 270 " model vdw 2.239 3.040 nonbonded pdb=" O GLN E 609 " pdb=" ND2 ASN E 614 " model vdw 2.266 3.120 nonbonded pdb=" OD1 ASN E 549 " pdb=" ND2 ASN E 584 " model vdw 2.274 3.120 ... (remaining 104126 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' and resid 354 through 638) selection = (chain 'F' and (resid 354 through 457 or resid 511 through 638)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.440 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.480 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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 : 0.003 0.035 13763 Z= 0.155 Angle : 0.686 9.891 18722 Z= 0.391 Chirality : 0.043 0.192 2219 Planarity : 0.005 0.102 2434 Dihedral : 14.152 83.150 5104 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.96 % Favored : 92.31 % Rotamer: Outliers : 0.97 % Allowed : 0.90 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.20), residues: 1782 helix: 0.68 (0.18), residues: 903 sheet: -2.19 (0.38), residues: 180 loop : -2.15 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 640 TYR 0.020 0.001 TYR D 34 PHE 0.008 0.001 PHE C 27 TRP 0.021 0.001 TRP E 548 HIS 0.005 0.001 HIS F 521 Details of bonding type rmsd covalent geometry : bond 0.00267 (13763) covalent geometry : angle 0.68602 (18722) hydrogen bonds : bond 0.19416 ( 691) hydrogen bonds : angle 6.19290 ( 2034) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.527 Fit side-chains REVERT: D 62 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7677 (tptp) REVERT: D 94 MET cc_start: 0.7560 (tmm) cc_final: 0.6690 (tmm) REVERT: E 421 MET cc_start: 0.7459 (ppp) cc_final: 0.7240 (ptt) REVERT: E 521 HIS cc_start: 0.9010 (m90) cc_final: 0.8505 (m-70) REVERT: E 528 ASP cc_start: 0.7386 (m-30) cc_final: 0.7145 (m-30) REVERT: F 439 ASN cc_start: 0.8766 (m-40) cc_final: 0.8550 (m-40) outliers start: 14 outliers final: 2 residues processed: 166 average time/residue: 0.0944 time to fit residues: 23.6471 Evaluate side-chains 124 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 62 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN D 101 ASN E 575 ASN E 614 ASN F 507 ASN F 521 HIS F 533 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.094934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.073347 restraints weight = 52314.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.075108 restraints weight = 27913.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.076262 restraints weight = 18467.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.076990 restraints weight = 14071.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.077410 restraints weight = 11765.218| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 13763 Z= 0.150 Angle : 0.629 10.057 18722 Z= 0.323 Chirality : 0.044 0.193 2219 Planarity : 0.005 0.093 2434 Dihedral : 4.891 56.724 1937 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.01 % Favored : 92.76 % Rotamer: Outliers : 1.03 % Allowed : 8.83 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.20), residues: 1782 helix: 1.01 (0.17), residues: 923 sheet: -2.16 (0.39), residues: 174 loop : -1.97 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 51 TYR 0.010 0.001 TYR F 578 PHE 0.011 0.001 PHE C 27 TRP 0.015 0.002 TRP E 628 HIS 0.006 0.001 HIS E 441 Details of bonding type rmsd covalent geometry : bond 0.00345 (13763) covalent geometry : angle 0.62893 (18722) hydrogen bonds : bond 0.04478 ( 691) hydrogen bonds : angle 4.41597 ( 2034) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: D 94 MET cc_start: 0.7443 (tmm) cc_final: 0.7026 (tmm) REVERT: E 357 MET cc_start: 0.7274 (mmm) cc_final: 0.7069 (mmm) REVERT: E 408 LYS cc_start: 0.8259 (ptpp) cc_final: 0.7093 (ptmm) REVERT: E 421 MET cc_start: 0.7466 (ppp) cc_final: 0.7246 (ptt) REVERT: E 521 HIS cc_start: 0.9068 (m90) cc_final: 0.8595 (m170) REVERT: F 439 ASN cc_start: 0.8731 (m-40) cc_final: 0.8304 (m110) REVERT: F 523 LEU cc_start: 0.8861 (tt) cc_final: 0.8620 (mt) outliers start: 15 outliers final: 14 residues processed: 141 average time/residue: 0.0886 time to fit residues: 19.6127 Evaluate side-chains 145 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 587 VAL Chi-restraints excluded: chain F residue 627 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 132 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 100 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 116 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 0.1980 chunk 163 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.096164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.074580 restraints weight = 52552.