Starting phenix.real_space_refine on Sun Sep 29 07:07:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk2_22359/09_2024/7jk2_22359.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk2_22359/09_2024/7jk2_22359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk2_22359/09_2024/7jk2_22359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk2_22359/09_2024/7jk2_22359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk2_22359/09_2024/7jk2_22359.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk2_22359/09_2024/7jk2_22359.cif" } resolution = 3.2 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= 0.003 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: 6 Type Number sf(0) Gaussians P 78 5.49 5 Mg 4 5.21 5 S 110 5.16 5 C 13528 2.51 5 N 3786 2.21 5 O 4113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21619 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 2290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2290 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 4 Chain: "C" Number of atoms: 4892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4892 Classifications: {'peptide': 609} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 585} Chain breaks: 7 Chain: "D" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3549 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 11, 'TRANS': 429} Chain breaks: 2 Chain: "E" Number of atoms: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3161 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "A" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3129 Classifications: {'peptide': 401} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 383} Chain: "G" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2974 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 13, 'TRANS': 358} Chain breaks: 2 Chain: "H" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 660 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "I" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 693 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.72, per 1000 atoms: 0.59 Number of scatterers: 21619 At special positions: 0 Unit cell: (127.449, 156.06, 121.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 110 16.00 P 78 15.00 Mg 4 11.99 O 4113 8.00 N 3786 7.00 C 13528 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: 5.09 Conformation dependent library (CDL) restraints added in 2.7 seconds 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4830 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 12 sheets defined 63.0% alpha, 6.9% beta 33 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 7.16 Creating SS restraints... Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 324 through 338 Processing helix chain 'B' and resid 339 through 349 removed outlier: 3.612A pdb=" N GLU B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 372 Processing helix chain 'B' and resid 389 through 401 removed outlier: 3.605A pdb=" N ILE B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 423 Processing helix chain 'B' and resid 444 through 456 removed outlier: 3.625A pdb=" N GLN B 448 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 474 removed outlier: 3.559A pdb=" N LEU B 473 " --> pdb=" O ASN B 470 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 474 " --> pdb=" O THR B 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 470 through 474' Processing helix chain 'B' and resid 476 through 483 Processing helix chain 'B' and resid 496 through 501 removed outlier: 3.860A pdb=" N THR B 500 " --> pdb=" O TYR B 496 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 501 " --> pdb=" O THR B 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 496 through 501' Processing helix chain 'B' and resid 516 through 525 removed outlier: 3.973A pdb=" N SER B 525 " --> pdb=" O SER B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 544 Processing helix chain 'B' and resid 554 through 565 removed outlier: 3.643A pdb=" N LEU B 558 " --> pdb=" O PRO B 554 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 565 " --> pdb=" O SER B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 584 removed outlier: 3.963A pdb=" N LEU B 574 " --> pdb=" O SER B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 615 removed outlier: 3.731A pdb=" N GLN B 615 " --> pdb=" O PHE B 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.653A pdb=" N VAL C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 88 removed outlier: 3.674A pdb=" N GLU C 51 " --> pdb=" O GLN C 47 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ARG C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N THR C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 109 through 122 removed outlier: 4.344A pdb=" N GLN C 113 " --> pdb=" O ASP C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 159 Processing helix chain 'C' and resid 184 through 197 removed outlier: 3.999A pdb=" N ASP C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 230 Processing helix chain 'C' and resid 245 through 253 removed outlier: 4.028A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 293 through 307 Processing helix chain 'C' and resid 310 through 327 Processing helix chain 'C' and resid 328 through 335 removed outlier: 5.853A pdb=" N ALA C 331 " --> pdb=" O GLY C 328 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 334 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS C 335 " --> pdb=" O PHE C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 349 through 358 removed outlier: 4.033A pdb=" N MET C 353 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 Processing helix chain 'C' and resid 383 through 416 Proline residue: C 390 - end of helix removed outlier: 4.247A pdb=" N ASP C 416 " --> pdb=" O GLU C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 436 removed outlier: 3.873A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG C 436 " --> pdb=" O ASN C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 453 removed outlier: 3.748A