Starting phenix.real_space_refine on Thu Mar 5 11:01:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jk3_22360/03_2026/7jk3_22360.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jk3_22360/03_2026/7jk3_22360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jk3_22360/03_2026/7jk3_22360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jk3_22360/03_2026/7jk3_22360.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jk3_22360/03_2026/7jk3_22360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jk3_22360/03_2026/7jk3_22360.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 111 5.16 5 C 13529 2.51 5 N 3818 2.21 5 O 4121 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21661 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: 4934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4934 Classifications: {'peptide': 614} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 590} Chain breaks: 6 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: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 684 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "I" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 669 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: 4.75, per 1000 atoms: 0.22 Number of scatterers: 21661 At special positions: 0 Unit cell: (128.14, 162.54, 120.4, 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 111 16.00 P 78 15.00 Mg 4 11.99 O 4121 8.00 N 3818 7.00 C 13529 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 1.0 seconds 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4840 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 13 sheets defined 63.1% alpha, 6.9% beta 32 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 2.77 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: 3.693A 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 400 removed outlier: 3.529A pdb=" N MET B 393 " --> pdb=" O THR B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 424 removed outlier: 3.974A pdb=" N LEU B 424 " --> pdb=" O GLU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 455 removed outlier: 3.680A pdb=" N GLN B 448 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 475 removed outlier: 3.560A pdb=" N LEU B 473 " --> pdb=" O ASN B 470 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 474 " --> pdb=" O THR B 471 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP B 475 " --> pdb=" O PRO B 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 470 through 475' Processing helix chain 'B' and resid 476 through 483 Processing helix chain 'B' and resid 516 through 524 Processing helix chain 'B' and resid 527 through 544 Processing helix chain 'B' and resid 554 through 565 removed outlier: 3.675A pdb=" N LEU B 558 " --> pdb=" O PRO B 554 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA B 565 " --> pdb=" O SER B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 584 removed outlier: 3.896A pdb=" N LEU B 574 " --> pdb=" O SER B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 615 removed outlier: 3.710A pdb=" N LEU B 608 " --> pdb=" O ASP B 604 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 615 " --> pdb=" O PHE B 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.848A pdb=" N VAL C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 41 through 46' Processing helix chain 'C' and resid 47 through 88 removed outlier: 3.610A pdb=" N GLU C 51 " --> pdb=" O GLN C 47 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ARG C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N THR C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 122 removed outlier: 5.721A pdb=" N SER C 112 " --> pdb=" O PRO C 108 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLN C 113 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE C 114 " --> pdb=" O HIS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.513A pdb=" N CYS C 137 " --> pdb=" O SER C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 159 Processing helix chain 'C' and resid 179 through 183 removed outlier: 3.652A pdb=" N CYS C 183 " --> pdb=" O ARG C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 196 Processing helix chain 'C' and resid 216 through 230 Processing helix chain 'C' and resid 245 through 253 removed outlier: 3.999A 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: 5.686A pdb=" N ALA C 331 " --> pdb=" O GLY C 328 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 334 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS C 335 " --> pdb=" O PHE C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 346 Processing helix chain 'C' and resid 349 through 357 removed outlier: 4.247A pdb=" N MET C 353 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU C 354 " --> pdb=" O HIS