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.076435 restraints weight = 27291.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.077634 restraints weight = 17776.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.078424 restraints weight = 13374.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.078871 restraints weight = 11066.693| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 13763 Z= 0.110 Angle : 0.577 7.472 18722 Z= 0.293 Chirality : 0.042 0.157 2219 Planarity : 0.005 0.103 2434 Dihedral : 4.577 55.844 1932 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.06 % Favored : 93.77 % Rotamer: Outliers : 0.83 % Allowed : 12.41 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.21), residues: 1782 helix: 1.14 (0.17), residues: 930 sheet: -1.99 (0.40), residues: 170 loop : -1.77 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 580 TYR 0.025 0.001 TYR E 358 PHE 0.008 0.001 PHE C 27 TRP 0.007 0.001 TRP E 628 HIS 0.007 0.001 HIS E 441 Details of bonding type rmsd covalent geometry : bond 0.00248 (13763) covalent geometry : angle 0.57747 (18722) hydrogen bonds : bond 0.03614 ( 691) hydrogen bonds : angle 4.03768 ( 2034) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 245 HIS cc_start: 0.8303 (m-70) cc_final: 0.8027 (m-70) REVERT: E 408 LYS cc_start: 0.8252 (ptpp) cc_final: 0.7143 (ptmm) REVERT: E 521 HIS cc_start: 0.9046 (m90) cc_final: 0.8557 (m170) REVERT: F 439 ASN cc_start: 0.8690 (m-40) cc_final: 0.8329 (m-40) outliers start: 12 outliers final: 8 residues processed: 151 average time/residue: 0.0889 time to fit residues: 20.8202 Evaluate side-chains 142 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain F residue 370 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 152 optimal weight: 0.2980 chunk 158 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.097642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.076719 restraints weight = 52809.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.078536 restraints weight = 27736.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.079732 restraints weight = 17948.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.080455 restraints weight = 13345.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.080992 restraints weight = 11021.849| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 13763 Z= 0.106 Angle : 0.565 8.417 18722 Z= 0.286 Chirality : 0.042 0.158 2219 Planarity : 0.005 0.109 2434 Dihedral : 4.493 56.552 1932 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.23 % Favored : 93.60 % Rotamer: Outliers : 1.24 % Allowed : 14.55 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.21), residues: 1782 helix: 1.25 (0.17), residues: 934 sheet: -1.85 (0.40), residues: 170 loop : -1.72 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 228 TYR 0.022 0.001 TYR E 358 PHE 0.008 0.001 PHE C 27 TRP 0.009 0.001 TRP E 628 HIS 0.005 0.001 HIS E 441 Details of bonding type rmsd covalent geometry : bond 0.00242 (13763) covalent geometry : angle 0.56532 (18722) hydrogen bonds : bond 0.03352 ( 691) hydrogen bonds : angle 3.85965 ( 2034) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.7668 (mtt) cc_final: 0.7445 (mtt) REVERT: C 232 THR cc_start: 0.7718 (OUTLIER) cc_final: 0.7381 (p) REVERT: D 94 MET cc_start: 0.7280 (tmm) cc_final: 0.6774 (tmm) REVERT: E 374 ASN cc_start: 0.7354 (p0) cc_final: 0.6884 (p0) REVERT: E 408 LYS cc_start: 