pdb=" N LYS C 445 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 477 removed outlier: 3.829A pdb=" N PHE C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 508 Proline residue: C 493 - end of helix Processing helix chain 'C' and resid 563 through 576 Processing helix chain 'C' and resid 599 through 607 removed outlier: 3.516A pdb=" N ILE C 607 " --> pdb=" O ARG C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 620 removed outlier: 3.574A pdb=" N ALA C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 643 through 654 removed outlier: 3.760A pdb=" N GLU C 654 " --> pdb=" O LYS C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 672 removed outlier: 3.780A pdb=" N TRP C 664 " --> pdb=" O ASN C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 703 Processing helix chain 'D' and resid 3 through 21 removed outlier: 3.885A pdb=" N LEU D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 45 Processing helix chain 'D' and resid 61 through 74 Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 95 through 107 Processing helix chain 'D' and resid 120 through 135 removed outlier: 3.505A pdb=" N GLY D 135 " --> pdb=" O CYS D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 154 removed outlier: 3.545A pdb=" N PHE D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 158 through 165 Processing helix chain 'D' and resid 185 through 189 removed outlier: 3.526A pdb=" N GLU D 188 " --> pdb=" O ASP D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 211 through 224 removed outlier: 3.551A pdb=" N TYR D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 223 " --> pdb=" O CYS D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 244 removed outlier: 3.964A pdb=" N ILE D 244 " --> pdb=" O ASN D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 removed outlier: 3.782A pdb=" N ARG D 253 " --> pdb=" O TYR D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 280 Processing helix chain 'D' and resid 282 through 295 Processing helix chain 'D' and resid 297 through 310 removed outlier: 3.820A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 333 removed outlier: 3.770A pdb=" N GLY D 333 " --> pdb=" O SER D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 341 Processing helix chain 'D' and resid 344 through 362 Processing helix chain 'D' and resid 367 through 380 removed outlier: 3.511A pdb=" N ILE D 371 " --> pdb=" O ASN D 367 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 403 removed outlier: 3.847A pdb=" N VAL D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 443 removed outlier: 3.570A pdb=" N ILE D 436 " --> pdb=" O THR D 432 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN D 441 " --> pdb=" O HIS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 454 Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 15 through 27 Processing helix chain 'E' and resid 47 through 62 removed outlier: 3.711A pdb=" N THR E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 89 removed outlier: 3.882A pdb=" N MET E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 removed outlier: 3.550A pdb=" N ALA E 95 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU E 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 96' Processing helix chain 'E' and resid 100 through 110 Processing helix chain 'E' and resid 128 through 134 removed outlier: 3.622A pdb=" N ARG E 132 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET E 134 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 143 removed outlier: 3.580A pdb=" N VAL E 141 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'E' and resid 184 through 194 Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.575A pdb=" N GLN E 206 " --> pdb=" O GLN E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 218 Processing helix chain 'E' and resid 222 through 238 removed outlier: 4.052A pdb=" N VAL E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 259 removed outlier: 4.080A pdb=" N LYS E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 265 Processing helix chain 'E' and resid 275 through 287 removed outlier: 3.535A pdb=" N ILE E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) Proline residue: E 282 - end of helix Processing helix chain 'E' and resid 322 through 338 Processing helix chain 'E' and resid 339 through 341 No H-bonds generated for 'chain 'E' and resid 339 through 341' Processing helix chain 'E' and resid 342 through 347 removed outlier: 3.975A pdb=" N PHE E 347 " --> pdb=" O ASP E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 394 removed outlier: 3.966A pdb=" N GLU E 394 " --> pdb=" O TYR E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 413 removed outlier: 4.065A pdb=" N LEU E 404 " --> pdb=" O THR E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 449 removed outlier: 3.704A pdb=" N VAL E 441 " --> pdb=" O GLY E 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 238 Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 571 through 588 Processing helix chain 'A' and resid 603 through 621 removed outlier: 3.515A pdb=" N GLN A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 652 removed outlier: 3.982A pdb=" N VAL A 645 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 652 " --> pdb=" O TYR A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 671 Processing helix chain 'A' and resid 686 through 689 Processing helix chain 'A' and resid 695 through 703 Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 728 through 736 removed outlier: 3.914A pdb=" N GLY A 736 " --> pdb=" O THR A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 759 Processing helix chain 'A' and resid 765 through 778 removed outlier: 3.692A pdb=" N VAL A 769 " --> pdb=" O LYS A 765 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 800 removed outlier: 4.051A pdb=" N ALA A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 818 removed outlier: 3.508A pdb=" N VAL A 810 " --> pdb=" O THR A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 828 removed outlier: 