C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 372 through 381 removed outlier: 3.618A pdb=" N THR C 380 " --> pdb=" O ILE C 376 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 416 Proline residue: C 390 - end of helix removed outlier: 4.305A pdb=" N ASP C 416 " --> pdb=" O GLU C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 436 removed outlier: 3.970A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG C 436 " --> pdb=" O ASN C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 440 Processing helix chain 'C' and resid 441 through 453 removed outlier: 3.713A pdb=" N LYS C 445 " --> pdb=" O THR C 441 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE C 453 " --> pdb=" O GLN C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 477 removed outlier: 3.501A pdb=" N GLU C 477 " --> pdb=" O PHE C 473 " (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 removed outlier: 3.786A pdb=" N LYS C 567 " --> pdb=" O ARG C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 581 removed outlier: 3.641A pdb=" N HIS C 580 " --> pdb=" O ILE C 576 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 581 " --> pdb=" O VAL C 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 576 through 581' Processing helix chain 'C' and resid 590 through 593 Processing helix chain 'C' and resid 599 through 607 Processing helix chain 'C' and resid 609 through 620 removed outlier: 3.594A 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 653 removed outlier: 3.527A pdb=" N VAL C 647 " --> pdb=" O PRO C 643 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 648 " --> pdb=" O ASP C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 672 Processing helix chain 'C' and resid 688 through 703 Processing helix chain 'D' and resid 3 through 21 removed outlier: 3.532A pdb=" N GLU D 7 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 3.820A 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 62 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 removed outlier: 3.910A pdb=" N ALA D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 134 Processing helix chain 'D' and resid 148 through 154 removed outlier: 3.555A pdb=" N PHE D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 165 Processing helix chain 'D' and resid 185 through 189 removed outlier: 3.597A 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 222 removed outlier: 3.576A pdb=" N TYR D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 244 removed outlier: 3.564A pdb=" N LEU D 231 " --> pdb=" O THR D 227 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE D 244 " --> pdb=" O ASN D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 removed outlier: 4.209A pdb=" N ARG D 253 " --> pdb=" O TYR D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 261 removed outlier: 3.828A pdb=" N GLU D 260 " --> pdb=" O ASP D 257 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR D 261 " --> pdb=" O PRO D 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 257 through 261' 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: 3.929A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 333 removed outlier: 3.616A pdb=" N MET D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 3.533A 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: 3.551A pdb=" N ILE D 371 " --> pdb=" O ASN D 367 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS D 380 " --> pdb=" O SER D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 403 removed outlier: 3.942A pdb=" N VAL D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA D 403 " --> pdb=" O HIS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 443 removed outlier: 3.765A pdb=" N ILE D 436 " --> pdb=" O THR D 432 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN D 441 " --> pdb=" O HIS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 456 removed outlier: 3.551A pdb=" N GLN D 455 " --> pdb=" O ALA D 451 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D 456 " --> pdb=" O GLN D 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 15 through 26 removed outlier: 3.723A pdb=" N ILE E 19 " --> pdb=" O ARG E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 62 Processing helix chain 'E' and resid 76 through 89 removed outlier: 3.844A pdb=" N MET E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 110 Processing helix chain 'E' and resid 127 through 131 Processing helix chain 'E' and resid 138 through 144 Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'E' and resid 162 through 166 removed outlier: 3.538A pdb=" N LYS E 165 " --> pdb=" O PRO E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 193 Processing helix chain 'E' and resid 195 through 205 Processing helix chain 'E' and resid 212 through 220 removed outlier: 3.843A pdb=" N GLU E 219 " --> pdb=" O