0.8197 (ptpp) cc_final: 0.7918 (ptpp) REVERT: E 521 HIS cc_start: 0.9058 (m90) cc_final: 0.8600 (m-70) REVERT: F 439 ASN cc_start: 0.8729 (m-40) cc_final: 0.8369 (m-40) REVERT: F 523 LEU cc_start: 0.8858 (tt) cc_final: 0.8642 (mt) REVERT: F 582 MET cc_start: 0.7707 (mpp) cc_final: 0.7503 (mpp) outliers start: 18 outliers final: 11 residues processed: 150 average time/residue: 0.0876 time to fit residues: 20.6965 Evaluate side-chains 146 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 506 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 15 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 100 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3849 r_free = 0.3849 target = 0.094565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.073918 restraints weight = 52282.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.075660 restraints weight = 27370.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.076803 restraints weight = 17618.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.077499 restraints weight = 13138.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.078013 restraints weight = 10864.424| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 13763 Z= 0.133 Angle : 0.595 8.674 18722 Z= 0.300 Chirality : 0.043 0.191 2219 Planarity : 0.005 0.112 2434 Dihedral : 4.594 58.497 1932 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.07 % Favored : 92.76 % Rotamer: Outliers : 1.45 % Allowed : 15.79 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.21), residues: 1782 helix: 1.26 (0.17), residues: 930 sheet: -2.04 (0.39), residues: 172 loop : -1.74 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 580 TYR 0.023 0.002 TYR E 583 PHE 0.010 0.001 PHE C 27 TRP 0.007 0.001 TRP E 648 HIS 0.004 0.001 HIS E 441 Details of bonding type rmsd covalent geometry : bond 0.00312 (13763) covalent geometry : angle 0.59505 (18722) hydrogen bonds : bond 0.03721 ( 691) hydrogen bonds : angle 3.92325 ( 2034) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.372 Fit side-chains REVERT: C 232 THR cc_start: 0.7812 (m) cc_final: 0.7595 (p) REVERT: D 94 MET cc_start: 0.7346 (tmm) cc_final: 0.6958 (tmm) REVERT: E 408 LYS cc_start: 0.8242 (ptpp) cc_final: 0.7998 (ptpp) REVERT: E 521 HIS cc_start: 0.9061 (m90) cc_final: 0.8542 (m-70) REVERT: F 439 ASN cc_start: 0.8724 (m-40) cc_final: 0.8349 (m-40) REVERT: F 448 GLN cc_start: 0.7550 (pp30) cc_final: 0.7242 (pp30) REVERT: F 582 MET cc_start: 0.7760 (mpp) cc_final: 0.7547 (mpp) outliers start: 21 outliers final: 13 residues processed: 144 average time/residue: 0.0810 time to fit residues: 18.4573 Evaluate side-chains 144 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 555 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 123 optimal weight: 0.0000 chunk 15 optimal weight: 7.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 HIS D 101 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.095455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.074369 restraints weight = 51671.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.076161 restraints weight = 26829.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.077327 restraints weight = 17273.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.078075 restraints weight = 12869.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.078501 restraints weight = 10589.801| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 13763 Z= 0.105 Angle : 0.576 10.865 18722 Z= 0.288 Chirality : 0.043 0.315 2219 Planarity : 0.005 0.113 2434 Dihedral : 4.479 58.684 1932 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.17 % Favored : 93.66 % Rotamer: Outliers : 1.24 % Allowed : 16.90 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.21), residues: 1782 helix: 1.33 (0.17), residues: 930 sheet: -1.82 (0.40), residues: 176 loop : -1.66 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 580 TYR 0.019 0.001 TYR E 358 PHE 0.008 0.001 PHE C 27 TRP 0.007 0.001 TRP E 648 HIS 0.005 0.001 HIS E 441 Details of