3.830A pdb=" N ILE A 826 " --> pdb=" O LYS A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 848 removed outlier: 3.524A pdb=" N ALA A 841 " --> pdb=" O LEU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 869 Processing helix chain 'A' and resid 874 through 888 removed outlier: 3.740A pdb=" N ARG A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 919 removed outlier: 3.627A pdb=" N ILE A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 918 " --> pdb=" O HIS A 914 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 260 removed outlier: 4.174A pdb=" N ASN G 260 " --> pdb=" O ARG G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 287 removed outlier: 3.668A pdb=" N GLN G 275 " --> pdb=" O GLU G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 311 Processing helix chain 'G' and resid 312 through 317 removed outlier: 6.204A pdb=" N ASP G 315 " --> pdb=" O ARG G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 345 Processing helix chain 'G' and resid 352 through 366 removed outlier: 3.644A pdb=" N LYS G 365 " --> pdb=" O GLN G 361 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR G 366 " --> pdb=" O ARG G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 382 Processing helix chain 'G' and resid 386 through 393 Processing helix chain 'G' and resid 394 through 398 Processing helix chain 'G' and resid 413 through 418 Processing helix chain 'G' and resid 419 through 425 removed outlier: 3.566A pdb=" N LEU G 422 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG G 425 " --> pdb=" O LEU G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 453 removed outlier: 3.600A pdb=" N ILE G 443 " --> pdb=" O SER G 439 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 476 removed outlier: 3.680A pdb=" N LEU G 465 " --> pdb=" O PRO G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 498 removed outlier: 3.534A pdb=" N ALA G 482 " --> pdb=" O ASP G 478 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL G 490 " --> pdb=" O GLY G 486 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN G 495 " --> pdb=" O GLU G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 542 removed outlier: 3.730A pdb=" N VAL G 534 " --> pdb=" O GLN G 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 557 through 573 Processing helix chain 'G' and resid 581 through 595 removed outlier: 3.541A pdb=" N VAL G 587 " --> pdb=" O ARG G 583 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG G 590 " --> pdb=" O GLU G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 601 through 614 removed outlier: 3.838A pdb=" N GLY G 607 " --> pdb=" O ALA G 603 " (cutoff:3.500A) Processing helix chain 'G' and resid 625 through 628 Processing helix chain 'G' and resid 636 through 645 Processing helix chain 'G' and resid 646 through 654 removed outlier: 3.989A pdb=" N SER G 652 " --> pdb=" O GLN G 648 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 485 through 488 removed outlier: 6.284A pdb=" N ASN B 352 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N TRP B 488 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU B 354 " --> pdb=" O TRP B 488 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 378 " --> pdb=" O TYR C 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AA3, first strand: chain 'C' and resid 127 through 131 removed outlier: 5.997A pdb=" N MET C 128 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE C 208 " --> pdb=" O MET C 128 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS C 130 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 101 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N PHE C 266 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA C 100 " --> pdb=" O PHE C 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 658 through 659 Processing sheet with id=AA5, first strand: chain 'D' and resid 83 through 89 removed outlier: 6.565A pdb=" N ASN D 50 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLY D 179 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU D 52 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 406 through 408 Processing sheet with id=AA7, first strand: chain 'E' and resid 64 through 70 removed outlier: 6.717A pdb=" N PHE E 121 " --> pdb=" O CYS E 154 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE E 156 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE E 123 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU E 158 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL E 125 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE E 37 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N SER E 159 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU E 39 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ALA E 36 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LEU E 178 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR E 38 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU E 180 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE E 40 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 380 through 381 removed outlier: 6.808A pdb=" N GLN E 433 " --> pdb=" O PHE E 418 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE E 418 " --> pdb=" O GLN E 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 627 through 633 removed outlier: 6.500A pdb=" N GLU A 628 " --> pdb=" O VAL A 680 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU A 682 " --> pdb=" O GLU A 628 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU A 630 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ASP A 684 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 632 " --> pdb=" O ASP A 684 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY A 592 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N THR A 715 " --> pdb=" O GLY A 592 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N MET A 594 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ALA A 717 " --> pdb=" O MET A 594 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL A 596 " --> pdb=" O ALA