Starting phenix.real_space_refine on Sun Nov 17 10:55:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh3_40032/11_2024/8gh3_40032.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh3_40032/11_2024/8gh3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh3_40032/11_2024/8gh3_40032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh3_40032/11_2024/8gh3_40032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh3_40032/11_2024/8gh3_40032.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gh3_40032/11_2024/8gh3_40032.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 8.46, per 1000 atoms: 0.63 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: 3.11 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.30 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: 3.61 Time building geometry restraints manager: 3.59 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: 3.580 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: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 30.070 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.760 ------------------------------------------------------------------------------- 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= 0.179 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 : 10.62 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (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 TRP 0.021 0.001 TRP E 548 HIS 0.005 0.001 HIS F 521 PHE 0.008 0.001 PHE C 27 TYR 0.020 0.001 TYR D 34 ARG 0.003 0.000 ARG E 640 *********************** 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 : 1.473 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: 0.2543 time to fit residues: 63.1651 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 : 1.561 ------------------------------------------------------------------------------- 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 150 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 103 optimal weight: 0.0170 chunk 161 optimal weight: 8.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 13763 Z= 0.188 Angle : 0.615 10.079 18722 Z= 0.315 Chirality : 0.044 0.198 2219 Planarity : 0.005 0.092 2434 Dihedral : 4.809 56.365 1937 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.51 % Favored : 93.27 % Rotamer: Outliers : 0.90 % Allowed : 8.55 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.20), residues: 1782 helix: 1.01 (0.17), residues: 930 sheet: -2.07 (0.39), residues: 170 loop : -1.93 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 628 HIS 0.006 0.001 HIS E 441 PHE 0.009 0.001 PHE C 27 TYR 0.009 0.001 TYR F 578 ARG 0.004 0.000 ARG B 228 *********************** 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 155 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 1.567 Fit side-chains revert: symmetry clash REVERT: C 232 THR cc_start: 0.7893 (m) cc_final: 0.7620 (p) REVERT: D 94 MET cc_start: 0.7436 (tmm) cc_final: 0.7039 (tmm) REVERT: E 357 MET cc_start: 0.7201 (mmm) cc_final: 0.6999 (mmm) REVERT: E 408 LYS cc_start: 0.8228 (ptpp) cc_final: 0.7118 (ptmm) REVERT: E 421 MET cc_start: 0.7436 (ppp) cc_final: 0.7222 (ptt) REVERT: E 521 HIS cc_start: 0.9074 (m90) cc_final: 0.8611 (m170) REVERT: F 439 ASN cc_start: 0.8712 (m-40) cc_final: 0.8309 (m110) REVERT: F 523 LEU cc_start: 0.8856 (tt) cc_final: 0.8616 (mt) outliers start: 13 outliers final: 12 residues processed: 146 average time/residue: 0.2234 time to fit residues: 50.6886 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 : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP 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 627 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 55 optimal weight: 0.0670 chunk 129 optimal weight: 2.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 13763 Z= 0.240 Angle : 0.610 7.451 18722 Z= 0.313 Chirality : 0.043 0.152 2219 Planarity : 0.005 0.104 2434 Dihedral : 4.780 56.917 1932 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.41 % Favored : 92.42 % Rotamer: Outliers : 1.45 % Allowed : 11.86 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1782 helix: 1.03 (0.17), residues: 930 sheet: -2.13 (0.39), residues: 176 loop : -1.86 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 628 HIS 0.005 0.001 HIS E 441 PHE 0.011 0.001 PHE C 27 TYR 0.024 0.002 TYR E 358 ARG 0.004 0.000 ARG B 228 *********************** 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 154 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.632 Fit side-chains REVERT: E 357 MET cc_start: 0.7431 (mmm) cc_final: 0.7218 (mmm) REVERT: E 408 LYS cc_start: 0.8260 (ptpp) cc_final: 0.7116 (ptmm) REVERT: E 521 HIS cc_start: 0.9045 (m90) cc_final: 0.8519 (m170) REVERT: F 439 ASN cc_start: 0.8696 (m-40) cc_final: 0.8326 (m110) outliers start: 21 outliers final: 17 residues processed: 142 average time/residue: 0.2392 time to fit residues: 53.0273 Evaluate side-chains 143 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.686 ------------------------------------------------------------------------------- 