bonding type rmsd covalent geometry : bond 0.00244 (13763) covalent geometry : angle 0.57584 (18722) hydrogen bonds : bond 0.03219 ( 691) hydrogen bonds : angle 3.79461 ( 2034) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: C 232 THR cc_start: 0.7817 (m) cc_final: 0.7460 (p) REVERT: D 94 MET cc_start: 0.7302 (tmm) cc_final: 0.7024 (tmm) REVERT: E 369 MET cc_start: 0.6612 (ppp) cc_final: 0.6348 (ppp) REVERT: E 408 LYS cc_start: 0.8259 (ptpp) cc_final: 0.8049 (ptpp) REVERT: E 521 HIS cc_start: 0.9071 (m90) cc_final: 0.8568 (m-70) REVERT: E 637 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.6162 (mt) REVERT: F 439 ASN cc_start: 0.8684 (m-40) cc_final: 0.8412 (m-40) outliers start: 18 outliers final: 14 residues processed: 149 average time/residue: 0.0840 time to fit residues: 19.7179 Evaluate side-chains 146 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 637 LEU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 555 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 163 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 170 optimal weight: 8.9990 chunk 152 optimal weight: 0.0070 chunk 98 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 HIS ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.093637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.072755 restraints weight = 51977.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.074482 restraints weight = 27289.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.075614 restraints weight = 17704.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.076327 restraints weight = 13232.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.076694 restraints weight = 10924.405| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 13763 Z= 0.149 Angle : 0.621 11.008 18722 Z= 0.312 Chirality : 0.044 0.346 2219 Planarity : 0.005 0.115 2434 Dihedral : 4.651 52.190 1932 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.46 % Favored : 92.31 % Rotamer: Outliers : 1.17 % Allowed : 17.52 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.21), residues: 1782 helix: 1.22 (0.17), residues: 934 sheet: -1.98 (0.40), residues: 167 loop : -1.73 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 580 TYR 0.026 0.002 TYR E 583 PHE 0.011 0.001 PHE C 27 TRP 0.009 0.001 TRP E 648 HIS 0.005 0.001 HIS E 441 Details of bonding type rmsd covalent geometry : bond 0.00349 (13763) covalent geometry : angle 0.62066 (18722) hydrogen bonds : bond 0.03886 ( 691) hydrogen bonds : angle 4.00633 ( 2034) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: C 232 THR cc_start: 0.7826 (m) cc_final: 0.7598 (p) REVERT: E 369 MET cc_start: 0.6630 (ppp) cc_final: 0.6358 (ppp) REVERT: E 521 HIS cc_start: 0.9072 (m90) cc_final: 0.8722 (m170) REVERT: E 637 LEU cc_start: 0.6381 (OUTLIER) cc_final: 0.6147 (mt) REVERT: F 363 MET cc_start: 0.5507 (tmm) cc_final: 0.5104 (tmm) REVERT: F 439 ASN cc_start: 0.8684 (m-40) cc_final: 0.8366 (m-40) outliers start: 17 outliers final: 14 residues processed: 140 average time/residue: 0.0816 time to fit residues: 18.0196 Evaluate side-chains 142 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain E residue 637 LEU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 435 VAL Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 521 HIS Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 583 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 99 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.095126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.074048 restraints weight = 51201.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.075802 restraints weight = 26867.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.076958 restraints weight = 17422.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.077711 restraints weight = 13059.