A 717 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 852 through 853 Processing sheet with id=AB2, first strand: chain 'G' and resid 320 through 326 removed outlier: 6.170A pdb=" N GLN G 321 " --> pdb=" O LEU G 372 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL G 374 " --> pdb=" O GLN G 321 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL G 323 " --> pdb=" O VAL G 374 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ASP G 376 " --> pdb=" O VAL G 323 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE G 325 " --> pdb=" O ASP G 376 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLY G 291 " --> pdb=" O LEU G 405 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N GLY G 407 " --> pdb=" O GLY G 291 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU G 293 " --> pdb=" O GLY G 407 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ALA G 409 " --> pdb=" O LEU G 293 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL G 295 " --> pdb=" O ALA G 409 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 579 through 580 removed outlier: 4.592A pdb=" N ILE G 579 " --> pdb=" O VAL G 631 " (cutoff:3.500A) 1053 hydrogen bonds defined for protein. 3075 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 7.69 Time building geometry restraints manager: 5.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5140 1.33 - 1.45: 4406 1.45 - 1.57: 12271 1.57 - 1.69: 150 1.69 - 1.81: 162 Bond restraints: 22129 Sorted by residual: bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.07e+01 bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.92e+01 bond pdb=" C4 ATP G 901 " pdb=" C5 ATP G 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.87e+01 bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.69e+01 bond pdb=" C5 ATP E 901 " pdb=" C6 ATP E 901 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.62e+01 ... (remaining 22124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.72: 29970 3.72 - 7.45: 187 7.45 - 11.17: 33 11.17 - 14.89: 4 14.89 - 18.62: 6 Bond angle restraints: 30200 Sorted by residual: angle pdb=" PB ATP G 901 " pdb=" O3B ATP G 901 " pdb=" PG ATP G 901 " ideal model delta sigma weight residual 139.87 121.25 18.62 1.00e+00 1.00e+00 3.47e+02 angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 121.27 18.60 1.00e+00 1.00e+00 3.46e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 121.96 17.91 1.00e+00 1.00e+00 3.21e+02 angle pdb=" PA ATP G 901 " pdb=" O3A ATP G 901 " pdb=" PB ATP G 901 " ideal model delta sigma weight residual 136.83 120.10 16.73 1.00e+00 1.00e+00 2.80e+02 angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 123.68 16.19 1.00e+00 1.00e+00 2.62e+02 ... (remaining 30195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 11488 17.90 - 35.80: 1351 35.80 - 53.71: 478 53.71 - 71.61: 106 71.61 - 89.51: 25 Dihedral angle restraints: 13448 sinusoidal: 6051 harmonic: 7397 Sorted by residual: dihedral pdb=" CA LYS C 712 " pdb=" C LYS C 712 " pdb=" N THR C 713 " pdb=" CA THR C 713 " ideal model delta harmonic sigma weight residual -180.00 -152.09 -27.91 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA LEU G 259 " pdb=" C LEU G 259 " pdb=" N ASN G 260 " pdb=" CA ASN G 260 " ideal model delta harmonic sigma weight residual 180.00 153.34 26.66 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ASN E 338 " pdb=" C ASN E 338 " pdb=" N ALA E 339 " pdb=" CA ALA E 339 " ideal model delta harmonic sigma weight residual 180.00 153.76 26.24 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 13445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3041 0.070 - 0.140: 409 0.140 - 0.210: 33 0.210 - 0.280: 2 0.280 - 0.350: 2 Chirality restraints: 3487 Sorted by residual: chirality pdb=" CG LEU A 750 " pdb=" CB LEU A 750 " pdb=" CD1 LEU A 750 " pdb=" CD2 LEU A 750 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CB ILE C 5 " pdb=" CA ILE C 5 " pdb=" CG1 ILE C 5 " pdb=" CG2 ILE C 5 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA THR B 471 " pdb=" N THR B 471 " pdb=" C THR B 471 " pdb=" CB THR B 471 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 3484 not shown) Planarity restraints: 3594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 664 " -0.030 2.00e-02 2.50e+03 2.13e-02 1.13e+01 pdb=" CG TRP C 664 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP C 664 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 664 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 664 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 664 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 664 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 664 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 664 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 664 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 9 " -0.054 5.00e-02 4.00e+02 8.04e-02 1.04e+01 pdb=" N PRO E 10 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO E 10 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 10 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 872 " 0.053 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO A 873 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 873 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 873 " 0.043 5.00e-02 4.00e+02 ... (remaining 3591 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 265 2.65 - 3.22: 18050 3.22 - 3.78: 33969 3.78 - 4.34: 47038 4.34 - 4.90: 75830 Nonbonded interactions: 175152 Sorted by model distance: nonbonded pdb=" OG1 THR D 63 " pdb="MG MG D 902 " model vdw 2.092 2.170 nonbonded pdb=" O2B ATP E 901 " pdb="MG MG E 902 " model vdw 2.112 2.170 nonbonded pdb=" OG1 THR A 605 " pdb="MG MG A1002 " model vdw 2.113 2.170 nonbonded pdb=" O2B ATP D 901 " pdb="MG MG D 902 " model vdw 2.121 2.170 nonbonded pdb=" OG1 THR E 48 " pdb="MG MG E 902 " model vdw 2.121 2.170 ... (remaining 175147 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.340 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: 0.030 Extract box with map and