GLU E 215 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 238 removed outlier: 4.015A pdb=" N VAL E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 259 removed outlier: 4.033A pdb=" N LYS E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 264 Processing helix chain 'E' and resid 275 through 287 Proline residue: E 282 - end of helix Processing helix chain 'E' and resid 288 through 290 No H-bonds generated for 'chain 'E' and resid 288 through 290' Processing helix chain 'E' and resid 322 through 337 Processing helix chain 'E' and resid 342 through 347 removed outlier: 3.778A pdb=" N LEU E 346 " --> pdb=" O GLN E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 394 removed outlier: 4.650A pdb=" N GLU E 394 " --> pdb=" O TYR E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 412 removed outlier: 4.139A pdb=" N LEU E 404 " --> pdb=" O THR E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 449 Processing helix chain 'F' and resid 224 through 238 removed outlier: 3.585A pdb=" N ALA F 238 " --> pdb=" O ALA F 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 529 removed outlier: 3.626A pdb=" N ALA A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 571 through 589 removed outlier: 3.624A pdb=" N PHE A 575 " --> pdb=" O ARG A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 621 Processing helix chain 'A' and resid 635 through 637 No H-bonds generated for 'chain 'A' and resid 635 through 637' Processing helix chain 'A' and resid 641 through 650 removed outlier: 3.880A pdb=" N VAL A 645 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 648 " --> pdb=" O TYR A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 671 removed outlier: 4.012A pdb=" N THR A 671 " --> pdb=" O LYS A 667 " (cutoff:3.500A) 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 removed outlier: 3.801A pdb=" N LEU A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 748 through 759 removed outlier: 3.892A pdb=" N VAL A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY A 759 " --> pdb=" O THR A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 777 Processing helix chain 'A' and resid 782 through 800 removed outlier: 4.096A pdb=" N ALA A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 800 " --> pdb=" O ILE A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 818 removed outlier: 3.680A pdb=" N VAL A 810 " --> pdb=" O THR A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 828 Processing helix chain 'A' and resid 830 through 848 Processing helix chain 'A' and resid 854 through 869 Processing helix chain 'A' and resid 874 through 888 removed outlier: 4.242A pdb=" N ARG A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 918 removed outlier: 3.695A pdb=" N ILE A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 260 removed outlier: 4.115A pdb=" N ASN G 260 " --> pdb=" O ARG G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 287 removed outlier: 3.910A pdb=" N SER G 287 " --> pdb=" O ASN G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 310 Processing helix chain 'G' and resid 313 through 319 Processing helix chain 'G' and resid 332 through 334 No H-bonds generated for 'chain 'G' and resid 332 through 334' Processing helix chain 'G' and resid 335 through 345 Processing helix chain 'G' and resid 352 through 366 removed outlier: 3.613A pdb=" N HIS G 356 " --> pdb=" O THR G 352 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS G 365 " --> pdb=" O GLN G 361 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR G 366 " --> pdb=" O ARG G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 381 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 420 through 425 removed outlier: 3.593A pdb=" N ARG G 425 " --> pdb=" O LEU G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 453 removed outlier: 3.519A pdb=" N ILE G 443 " --> pdb=" O SER G 439 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 476 removed outlier: 3.673A pdb=" N LEU G 465 " --> pdb=" O PRO G 461 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA G 474 " --> pdb=" O ALA G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 498 removed outlier: 3.764A pdb=" N ALA G 482 " --> pdb=" O ASP G 478 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL G 490 " --> pdb=" O GLY G 486 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN G 495 " --> pdb=" O GLU G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 542 removed outlier: 3.788A 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 580 through 595 removed outlier: 3.563A pdb=" N LEU G 584 " --> pdb=" O SER G 580 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG G 590 " --> pdb=" O GLU G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 601 through 614 removed outlier: 4.014A pdb=" N GLY G 607 " --> pdb=" O ALA G 603 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR G 614 " --> pdb=" O ASP G 610 " (cutoff:3.500A) Processing helix chain 'G' and resid 636 through 645 removed outlier: 3.761A pdb=" N SER G 645 " --> pdb=" O HIS G 641 " (cutoff:3.500A) Processing helix chain 'G' and resid 646 through 654 removed outlier: 3.709A pdb=" N SER G 652 " --> pdb=" O GLN G 648 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU G 654 " --> pdb=" O ILE G 650 " (cutoff:3.500A) Processing helix chain 'G' and resid 656 through 660 removed outlier: 4.383A pdb=" N CYS G 659 " --> pdb=" O ASP G 656 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU G 660 " --> pdb=" O THR G 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 656 through 660' Processing sheet with id=AA1, first strand: chain 'B' and resid 487 through 488 removed outlier: 6.161A pdb=" N LEU B 354 " --> pdb=" O TRP B 488 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU B 430 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU B 463 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU B 432 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N SER B 465 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL B 434 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR B 377 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ILE B 433 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU B 379 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N HIS B 435 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 381 " --> pdb=" O HIS B 435 " (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: 6.016A pdb=" N MET C 128 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE C 208 " --> pdb=" O MET C 128 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS C 130 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LEU C 205 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL C 239 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL C 207 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA C 99 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 291 through 292 removed outlier: 7.610A pdb=" N HIS C 291 " --> pdb=" O PHE C 596 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 658 through 660 Processing sheet with id=AA6, first strand: chain 'D' and resid 83 through 89 removed outlier: 6.852A pdb=" N LEU D 84 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE D 145 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL D 86 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLU D 147 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU D 88 " --> pdb=" O GLU D 147 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL D 142 " --> pdb=" O CYS D 176 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LEU D 178 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE D 144 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL D 180 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU D 146 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASN D 50 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLY D 179 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU D 52 " --> pdb=" O GLY D 179 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N THR D 181 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU D 54 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 406 through 408 Processing sheet with id=AA8, first strand: chain 'E' and resid 64 through 70 removed outlier: 3.527A pdb=" N ASP E 126 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE E 121 " --> pdb=" O CYS E 154 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE E 156 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE E 123 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU E 158 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL E 125 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE E 37 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N SER E 159 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU E 39 " --> pdb=" O SER E 159 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 416 through 420 removed outlier: 5.514A pdb=" N PHE E 418 " --> pdb=" O GLN E 433 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN E 433 " --> pdb=" O PHE E 418 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER E 420 " --> pdb=" O ARG E 431 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG E 431 " --> pdb=" O SER E 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 627 through 633 removed outlier: 6.488A pdb=" N GLU A 628 " --> pdb=" O VAL A 680 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU A 682 " --> pdb=" O GLU A 628 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 630 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASP A 684 