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.078211 restraints weight = 10781.676| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 13763 Z= 0.109 Angle : 0.608 12.438 18722 Z= 0.300 Chirality : 0.043 0.336 2219 Planarity : 0.005 0.115 2434 Dihedral : 4.365 41.028 1931 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.29 % Favored : 93.55 % Rotamer: Outliers : 1.10 % Allowed : 17.86 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.21), residues: 1782 helix: 1.31 (0.17), residues: 930 sheet: -1.81 (0.40), residues: 176 loop : -1.62 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 228 TYR 0.028 0.001 TYR F 568 PHE 0.008 0.001 PHE C 27 TRP 0.009 0.001 TRP E 648 HIS 0.005 0.001 HIS E 441 Details of bonding type rmsd covalent geometry : bond 0.00252 (13763) covalent geometry : angle 0.60802 (18722) hydrogen bonds : bond 0.03318 ( 691) hydrogen bonds : angle 3.83371 ( 2034) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.372 Fit side-chains REVERT: C 232 THR cc_start: 0.7804 (m) cc_final: 0.7425 (p) REVERT: D 94 MET cc_start: 0.7187 (tmm) cc_final: 0.6520 (tmm) REVERT: E 421 MET cc_start: 0.6850 (ppp) cc_final: 0.6552 (pmm) REVERT: E 521 HIS cc_start: 0.9090 (m90) cc_final: 0.8690 (m-70) REVERT: E 547 MET cc_start: 0.8272 (ttt) cc_final: 0.7589 (tmm) REVERT: E 637 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.6199 (mt) REVERT: F 363 MET cc_start: 0.5711 (tmm) cc_final: 0.5349 (tmm) REVERT: F 439 ASN cc_start: 0.8674 (m-40) cc_final: 0.8390 (m-40) REVERT: F 582 MET cc_start: 0.7714 (mpp) cc_final: 0.7485 (mpp) REVERT: F 628 TRP cc_start: 0.7160 (t60) cc_final: 0.6688 (t60) outliers start: 16 outliers final: 11 residues processed: 145 average time/residue: 0.0816 time to fit residues: 18.6976 Evaluate side-chains 144 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 637 LEU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 555 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 173 optimal weight: 1.9990 chunk 138 optimal weight: 0.0050 chunk 4 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 148 optimal weight: 0.3980 chunk 58 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 97 optimal weight: 0.6980 chunk 160 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.098479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.077578 restraints weight = 52471.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.079399 restraints weight = 27592.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.080584 restraints weight = 17868.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.081294 restraints weight = 13288.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.081849 restraints weight = 10996.324| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 13763 Z= 0.104 Angle : 0.618 12.586 18722 Z= 0.301 Chirality : 0.043 0.331 2219 Planarity : 0.005 0.115 2434 Dihedral : 4.211 39.087 1931 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.95 % Favored : 93.88 % Rotamer: Outliers : 0.90 % Allowed : 18.55 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.21), residues: 1782 helix: 1.29 (0.18), residues: 935 sheet: -1.74 (0.42), residues: 162 loop : -1.57 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 580 TYR 0.025 0.001 TYR E 583 PHE 0.006 0.001 PHE C 27 TRP 0.010 0.001 TRP E 648 HIS 0.005 0.000 HIS E 441 Details of bonding type rmsd covalent geometry : bond 0.00241 (13763) covalent geometry : angle 0.61805 (18722) hydrogen bonds : bond 0.02984 ( 691) hydrogen bonds : angle 3.73944 ( 2034) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.443 Fit side-chains REVERT: C 232 THR cc_start: 0.7682 (m) cc_final: 0.7344 (p) REVERT: D 94 MET cc_start: 0.6959 (tmm) cc_final: 0.6451 (tmm) REVERT: E 521 HIS cc_start: 0.9059 (m90) cc_final: 0.8738 (m90) REVERT: E 547 MET cc_start: 0.8232 (ttt) cc_final: 0.7586 (tmm) REVERT: E 600 LYS cc_start: 0.8105 (mmtt) cc_final: 0.7480 (mmmt) REVERT: F 363 MET cc_start: 0.5730 (tmm) cc_final: 0.5450 (tmm) REVERT: F 523 LEU cc_start: 0.8704 (mm) cc_final: 0.8310 (tt) REVERT: F 582 MET cc_start: 0.7782 (mpp) cc_final: 0.7563 (mpp) REVERT: F 628 TRP cc_start: 0.7192 (t60) cc_final: 0.6754 (t60) outliers start: 13 outliers final: 8 residues processed: 152 average time/residue: 0.0808 time to fit residues: 19.3466 Evaluate side-chains 143 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 506 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.095331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.074417 restraints weight = 52527.