model: 0.960 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 51.840 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 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 : 0.006 0.078 22129 Z= 0.343 Angle : 0.916 18.617 30200 Z= 0.568 Chirality : 0.048 0.350 3487 Planarity : 0.007 0.080 3594 Dihedral : 17.904 89.509 8618 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.23 % Allowed : 8.00 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -3.50 (0.13), residues: 2471 helix: -2.34 (0.10), residues: 1449 sheet: -1.53 (0.31), residues: 225 loop : -2.07 (0.18), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP C 664 HIS 0.006 0.001 HIS B 468 PHE 0.021 0.002 PHE D 304 TYR 0.018 0.002 TYR G 588 ARG 0.006 0.001 ARG A 785 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 290 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9140 (tpp) cc_final: 0.8713 (mmm) REVERT: B 555 PHE cc_start: 0.7807 (t80) cc_final: 0.7510 (t80) REVERT: C 145 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8067 (mt-10) REVERT: C 326 PHE cc_start: 0.8955 (m-10) cc_final: 0.8542 (m-10) REVERT: C 417 LEU cc_start: 0.8562 (tp) cc_final: 0.8287 (tp) REVERT: C 573 GLU cc_start: 0.8444 (tt0) cc_final: 0.8206 (tm-30) REVERT: C 658 MET cc_start: 0.7999 (tpt) cc_final: 0.7477 (mmm) REVERT: D 347 GLU cc_start: 0.8750 (mp0) cc_final: 0.8383 (mp0) REVERT: E 82 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8239 (mt-10) REVERT: E 394 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7501 (pp20) REVERT: A 618 MET cc_start: 0.8689 (mtp) cc_final: 0.8477 (mtt) REVERT: A 666 GLU cc_start: 0.8629 (tp30) cc_final: 0.8351 (tp30) outliers start: 5 outliers final: 4 residues processed: 294 average time/residue: 0.3969 time to fit residues: 169.2362 Evaluate side-chains 189 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 185 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 750 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 148 optimal weight: 0.0270 chunk 231 optimal weight: 1.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 ASN B 366 GLN B 544 ASN C 16 ASN C 78 GLN C 449 GLN C 464 ASN D 82 ASN D 157 ASN D 202 GLN E 218 GLN ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 GLN E 454 GLN A 650 GLN A 749 GLN A 838 GLN G 254 ASN G 356 HIS G 533 GLN G 596 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22129 Z= 0.178 Angle : 0.553 8.721 30200 Z= 0.296 Chirality : 0.038 0.175 3487 Planarity : 0.004 0.061 3594 Dihedral : 16.891 68.984 3666 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.22 % Allowed : 10.75 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.04 (0.16), residues: 2471 helix: -0.10 (0.13), residues: 1463 sheet: -1.16 (0.33), residues: 226 loop : -1.44 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 664 HIS 0.004 0.001 HIS C 580 PHE 0.017 0.001 PHE C 459 TYR 0.013 0.001 TYR C 365 ARG 0.006 0.000 ARG A 641 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 204 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9179 (tpp) cc_final: 0.8794 (mmm) REVERT: B 419 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8259 (mt-10) REVERT: C 145 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8130 (mt-10) REVERT: C 384 TYR cc_start: 0.8328 (t80) cc_final: 0.7945 (t80) REVERT: C 586 ASP cc_start: 0.7589 (m-30) cc_final: 0.6986 (p0) REVERT: C 598 ASP cc_start: 0.7530 (t0) cc_final: 0.7323 (t0) REVERT: D 347 GLU cc_start: 0.8836 (mp0) cc_final: 0.8571 (mp0) REVERT: D 423 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8494 (mp0) REVERT: A 666 GLU cc_start: 0.8674 (tp30) cc_final: 0.8277 (tp30) REVERT: A 788 ASP cc_start: 0.8807 (m-30) cc_final: 0.8376 (t0) REVERT: A 915 TYR cc_start: 0.9262 (t80) cc_final: 0.8887 (t80) REVERT: G 324 TYR cc_start: 0.9233 (t80) cc_final: 0.9009 (t80) outliers start: 27 outliers final: 15 residues processed: 225 average time/residue: 0.3508 time to fit residues: 121.5037 Evaluate side-chains 183 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 168 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 0.2980 chunk 71 optimal weight: 4.9990 chunk 192 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 231 optimal weight: 0.9990 chunk 250 optimal weight: 6.9990 chunk 206 optimal weight: 0.9990 chunk 230 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 186 optimal weight: 0.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 HIS B 435 HIS C 325 HIS ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22129 Z= 0.161 Angle : 0.512 8.379 30200 Z= 0.273 Chirality : 0.037 0.161 3487 Planarity : 0.004 0.051 3594 Dihedral : 16.961 71.296 3663 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.54 % Allowed : 11.66 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 0.16 (0.17), residues: 2471 helix: 0.93 (0.14), residues: 1459 sheet: -1.08 (0.32), residues: 250 loop : -0.95 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 664 HIS 0.004 0.001 HIS C 110 PHE 0.015 0.001 PHE C 459 TYR 0.022 0.001 TYR C 72 ARG 0.006 0.000 ARG A 617 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 177 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 344 MET cc_start: 0.9097 (mmm) cc_final: 0.8876 (tpt) REVERT: C 145 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8147 (mt-10) REVERT: C 323 MET cc_start: 0.9073 (ttp) cc_final: 0.8827 (ttp) REVERT: C 384 TYR cc_start: 0.8225 (t80) cc_final: 0.7878 (t80) REVERT: C 586 ASP cc_start: 0.7625 (m-30) cc_final: 0.6999 (p0) REVERT: C 598 ASP cc_start: 0.7669 (t0) cc_final: 0.7388 (t0) REVERT: C 710 LYS cc_start: 0.9187 (mmtt) cc_final: 0.8916 (tttt) REVERT: D 6 ARG cc_start: 0.8282 (mpt180) cc_final: 0.7985 (mpt180) REVERT: D 423 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8477 (mp0) REVERT: A 666 GLU cc_start: 0.8645 (tp30) cc_final: 0.8293 (tp30) REVERT: G 324 TYR cc_start: 0.9230 (t80) cc_final: 0.8946 (t80) outliers start: 34 outliers final: 21 residues processed: 204 average time/residue: 0.3372 time to fit residues: 110.6170 Evaluate side-chains 180 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 3.