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE A 632 " --> pdb=" O ASP A 684 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR A 679 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL A 714 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU A 681 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE A 716 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL A 683 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY A 592 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N THR A 715 " --> pdb=" O GLY A 592 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N MET A 594 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA A 717 " --> pdb=" O MET A 594 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 596 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N LEU A 740 " --> pdb=" O CYS A 593 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR A 595 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N PHE A 742 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N SER A 597 " --> pdb=" O PHE A 742 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 852 through 853 Processing sheet with id=AB3, first strand: chain 'G' and resid 320 through 326 removed outlier: 6.432A pdb=" N GLN G 321 " --> pdb=" O LEU G 372 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL G 374 " --> pdb=" O GLN G 321 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL G 323 " --> pdb=" O VAL G 374 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ASP G 376 " --> pdb=" O VAL G 323 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE G 325 " --> pdb=" O ASP G 376 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY G 291 " --> pdb=" O LEU G 405 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N GLY G 407 " --> pdb=" O GLY G 291 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU G 293 " --> pdb=" O GLY G 407 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ALA G 409 " --> pdb=" O LEU G 293 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL G 295 " --> pdb=" O ALA G 409 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG G 431 " --> pdb=" O SER G 292 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 618 through 621 991 hydrogen bonds defined for protein. 2895 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 3.98 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5825 1.34 - 1.46: 4252 1.46 - 1.58: 11782 1.58 - 1.70: 150 1.70 - 1.82: 163 Bond restraints: 22172 Sorted by residual: bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.52e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.51e+01 bond pdb=" C4 ATP G 901 " pdb=" C5 ATP G 901 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.37e+01 bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.25e+01 bond pdb=" C5 ATP G 901 " pdb=" C6 ATP G 901 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.67e+01 ... (remaining 22167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 30089 3.96 - 7.92: 142 7.92 - 11.87: 19 11.87 - 15.83: 3 15.83 - 19.79: 5 Bond angle restraints: 30258 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 120.08 19.79 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 120.96 18.91 1.00e+00 1.00e+00 3.57e+02 angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 120.99 18.88 1.00e+00 1.00e+00 3.56e+02 angle pdb=" PB ATP G 901 " pdb=" O3B ATP G 901 " pdb=" PG ATP G 901 " ideal model delta sigma weight residual 139.87 122.02 17.85 1.00e+00 1.00e+00 3.19e+02 angle pdb=" PA ATP E 901 " pdb=" O3A ATP E 901 " pdb=" PB ATP E 901 " ideal model delta sigma weight residual 136.83 119.72 17.11 1.00e+00 1.00e+00 2.93e+02 ... (remaining 30253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11510 17.95 - 35.91: 1282 35.91 - 53.86: 458 53.86 - 71.82: 113 71.82 - 89.77: 27 Dihedral angle restraints: 13390 sinusoidal: 5977 harmonic: 7413 Sorted by residual: 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 180.00 153.30 26.70 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA MET E 134 " pdb=" C MET E 134 " pdb=" N ASP E 135 " pdb=" CA ASP E 135 " ideal model delta harmonic sigma weight residual -180.00 -158.08 -21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ASP E 135 " pdb=" C ASP E 135 " pdb=" N ALA E 136 " pdb=" CA ALA E 136 " ideal model delta harmonic sigma weight residual 180.00 158.56 21.44 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 13387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2487 0.044 - 0.089: 774 0.089 - 0.133: 188 0.133 - 0.178: 36 0.178 - 0.222: 7 Chirality restraints: 3492 Sorted by residual: chirality pdb=" CA ASP C 714 " pdb=" N ASP C 714 " pdb=" C ASP C 714 " pdb=" CB ASP C 714 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB THR A 679 " pdb=" CA THR A 679 " pdb=" OG1 THR A 679 " pdb=" CG2 THR