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 130 VAL 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 111 VAL Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 583 TYR Chi-restraints excluded: chain F residue 587 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 5.9990 chunk 121 optimal weight: 0.0270 chunk 84 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 162 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 154 optimal weight: 30.0000 chunk 46 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 13763 Z= 0.214 Angle : 0.601 9.403 18722 Z= 0.305 Chirality : 0.043 0.312 2219 Planarity : 0.005 0.109 2434 Dihedral : 4.785 59.283 1932 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.30 % Favored : 92.54 % Rotamer: Outliers : 1.38 % Allowed : 14.90 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.20), residues: 1782 helix: 1.03 (0.17), residues: 935 sheet: -1.98 (0.38), residues: 184 loop : -1.86 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 648 HIS 0.005 0.001 HIS E 441 PHE 0.011 0.001 PHE C 27 TYR 0.033 0.002 TYR E 583 ARG 0.004 0.000 ARG B 228 *********************** 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 150 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 1.629 Fit side-chains REVERT: D 94 MET cc_start: 0.7443 (tmm) cc_final: 0.6818 (tmm) REVERT: E 357 MET cc_start: 0.7641 (mmm) cc_final: 0.7374 (mmm) REVERT: E 408 LYS cc_start: 0.8280 (ptpp) cc_final: 0.8012 (ptpp) REVERT: E 521 HIS cc_start: 0.9090 (m90) cc_final: 0.8629 (m170) REVERT: F 439 ASN cc_start: 0.8699 (m-40) cc_final: 0.8314 (m110) REVERT: F 448 GLN cc_start: 0.7623 (pp30) cc_final: 0.7340 (pp30) outliers start: 20 outliers final: 14 residues processed: 139 average time/residue: 0.2229 time to fit residues: 48.5231 Evaluate side-chains 139 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 1.550 ------------------------------------------------------------------------------- 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 130 VAL 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 293 ILE 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 506 MET Chi-restraints excluded: chain F residue 583 TYR Chi-restraints excluded: chain F residue 587 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 154 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 13763 Z= 0.176 Angle : 0.583 8.201 18722 Z= 0.294 Chirality : 0.043 0.286 2219 Planarity : 0.005 0.112 2434 Dihedral : 4.649 57.062 1932 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.79 % Favored : 93.04 % Rotamer: Outliers : 2.00 % Allowed : 15.79 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.21), residues: 1782 helix: 1.17 (0.17), residues: 931 sheet: -2.04 (0.39), residues: 174 loop : -1.78 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 648 HIS 0.005 0.001 HIS E 441 PHE 0.009 0.001 PHE C 27 TYR 0.024 0.001 TYR E 583 ARG 0.003 0.000 ARG B 228 *********************** 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 164 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 1.498 Fit side-chains REVERT: C 232 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7441 (p) REVERT: E 357 MET cc_start: 0.7766 (mmm) cc_final: 0.7415 (mmm) REVERT: E 408 LYS cc_start: 0.8247 (ptpp) cc_final: 0.8026 (ptpp) REVERT: E 521 HIS cc_start: 0.9102 (m90) cc_final: 0.8685 (m170) REVERT: F 439 ASN cc_start: 0.8691 (m-40) cc_final: 0.8327 (m110) REVERT: F 523 LEU cc_start: 0.8850 (tt) cc_final: 0.8612 (mt) outliers start: 29 outliers final: 17 residues processed: 152 average time/residue: 0.2255 time to fit residues: 53.1650 Evaluate side-chains 148 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain B residue 130 VAL 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 232 THR 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 F residue 370 LEU Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 587 VAL Chi-restraints excluded: chain F residue 633 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 172 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 166 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2096 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= 0.157 Angle : 0.577 8.963 18722 Z= 0.290 Chirality : 0.042 0.168 2219 Planarity : 0.005 0.114 2434 Dihedral : 4.513 52.133 1932 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.68 % Favored : 93.15 % Rotamer: Outliers : 1.52 % Allowed : 16.41 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1782 helix: 1.22 (0.17), residues: 929 sheet: -1.95 (0.39), residues: 178 loop : -1.76 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 648 HIS 0.005 0.001 HIS E 441 PHE 0.008 0.001 PHE C 27 TYR 0.019 0.001 TYR D 34 ARG 0.004 0.000 ARG B 228 *********************** 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 162 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.467 Fit side-chains REVERT: B 235 MET cc_start: 0.7662 (mtt) cc_final: 0.7448 (mtt) REVERT: C 232 THR cc_start: 0.7857 (m) cc_final: 0.7477 (p) REVERT: D 94 MET cc_start: 0.7293 (tmm) cc_final: 