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 2.9990 chunk 174 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 232 optimal weight: 3.9990 chunk 246 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 220 optimal weight: 0.0980 chunk 66 optimal weight: 3.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22129 Z= 0.281 Angle : 0.563 12.054 30200 Z= 0.293 Chirality : 0.039 0.154 3487 Planarity : 0.004 0.046 3594 Dihedral : 16.958 81.707 3663 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.76 % Allowed : 12.88 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 0.73 (0.17), residues: 2471 helix: 1.43 (0.14), residues: 1465 sheet: -0.91 (0.32), residues: 250 loop : -0.79 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 276 HIS 0.008 0.001 HIS C 580 PHE 0.025 0.001 PHE C 290 TYR 0.035 0.001 TYR C 72 ARG 0.006 0.000 ARG A 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 160 time to evaluate : 2.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9255 (mmm) cc_final: 0.8895 (mmm) REVERT: C 128 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7986 (mtp) REVERT: C 145 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8254 (mt-10) REVERT: C 323 MET cc_start: 0.9111 (ttp) cc_final: 0.8809 (ttp) REVERT: C 384 TYR cc_start: 0.8193 (t80) cc_final: 0.7851 (t80) REVERT: C 449 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8498 (mt0) REVERT: C 586 ASP cc_start: 0.7804 (m-30) cc_final: 0.7432 (p0) REVERT: C 598 ASP cc_start: 0.7781 (t0) cc_final: 0.7540 (t0) REVERT: C 710 LYS cc_start: 0.9178 (mmtt) cc_final: 0.8896 (tttt) REVERT: D 6 ARG cc_start: 0.8349 (mpt180) cc_final: 0.8055 (mpt180) REVERT: D 45 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: D 423 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8517 (mp0) REVERT: D 426 MET cc_start: 0.8819 (mmm) cc_final: 0.8559 (mmt) REVERT: E 446 LYS cc_start: 0.9179 (tmmt) cc_final: 0.8806 (ptpp) REVERT: A 666 GLU cc_start: 0.8679 (tp30) cc_final: 0.8241 (tp30) REVERT: A 788 ASP cc_start: 0.8869 (m-30) cc_final: 0.8498 (t0) REVERT: G 324 TYR cc_start: 0.9245 (t80) cc_final: 0.9018 (t80) outliers start: 39 outliers final: 29 residues processed: 188 average time/residue: 0.3323 time to fit residues: 99.7614 Evaluate side-chains 180 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 149 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 381 LEU Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 570 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 183 optimal weight: 0.0050 chunk 101 optimal weight: 0.9980 chunk 210 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 125 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22129 Z= 0.185 Angle : 0.524 11.819 30200 Z= 0.273 Chirality : 0.037 0.164 3487 Planarity : 0.003 0.046 3594 Dihedral : 16.897 87.858 3663 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.76 % Allowed : 13.60 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 1.17 (0.18), residues: 2471 helix: 1.73 (0.14), residues: 1462 sheet: -0.69 (0.33), residues: 249 loop : -0.49 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 276 HIS 0.004 0.001 HIS C 580 PHE 0.018 0.001 PHE C 459 TYR 0.024 0.001 TYR C 72 ARG 0.006 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 158 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9249 (mmm) cc_final: 0.8920 (mmm) REVERT: C 145 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8220 (mt-10) REVERT: C 323 MET cc_start: 0.9096 (ttp) cc_final: 0.8788 (ttp) REVERT: C 353 MET cc_start: 0.9067 (mmm) cc_final: 0.8839 (mmm) REVERT: C 384 TYR cc_start: 0.8223 (t80) cc_final: 0.7903 (t80) REVERT: C 449 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8504 (mt0) REVERT: C 586 ASP cc_start: 0.7873 (m-30) cc_final: 0.7481 (p0) REVERT: C 598 ASP cc_start: 0.7826 (t0) cc_final: 0.7622 (t0) REVERT: C 710 LYS cc_start: 0.9163 (mmtt) cc_final: 0.8814 (ptmt) REVERT: D 6 ARG cc_start: 0.8321 (mpt180) cc_final: 0.8042 (mpt180) REVERT: D 45 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: D 423 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8453 (mp0) REVERT: E 446 LYS cc_start: 0.9165 (tmmt) cc_final: 0.8755 (ptpp) REVERT: A 666 GLU cc_start: 0.8652 (tp30) cc_final: 0.8239 (tp30) REVERT: A 788 ASP cc_start: 0.8873 (m-30) cc_final: 0.8442 (t0) REVERT: G 324 TYR cc_start: 0.9237 (t80) cc_final: 0.8936 (t80) REVERT: G 484 ASP cc_start: 0.8983 (t0) cc_final: 0.8595 (t0) outliers start: 39 outliers final: 26 residues processed: 189 average time/residue: 0.3152 time to fit residues: 95.1818 Evaluate side-chains 180 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 381 LEU Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 570 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 144 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 204 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 chunk 129 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22129 Z= 0.191 Angle : 0.518 12.392 30200 Z= 0.270 Chirality : 0.037 0.149 3487 Planarity : 0.003 0.045 3594 Dihedral : 16.817 86.380 3663 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.58 % Allowed : 14.10 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 1.39 (0.18), residues: 2471 helix: 1.91 (0.14), residues: 1458 sheet: -0.58 (0.33), residues: 250 loop : -0.43 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 276 HIS 0.004 0.001 HIS C 580 PHE 0.019 0.001 PHE C 326 TYR 0.036 0.001 TYR C 72 ARG 0.006 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 3.