A 679 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA GLU E 260 " pdb=" N GLU E 260 " pdb=" C GLU E 260 " pdb=" CB GLU E 260 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 3489 not shown) Planarity restraints: 3603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 712 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.40e+00 pdb=" C LYS C 712 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS C 712 " -0.020 2.00e-02 2.50e+03 pdb=" N THR C 713 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP G 395 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO G 396 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO G 396 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 396 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 74 " 0.049 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO D 75 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " 0.042 5.00e-02 4.00e+02 ... (remaining 3600 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 23 2.35 - 2.99: 9278 2.99 - 3.62: 31585 3.62 - 4.26: 48614 4.26 - 4.90: 81904 Nonbonded interactions: 171404 Sorted by model distance: nonbonded pdb=" NH1 ARG C 711 " pdb=" O3' DA I 43 " model vdw 1.709 3.120 nonbonded pdb=" OG1 THR G 304 " pdb="MG MG G 902 " model vdw 2.106 2.170 nonbonded pdb=" OG1 THR D 63 " pdb="MG MG D 902 " model vdw 2.117 2.170 nonbonded pdb=" O2B ATP A1001 " pdb="MG MG A1002 " model vdw 2.122 2.170 nonbonded pdb=" OG1 THR E 48 " pdb="MG MG E 902 " model vdw 2.128 2.170 ... (remaining 171399 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: 1.830 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: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 21.600 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 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 : 0.005 0.081 22172 Z= 0.282 Angle : 0.866 19.789 30258 Z= 0.553 Chirality : 0.046 0.222 3492 Planarity : 0.007 0.076 3603 Dihedral : 17.808 89.771 8550 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.18 % Allowed : 5.82 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.87 (0.13), residues: 2478 helix: -2.55 (0.09), residues: 1448 sheet: -1.77 (0.30), residues: 228 loop : -2.42 (0.17), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 675 TYR 0.015 0.001 TYR E 258 PHE 0.019 0.002 PHE D 256 TRP 0.013 0.001 TRP C 57 HIS 0.011 0.001 HIS G 629 Details of bonding type rmsd covalent geometry : bond 0.00458 (22172) covalent geometry : angle 0.86610 (30258) hydrogen bonds : bond 0.13487 ( 1075) hydrogen bonds : angle 6.01061 ( 3059) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 208 time to evaluate : 0.809 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 562 CYS cc_start: 0.9246 (m) cc_final: 0.8941 (p) REVERT: C 52 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8212 (mm-30) REVERT: C 353 MET cc_start: 0.9122 (mmt) cc_final: 0.8864 (mmm) REVERT: C 383 ASP cc_start: 0.9088 (m-30) cc_final: 0.8859 (p0) REVERT: C 454 LEU cc_start: 0.7557 (tp) cc_final: 0.6947 (tt) REVERT: C 699 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7537 (mt-10) REVERT: D 426 MET cc_start: 0.8449 (mmm) cc_final: 0.8223 (mmp) REVERT: F 224 ASP cc_start: 0.9297 (t0) cc_final: 0.8987 (t70) REVERT: F 226 GLU cc_start: 0.9523 (mm-30) cc_final: 0.9253 (mp0) REVERT: A 622 ASN cc_start: 0.9018 (t0) cc_final: 0.8797 (t0) REVERT: A 631 GLU cc_start: 0.8033 (pp20) cc_final: 0.7827 (pm20) REVERT: A 817 MET cc_start: 0.8916 (mmm) cc_final: 0.7755 (mmm) REVERT: G 491 GLU cc_start: 0.8308 (tt0) cc_final: 0.7859 (pt0) REVERT: G 563 MET cc_start: 0.8405 (tmm) cc_final: 0.7867 (tmm) REVERT: G 592 CYS cc_start: 0.9046 (m) cc_final: 0.8462 (m) outliers start: 4 outliers final: 0 residues processed: 212 average time/residue: 0.1702 time to fit residues: 54.3847 Evaluate side-chains 133 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 0.0770 chunk 71 optimal weight: 5.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 HIS B 330 ASN B 348 ASN B 374 HIS B 498 ASN B 577 GLN C 368 GLN C 578 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 HIS D 138 HIS D 455 GLN E 150 ASN E 414 ASN E 433 GLN A 621 GLN A 718 ASN A 747 HIS A 749 GLN A 809 HIS A 838 GLN A 902 GLN G 265 GLN G 284 HIS G 386 GLN G 585 HIS G 634 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.068407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.048063 restraints weight = 73506.283| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.53 r_work: 0.2691 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22172 Z= 0.148 Angle : 0.553 10.779 30258 Z= 0.291 Chirality : 0.038 0.162 3492 Planarity : 0.004 0.054 3603 Dihedral : 17.379 88.311 3578 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.81 % Allowed : 9.47 