0.6698 (tmm) REVERT: E 357 MET cc_start: 0.7679 (mmm) cc_final: 0.7337 (mmm) REVERT: E 521 HIS cc_start: 0.9107 (m90) cc_final: 0.8705 (m-70) REVERT: E 637 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6198 (mt) REVERT: F 439 ASN cc_start: 0.8690 (m-40) cc_final: 0.8335 (m-40) REVERT: F 523 LEU cc_start: 0.8883 (tt) cc_final: 0.8677 (mt) outliers start: 22 outliers final: 14 residues processed: 154 average time/residue: 0.2321 time to fit residues: 55.0460 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 : 1.484 ------------------------------------------------------------------------------- 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 130 VAL 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 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 Chi-restraints excluded: chain F residue 633 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 125 optimal weight: 0.0170 chunk 97 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 13763 Z= 0.167 Angle : 0.598 9.356 18722 Z= 0.299 Chirality : 0.043 0.175 2219 Planarity : 0.005 0.115 2434 Dihedral : 4.339 40.657 1931 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.51 % Favored : 93.32 % Rotamer: Outliers : 1.38 % Allowed : 17.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1782 helix: 1.26 (0.17), residues: 930 sheet: -1.86 (0.40), residues: 167 loop : -1.68 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 648 HIS 0.004 0.001 HIS E 441 PHE 0.008 0.001 PHE C 27 TYR 0.025 0.001 TYR E 583 ARG 0.004 0.000 ARG D 51 *********************** 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 152 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.643 Fit side-chains REVERT: C 232 THR cc_start: 0.7856 (m) cc_final: 0.7481 (p) REVERT: E 357 MET cc_start: 0.7636 (mmm) cc_final: 0.7320 (mmm) REVERT: E 520 LEU cc_start: 0.9122 (tp) cc_final: 0.8868 (tp) REVERT: E 521 HIS cc_start: 0.9091 (m90) cc_final: 0.8690 (m-70) REVERT: E 547 MET cc_start: 0.7467 (ppp) cc_final: 0.7223 (tmm) REVERT: E 637 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.6148 (mt) REVERT: F 363 MET cc_start: 0.5585 (tmm) cc_final: 0.5171 (tmm) REVERT: F 439 ASN cc_start: 0.8702 (m-40) cc_final: 0.8335 (m-40) REVERT: F 628 TRP cc_start: 0.7234 (t60) cc_final: 0.6672 (t60) outliers start: 20 outliers final: 15 residues processed: 142 average time/residue: 0.2209 time to fit residues: 49.3685 Evaluate side-chains 147 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 1.496 ------------------------------------------------------------------------------- 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 130 VAL 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 521 HIS Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 633 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 134 optimal weight: 0.2980 chunk 156 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN B 185 HIS ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2346 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= 0.156 Angle : 0.600 11.251 18722 Z= 0.296 Chirality : 0.043 0.287 2219 Planarity : 0.005 0.115 2434 Dihedral : 4.262 38.809 1931 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.40 % Favored : 93.43 % Rotamer: Outliers : 1.31 % Allowed : 18.07 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.21), residues: 1782 helix: 1.23 (0.17), residues: 937 sheet: -1.79 (0.42), residues: 162 loop : -1.64 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 648 HIS 0.004 0.001 HIS E 441 PHE 0.007 0.001 PHE C 27 TYR 0.025 0.001 TYR E 583 ARG 0.003 0.000 ARG E 580 *********************** 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 156 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 1.488 Fit side-chains REVERT: C 232 THR cc_start: 0.7770 (m) cc_final: 0.7434 (p) REVERT: E 357 MET cc_start: 0.7636 (mmm) cc_final: 0.7377 (mmm) REVERT: E 520 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8911 (tp) REVERT: E 521 HIS cc_start: 0.9105 (m90) cc_final: 0.8700 (m-70) REVERT: E 547 MET cc_start: 0.7402 (ppp) cc_final: 0.7144 (tmm) REVERT: E 637 LEU cc_start: 0.6428 (OUTLIER) cc_final: 0.6203 (mt) REVERT: F 363 MET cc_start: 0.5767 (tmm) cc_final: 0.5455 (tmm) REVERT: F 439 ASN cc_start: 0.8731 (m-40) cc_final: 0.8409 (m-40) outliers start: 19 outliers final: 13 residues processed: 146 average time/residue: 0.2222 time to fit residues: 51.9560 Evaluate side-chains 147 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.542 ------------------------------------------------------------------------------- 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 130 VAL 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 520 LEU 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 149 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 164 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 125 optimal weight: 0.4980 chunk 49 optimal weight: 0.4980 chunk 144 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 HIS F 457 GLN ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 13763 Z= 