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9244 (mmm) cc_final: 0.8923 (mmm) REVERT: B 425 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9037 (tp) REVERT: B 476 ASP cc_start: 0.8590 (p0) cc_final: 0.8296 (p0) REVERT: C 128 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7879 (mtp) REVERT: C 145 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8251 (mt-10) REVERT: C 323 MET cc_start: 0.9120 (ttp) cc_final: 0.8826 (ttp) REVERT: C 326 PHE cc_start: 0.8633 (m-80) cc_final: 0.8301 (m-10) REVERT: C 353 MET cc_start: 0.9081 (mmm) cc_final: 0.8845 (mmm) REVERT: C 384 TYR cc_start: 0.8147 (t80) cc_final: 0.7870 (t80) REVERT: C 449 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8488 (mt0) REVERT: C 586 ASP cc_start: 0.7915 (m-30) cc_final: 0.7480 (p0) REVERT: C 598 ASP cc_start: 0.7838 (t0) cc_final: 0.7635 (t0) REVERT: C 710 LYS cc_start: 0.9151 (mmtt) cc_final: 0.8798 (ptmt) REVERT: D 6 ARG cc_start: 0.8341 (mpt180) cc_final: 0.8109 (mpt180) REVERT: D 45 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: D 423 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8461 (mp0) REVERT: D 426 MET cc_start: 0.8821 (mmm) cc_final: 0.8324 (mmm) REVERT: E 446 LYS cc_start: 0.9179 (tmmt) cc_final: 0.8772 (ptpp) REVERT: F 231 ARG cc_start: 0.8466 (tmm-80) cc_final: 0.7665 (tmm-80) REVERT: A 666 GLU cc_start: 0.8642 (tp30) cc_final: 0.8233 (tp30) REVERT: A 788 ASP cc_start: 0.8876 (m-30) cc_final: 0.8432 (t0) REVERT: G 324 TYR cc_start: 0.9232 (t80) cc_final: 0.8925 (t80) REVERT: G 484 ASP cc_start: 0.8993 (t0) cc_final: 0.8628 (t0) outliers start: 35 outliers final: 26 residues processed: 191 average time/residue: 0.3349 time to fit residues: 101.8135 Evaluate side-chains 182 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 153 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 381 LEU Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 570 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 245 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 113 optimal weight: 0.0170 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22129 Z= 0.174 Angle : 0.526 16.077 30200 Z= 0.271 Chirality : 0.037 0.150 3487 Planarity : 0.003 0.045 3594 Dihedral : 16.749 82.463 3663 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.85 % Allowed : 14.37 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 1.52 (0.18), residues: 2471 helix: 1.97 (0.14), residues: 1462 sheet: -0.42 (0.34), residues: 239 loop : -0.33 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 191 HIS 0.007 0.001 HIS C 580 PHE 0.019 0.001 PHE C 459 TYR 0.028 0.001 TYR C 72 ARG 0.008 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 162 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9257 (mmm) cc_final: 0.8940 (mmm) REVERT: B 395 ASP cc_start: 0.8358 (p0) cc_final: 0.8011 (p0) REVERT: B 425 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9037 (tp) REVERT: B 476 ASP cc_start: 0.8543 (p0) cc_final: 0.8261 (p0) REVERT: C 1 MET cc_start: 0.5065 (OUTLIER) cc_final: 0.4832 (ttm) REVERT: C 145 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8268 (mt-10) REVERT: C 323 MET cc_start: 0.9126 (ttp) cc_final: 0.8853 (ttp) REVERT: C 384 TYR cc_start: 0.8132 (t80) cc_final: 0.7878 (t80) REVERT: C 449 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8470 (mt0) REVERT: C 586 ASP cc_start: 0.7978 (m-30) cc_final: 0.7498 (p0) REVERT: C 710 LYS cc_start: 0.9139 (mmtt) cc_final: 0.8788 (ptmt) REVERT: D 6 ARG cc_start: 0.8353 (mpt180) cc_final: 0.8100 (mpt180) REVERT: D 45 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: D 423 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8403 (mp0) REVERT: D 426 MET cc_start: 0.8829 (mmm) cc_final: 0.8337 (mmm) REVERT: E 446 LYS cc_start: 0.9167 (tmmt) cc_final: 0.8961 (ptmm) REVERT: F 232 MET cc_start: 0.8658 (tpp) cc_final: 0.8411 (ttm) REVERT: A 666 GLU cc_start: 0.8633 (tp30) cc_final: 0.8216 (tp30) REVERT: A 788 ASP cc_start: 0.8900 (m-30) cc_final: 0.8443 (t0) REVERT: G 324 TYR cc_start: 0.9234 (t80) cc_final: 0.8925 (t80) REVERT: G 484 ASP cc_start: 0.9000 (t0) cc_final: 0.8636 (t0) outliers start: 41 outliers final: 30 residues processed: 195 average time/residue: 0.3301 time to fit residues: 103.0543 Evaluate side-chains 187 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 154 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 277 ARG Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 570 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 74 optimal weight: 0.1980 chunk 48 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22129 Z= 0.151 Angle : 0.519 12.571 30200 Z= 0.267 Chirality : 0.037 0.149 3487 Planarity : 0.003 0.044 3594 Dihedral : 16.643 79.222 3663 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.58 % Allowed : 14.60 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 1.64 (0.18), residues: 2471 helix: 2.06 (0.14), residues: 1463 sheet: -0.37 (0.34), residues: 244 loop : -0.25 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 191 HIS 0.006 0.001 HIS C 580 PHE 0.025 0.001 PHE C 326 TYR 0.025 0.001 TYR C 72 ARG 0.009 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9259 (mmm) cc_final: 0.8962 (mmm) REVERT: B 425 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9050 (tp) REVERT: B 476 ASP cc_start: 0.8512 (p0) cc_final: 0.8233 (p0) REVERT: C 145 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8264 (mt-10) REVERT: C 323 MET cc_start: 0.9131 (ttp) cc_final: 0.8859 (ttp) REVERT: C 449 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8473 (mt0) REVERT: C 586 ASP cc_start: 0.8008 (m-30) cc_final: 0.7509 (p0) REVERT: C 637 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6890 (mm) REVERT: C 710 LYS cc_start: 0.9094 (mmtt) cc_final: 0.8757 (ptmt) REVERT: D 6 ARG cc_start: 0.8347 (mpt180) cc_final: 0.8019 (mpt180) REVERT: D 423 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8313 (mp0) REVERT: D 426 MET cc_start: 0.8849 (mmm) cc_final: 0.8389 (mmm) REVERT: E 446 LYS cc_start: 0.9157 (tmmt) cc_final: 0.8947 (ptmm) REVERT: A 666 GLU cc_start: 0.8602 (tp30) cc_final: 0.8255 (tp30) REVERT: A 788 ASP cc_start: 0.8897 (m-30) cc_final: 0.8420 (t0) REVERT: G 324 TYR cc_start: 0.9233 (t80) cc_final: 0.9006 (t80) REVERT: G 484 ASP cc_start: 0.8961 (t0) cc_final: 0.8604 (t0) outliers start: 35 outliers final: 24 residues processed: 191 average time/residue: 0.3178 time to fit residues: 