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.16), residues: 2478 helix: -0.34 (0.13), residues: 1474 sheet: -1.39 (0.31), residues: 227 loop : -1.70 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 604 TYR 0.016 0.001 TYR A 629 PHE 0.010 0.001 PHE E 104 TRP 0.009 0.001 TRP E 276 HIS 0.004 0.001 HIS C 615 Details of bonding type rmsd covalent geometry : bond 0.00324 (22172) covalent geometry : angle 0.55324 (30258) hydrogen bonds : bond 0.03977 ( 1075) hydrogen bonds : angle 3.88308 ( 3059) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9482 (m-40) cc_final: 0.9118 (m110) REVERT: B 420 GLU cc_start: 0.9453 (mm-30) cc_final: 0.9215 (tp30) REVERT: B 540 TYR cc_start: 0.8390 (t80) cc_final: 0.8041 (t80) REVERT: B 562 CYS cc_start: 0.9268 (m) cc_final: 0.8944 (m) REVERT: C 324 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8688 (tm-30) REVERT: C 699 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8247 (mt-10) REVERT: D 347 GLU cc_start: 0.9021 (mp0) cc_final: 0.8607 (mp0) REVERT: D 440 MET cc_start: 0.9012 (mmp) cc_final: 0.8722 (mmm) REVERT: E 1 MET cc_start: 0.7958 (ppp) cc_final: 0.7757 (ppp) REVERT: E 249 LEU cc_start: 0.9341 (mt) cc_final: 0.8968 (tt) REVERT: E 254 CYS cc_start: 0.8100 (m) cc_final: 0.7669 (t) REVERT: A 622 ASN cc_start: 0.9392 (t0) cc_final: 0.9100 (t0) REVERT: A 631 GLU cc_start: 0.8884 (pp20) cc_final: 0.8469 (pm20) REVERT: G 491 GLU cc_start: 0.8527 (tt0) cc_final: 0.7938 (pt0) REVERT: G 575 ARG cc_start: 0.7618 (tpt90) cc_final: 0.7260 (tpt90) REVERT: G 592 CYS cc_start: 0.9120 (m) cc_final: 0.8624 (m) outliers start: 18 outliers final: 12 residues processed: 151 average time/residue: 0.1468 time to fit residues: 35.5438 Evaluate side-chains 139 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain G residue 382 CYS Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 150 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 11 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.068600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.048552 restraints weight = 73789.782| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.52 r_work: 0.2702 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22172 Z= 0.113 Angle : 0.510 8.567 30258 Z= 0.264 Chirality : 0.037 0.155 3492 Planarity : 0.003 0.053 3603 Dihedral : 17.253 89.302 3578 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.04 % Allowed : 10.87 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2478 helix: 0.61 (0.14), residues: 1463 sheet: -1.09 (0.32), residues: 228 loop : -1.25 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 284 TYR 0.012 0.001 TYR E 258 PHE 0.009 0.001 PHE D 121 TRP 0.009 0.001 TRP E 276 HIS 0.014 0.001 HIS C 652 Details of bonding type rmsd covalent geometry : bond 0.00245 (22172) covalent geometry : angle 0.50966 (30258) hydrogen bonds : bond 0.03536 ( 1075) hydrogen bonds : angle 3.55202 ( 3059) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9486 (m-40) cc_final: 0.9152 (m110) REVERT: B 420 GLU cc_start: 0.9454 (mm-30) cc_final: 0.9197 (tp30) REVERT: B 540 TYR cc_start: 0.8312 (t80) cc_final: 0.7826 (t80) REVERT: B 562 CYS cc_start: 0.9255 (m) cc_final: 0.8924 (m) REVERT: C 324 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8650 (tm-30) REVERT: C 383 ASP cc_start: 0.9298 (m-30) cc_final: 0.8914 (p0) REVERT: C 413 LEU cc_start: 0.9049 (tt) cc_final: 0.8830 (tp) REVERT: C 435 ASN cc_start: 0.9434 (t0) cc_final: 0.9004 (p0) REVERT: C 699 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8224 (mt-10) REVERT: D 131 CYS cc_start: 0.9702 (t) cc_final: 0.9342 (t) REVERT: D 347 GLU cc_start: 0.9060 (mp0) cc_final: 0.8622 (mp0) REVERT: E 249 LEU cc_start: 0.9295 (mt) cc_final: 0.8934 (tt) REVERT: E 254 CYS cc_start: 0.8034 (m) cc_final: 0.7681 (t) REVERT: A 622 ASN cc_start: 0.9390 (t0) cc_final: 0.9125 (t0) REVERT: A 628 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7918 (tm-30) REVERT: A 631 GLU cc_start: 0.8862 (pp20) cc_final: 0.8456 (pm20) REVERT: A 635 MET cc_start: 0.9290 (tpp) cc_final: 0.8919 (mmm) REVERT: G 491 GLU cc_start: 0.8498 (tt0) cc_final: 0.7884 (pt0) REVERT: G 575 ARG cc_start: 0.7703 (tpt90) cc_final: 0.7358 (tpt90) REVERT: G 592 CYS cc_start: 0.9001 (m) cc_final: 0.8562 (m) outliers start: 23 outliers final: 13 residues processed: 152 average time/residue: 0.1447 time to fit residues: 35.4412 Evaluate side-chains 138 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 382 CYS Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 135 optimal weight: 9.9990 chunk 173 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 175 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 GLN C 652 HIS D 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.067258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.047050 