0.283 Angle : 0.685 12.031 18722 Z= 0.342 Chirality : 0.045 0.336 2219 Planarity : 0.005 0.113 2434 Dihedral : 4.694 47.755 1931 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.14 % Favored : 91.64 % Rotamer: Outliers : 1.38 % Allowed : 18.28 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.21), residues: 1782 helix: 1.01 (0.17), residues: 936 sheet: -1.97 (0.37), residues: 198 loop : -1.77 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 648 HIS 0.005 0.001 HIS B 185 PHE 0.012 0.002 PHE C 27 TYR 0.032 0.002 TYR E 583 ARG 0.003 0.000 ARG E 580 *********************** 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 146 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.548 Fit side-chains REVERT: C 232 THR cc_start: 0.7846 (m) cc_final: 0.7592 (p) REVERT: D 91 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7834 (tppt) REVERT: E 357 MET cc_start: 0.7828 (mmm) cc_final: 0.7454 (mmm) REVERT: E 421 MET cc_start: 0.6908 (ppp) cc_final: 0.6583 (pmm) REVERT: E 521 HIS cc_start: 0.9105 (m90) cc_final: 0.8832 (m170) REVERT: E 547 MET cc_start: 0.7373 (ppp) cc_final: 0.7116 (tmm) REVERT: E 637 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.6277 (mt) REVERT: F 357 MET cc_start: 0.7324 (tpp) cc_final: 0.5525 (tmm) REVERT: F 363 MET cc_start: 0.5795 (tmm) cc_final: 0.5519 (tmm) REVERT: F 439 ASN cc_start: 0.8710 (m-40) cc_final: 0.8373 (m-40) outliers start: 20 outliers final: 15 residues processed: 138 average time/residue: 0.2246 time to fit residues: 48.6391 Evaluate side-chains 142 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 1.614 ------------------------------------------------------------------------------- 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 130 VAL 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 D residue 91 LYS 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 521 HIS Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 583 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.0970 chunk 80 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2390 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= 0.183 Angle : 0.646 12.023 18722 Z= 0.317 Chirality : 0.044 0.333 2219 Planarity : 0.005 0.115 2434 Dihedral : 4.513 43.130 1931 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.85 % Favored : 92.99 % Rotamer: Outliers : 1.03 % Allowed : 18.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.21), residues: 1782 helix: 1.16 (0.17), residues: 932 sheet: -1.77 (0.39), residues: 186 loop : -1.71 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 648 HIS 0.005 0.001 HIS E 441 PHE 0.009 0.001 PHE C 27 TYR 0.024 0.001 TYR E 583 ARG 0.003 0.000 ARG B 228 ********************** 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 145 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.723 Fit side-chains REVERT: C 232 THR cc_start: 0.7752 (m) cc_final: 0.7520 (p) REVERT: D 91 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7785 (tppt) REVERT: E 357 MET cc_start: 0.7747 (mmm) cc_final: 0.7405 (mmm) REVERT: E 521 HIS cc_start: 0.9055 (m90) cc_final: 0.8664 (m-70) REVERT: E 547 MET cc_start: 0.7349 (ppp) cc_final: 0.7063 (tmm) REVERT: E 637 LEU cc_start: 0.6454 (OUTLIER) cc_final: 0.6210 (mt) REVERT: F 357 MET cc_start: 0.7288 (tpp) cc_final: 0.5460 (tmm) REVERT: F 363 MET cc_start: 0.5743 (tmm) cc_final: 0.5489 (tmm) REVERT: F 523 LEU cc_start: 0.8569 (mt) cc_final: 0.8079 (tt) outliers start: 15 outliers final: 13 residues processed: 139 average time/residue: 0.2177 time to fit residues: 47.5055 Evaluate side-chains 145 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain B 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 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 D residue 91 LYS 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 Chi-restraints excluded: chain F residue 583 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 141 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 145 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.097192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.076295 restraints weight = 52276.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.078124 restraints weight = 27242.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.079288 restraints weight = 17513.149| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 13763 Z= 0.161 Angle : 0.624 12.114 18722 Z= 0.306 Chirality : 0.044 0.307 2219 Planarity : 0.005 0.116 2434 Dihedral : 4.329 38.668 1931 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.85 % Favored : 92.99 % Rotamer: Outliers : 0.90 % Allowed : 19.03 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1782 helix: 1.22 (0.18), residues: 937 sheet: -1.74 (0.41), residues: 172 loop : -1.66 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 648 HIS 0.005 0.001 HIS E 441 PHE 0.007 0.001 PHE C 27 TYR 0.022 0.001 TYR E 583 ARG 0.004 0.000 ARG E 580 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2396.19 seconds wall clock time: 45 minutes 9.79 seconds (2709.79 seconds total)