95.1991 Evaluate side-chains 178 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 632 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 179 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 228 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22129 Z= 0.213 Angle : 0.555 12.483 30200 Z= 0.281 Chirality : 0.038 0.144 3487 Planarity : 0.003 0.081 3594 Dihedral : 16.643 78.917 3663 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.54 % Allowed : 14.96 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 1.68 (0.18), residues: 2471 helix: 2.09 (0.14), residues: 1463 sheet: -0.38 (0.34), residues: 244 loop : -0.25 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 276 HIS 0.006 0.001 HIS C 580 PHE 0.020 0.001 PHE C 459 TYR 0.024 0.001 TYR C 72 ARG 0.016 0.000 ARG B 575 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 156 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 425 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9040 (tp) REVERT: B 476 ASP cc_start: 0.8522 (p0) cc_final: 0.8235 (p0) REVERT: C 145 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8258 (mt-10) REVERT: C 323 MET cc_start: 0.9157 (ttp) cc_final: 0.8889 (ttp) REVERT: C 449 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8473 (mt0) REVERT: C 586 ASP cc_start: 0.8031 (m-30) cc_final: 0.7577 (p0) REVERT: C 637 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6915 (mm) REVERT: C 710 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8738 (ptmt) REVERT: D 6 ARG cc_start: 0.8385 (mpt180) cc_final: 0.8035 (mpt180) REVERT: D 45 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: D 423 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8556 (mp0) REVERT: D 426 MET cc_start: 0.8812 (mmm) cc_final: 0.8288 (mmm) REVERT: F 231 ARG cc_start: 0.8434 (tmm-80) cc_final: 0.7641 (tmm-80) REVERT: A 666 GLU cc_start: 0.8642 (tp30) cc_final: 0.8228 (tp30) REVERT: A 788 ASP cc_start: 0.8926 (m-30) cc_final: 0.8448 (t0) REVERT: G 433 MET cc_start: 0.8213 (ttm) cc_final: 0.7984 (ttm) REVERT: G 484 ASP cc_start: 0.8979 (t0) cc_final: 0.8622 (t0) outliers start: 34 outliers final: 27 residues processed: 183 average time/residue: 0.3285 time to fit residues: 95.8396 Evaluate side-chains 181 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 151 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 570 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 0.9980 chunk 242 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 254 optimal weight: 7.9990 chunk 233 optimal weight: 0.0270 chunk 202 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22129 Z= 0.173 Angle : 0.546 15.665 30200 Z= 0.276 Chirality : 0.037 0.146 3487 Planarity : 0.003 0.075 3594 Dihedral : 16.593 79.819 3663 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.40 % Allowed : 15.09 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 1.73 (0.18), residues: 2471 helix: 2.12 (0.14), residues: 1465 sheet: -0.31 (0.34), residues: 244 loop : -0.22 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 276 HIS 0.005 0.001 HIS E 278 PHE 0.020 0.001 PHE C 459 TYR 0.024 0.001 TYR C 72 ARG 0.016 0.000 ARG B 575 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9237 (mmm) cc_final: 0.8960 (mmm) REVERT: B 425 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9063 (tp) REVERT: B 476 ASP cc_start: 0.8493 (p0) cc_final: 0.8203 (p0) REVERT: B 535 MET cc_start: 0.7980 (tmm) cc_final: 0.6961 (tpp) REVERT: C 145 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8266 (mt-10) REVERT: C 185 MET cc_start: 0.8611 (mmm) cc_final: 0.8352 (mmm) REVERT: C 323 MET cc_start: 0.9161 (ttp) cc_final: 0.8897 (ttp) REVERT: C 449 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8474 (mt0) REVERT: C 710 LYS cc_start: 0.9073 (mmtt) cc_final: 0.8754 (ptmt) REVERT: D 6 ARG cc_start: 0.8372 (mpt180) cc_final: 0.8027 (mpt180) REVERT: D 45 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7601 (mp0) REVERT: D 423 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8573 (mp0) REVERT: D 426 MET cc_start: 0.8857 (mmm) cc_final: 0.8634 (mmt) REVERT: A 579 TYR cc_start: 0.8784 (t80) cc_final: 0.8393 (t80) REVERT: A 618 MET cc_start: 0.8621 (mtt) cc_final: 0.8286 (mtt) REVERT: A 666 GLU cc_start: 0.8626 (tp30) cc_final: 0.8281 (tp30) REVERT: A 788 ASP cc_start: 0.8916 (m-30) cc_final: 0.8443 (t0) REVERT: G 324 TYR cc_start: 0.9236 (t80) cc_final: 0.8995 (t80) REVERT: G 433 MET cc_start: 0.8243 (ttm) cc_final: 0.8018 (ttm) REVERT: G 484 ASP cc_start: 0.8968 (t0) cc_final: 0.8617 (t0) outliers start: 31 outliers final: 24 residues processed: 184 average time/residue: 0.3307 time to fit residues: 96.4262 Evaluate side-chains 179 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 153 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 61 optimal weight: 0.0980 chunk 186 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 202 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 208 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 ASN ** E 150 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 = 0.3604 r_free = 0.3604 target = 0.091780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.064212 restraints weight = 55229.966| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.32 r_work: 0.2868 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22129 Z= 0.165 Angle : 0.551 14.924 30200 Z= 0.277 Chirality : 0.037 0.145 3487 Planarity : 0.003 0.048 3594 Dihedral : 16.524 81.511 3663 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.27 % Allowed : 15.32 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 1.80 (0.18), residues: 2471 helix: 2.18 (0.14), residues: 1463 sheet: -0.30 (0.34), residues: 244 loop : -0.19 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 276 HIS 0.005 0.001 HIS E 278 PHE 0.023 0.001 PHE B 523 TYR 0.023 0.001 TYR C 72 ARG 0.011 0.000 ARG G 575 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4054.33 seconds wall clock time: 76 minutes 35.09 seconds (4595.09 seconds total)