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.076147 restraints weight = 27719.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.077295 restraints weight = 18100.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.078040 restraints weight = 13533.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.078530 restraints weight = 11169.241| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 13763 Z= 0.152 Angle : 0.661 12.374 18722 Z= 0.326 Chirality : 0.044 0.332 2219 Planarity : 0.005 0.115 2434 Dihedral : 4.488 45.588 1931 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.63 % Favored : 92.20 % Rotamer: Outliers : 0.62 % Allowed : 18.90 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.21), residues: 1782 helix: 1.24 (0.17), residues: 929 sheet: -1.95 (0.38), residues: 188 loop : -1.63 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 228 TYR 0.023 0.002 TYR E 583 PHE 0.011 0.001 PHE C 27 TRP 0.011 0.001 TRP E 648 HIS 0.006 0.001 HIS E 441 Details of bonding type rmsd covalent geometry : bond 0.00357 (13763) covalent geometry : angle 0.66108 (18722) hydrogen bonds : bond 0.03836 ( 691) hydrogen bonds : angle 4.00298 ( 2034) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.361 Fit side-chains REVERT: C 232 THR cc_start: 0.7717 (m) cc_final: 0.7482 (p) REVERT: D 94 MET cc_start: 0.7177 (tmm) cc_final: 0.6623 (tmm) REVERT: E 421 MET cc_start: 0.6867 (ppp) cc_final: 0.6507 (pmm) REVERT: E 521 HIS cc_start: 0.9060 (m90) cc_final: 0.8742 (m170) REVERT: E 547 MET cc_start: 0.8294 (ttt) cc_final: 0.7611 (tmm) REVERT: F 357 MET cc_start: 0.7134 (tpp) cc_final: 0.5324 (tmm) REVERT: F 363 MET cc_start: 0.5764 (tmm) cc_final: 0.5495 (tmm) REVERT: F 523 LEU cc_start: 0.8683 (mm) cc_final: 0.8232 (tt) REVERT: F 582 MET cc_start: 0.7812 (mpp) cc_final: 0.7586 (mpp) REVERT: F 628 TRP cc_start: 0.7257 (t60) cc_final: 0.6788 (t60) outliers start: 9 outliers final: 7 residues processed: 135 average time/residue: 0.0758 time to fit residues: 16.3395 Evaluate side-chains 135 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 506 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 147 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 27 optimal weight: 0.0270 chunk 14 optimal weight: 2.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.097888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.076846 restraints weight = 52715.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.078717 restraints weight = 27377.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.079932 restraints weight = 17602.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.080701 restraints weight = 13034.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.081223 restraints weight = 10687.181| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 13763 Z= 0.107 Angle : 0.632 12.080 18722 Z= 0.307 Chirality : 0.043 0.303 2219 Planarity : 0.005 0.116 2434 Dihedral : 4.306 40.422 1931 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.23 % Favored : 93.60 % Rotamer: Outliers : 0.69 % Allowed : 19.03 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.21), residues: 1782 helix: 1.28 (0.17), residues: 935 sheet: -1.78 (0.42), residues: 162 loop : -1.59 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 228 TYR 0.021 0.001 TYR E 583 PHE 0.007 0.001 PHE C 27 TRP 0.010 0.001 TRP E 648 HIS 0.006 0.001 HIS E 441 Details of bonding type rmsd covalent geometry : bond 0.00251 (13763) covalent geometry : angle 0.63223 (18722) hydrogen bonds : bond 0.03144 ( 691) hydrogen bonds : angle 3.81368 ( 2034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1985.58 seconds wall clock time: 35 minutes 0.33 seconds (2100.33 seconds total)