restraints weight = 74618.235| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 3.55 r_work: 0.2652 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22172 Z= 0.164 Angle : 0.529 8.775 30258 Z= 0.271 Chirality : 0.038 0.238 3492 Planarity : 0.003 0.047 3603 Dihedral : 17.134 89.744 3578 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.13 % Allowed : 11.36 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.17), residues: 2478 helix: 1.18 (0.14), residues: 1474 sheet: -0.81 (0.33), residues: 228 loop : -0.99 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 374 TYR 0.013 0.001 TYR A 915 PHE 0.010 0.001 PHE E 237 TRP 0.011 0.001 TRP E 276 HIS 0.005 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00371 (22172) covalent geometry : angle 0.52854 (30258) hydrogen bonds : bond 0.03679 ( 1075) hydrogen bonds : angle 3.45194 ( 3059) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9502 (m-40) cc_final: 0.9164 (m110) REVERT: B 420 GLU cc_start: 0.9523 (mm-30) cc_final: 0.9262 (tp30) REVERT: B 540 TYR cc_start: 0.8294 (t80) cc_final: 0.7859 (t80) REVERT: B 562 CYS cc_start: 0.9212 (m) cc_final: 0.8725 (p) REVERT: C 324 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8724 (tm-30) REVERT: C 353 MET cc_start: 0.9095 (mmt) cc_final: 0.8883 (mmm) REVERT: C 383 ASP cc_start: 0.9255 (m-30) cc_final: 0.8945 (p0) REVERT: C 435 ASN cc_start: 0.9453 (t0) cc_final: 0.8966 (p0) REVERT: C 699 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8263 (mt-10) REVERT: D 131 CYS cc_start: 0.9694 (t) cc_final: 0.9373 (t) REVERT: D 347 GLU cc_start: 0.9094 (mp0) cc_final: 0.8545 (mp0) REVERT: E 249 LEU cc_start: 0.9292 (mt) cc_final: 0.8927 (tt) REVERT: E 254 CYS cc_start: 0.8078 (m) cc_final: 0.7707 (t) REVERT: E 276 TRP cc_start: 0.8346 (t-100) cc_final: 0.8042 (t-100) REVERT: A 622 ASN cc_start: 0.9415 (t0) cc_final: 0.9186 (t0) REVERT: A 628 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7691 (tm-30) REVERT: A 631 GLU cc_start: 0.8817 (pp20) cc_final: 0.8559 (pp20) REVERT: A 635 MET cc_start: 0.9405 (tpp) cc_final: 0.9057 (mmm) REVERT: G 491 GLU cc_start: 0.8559 (tt0) cc_final: 0.7938 (pt0) REVERT: G 592 CYS cc_start: 0.8937 (m) cc_final: 0.8631 (m) outliers start: 25 outliers final: 18 residues processed: 146 average time/residue: 0.1422 time to fit residues: 33.5876 Evaluate side-chains 139 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 54 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 241 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 180 optimal weight: 9.9990 chunk 240 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 223 optimal weight: 9.9990 chunk 160 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 HIS A 650 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.067866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.047355 restraints weight = 74346.959| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.63 r_work: 0.2655 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22172 Z= 0.108 Angle : 0.500 12.021 30258 Z= 0.254 Chirality : 0.037 0.279 3492 Planarity : 0.003 0.045 3603 Dihedral : 17.039 89.357 3578 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.53 % Allowed : 11.99 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.17), residues: 2478 helix: 1.50 (0.14), residues: 1471 sheet: -0.62 (0.34), residues: 228 loop : -0.73 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 231 TYR 0.014 0.001 TYR A 915 PHE 0.009 0.001 PHE E 237 TRP 0.007 0.001 TRP A 658 HIS 0.003 0.000 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00238 (22172) covalent geometry : angle 0.50000 (30258) hydrogen bonds : bond 0.03281 ( 1075) hydrogen bonds : angle 3.30916 ( 3059) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9505 (m-40) cc_final: 0.9163 (m110) REVERT: B 420 GLU cc_start: 0.9555 (mm-30) cc_final: 0.9328 (tp30) REVERT: B 432 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8968 (pp) REVERT: B 540 TYR cc_start: 0.8181 (t80) cc_final: 0.7808 (t80) REVERT: B 562 CYS cc_start: 0.9212 (m) cc_final: 0.8688 (p) REVERT: C 324 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8712 (tm-30) REVERT: C 353 MET cc_start: 0.9150 (mmt) cc_final: 0.8837 (mmm) REVERT: C 368 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8647 (pp30) REVERT: C 383 ASP cc_start: 0.9269 (m-30) cc_final: 0.8964 (p0) REVERT: C 435 ASN cc_start: 0.9468 (t0) cc_final: 0.9111 (m110) REVERT: C 699 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8287 (mt-10) REVERT: D 131 CYS cc_start: 0.9655 (t) cc_final: 0.9363 (t) REVERT: D 347 GLU cc_start: 0.9120 (mp0) cc_final: 0.8530 (mp0) REVERT: D 362 ASP cc_start: 0.9202 (t0) cc_final: 0.8961 (m-30) REVERT: E 249 LEU cc_start: 0.9279 (mt) cc_final: 0.8934 (tt) REVERT: E 254 CYS cc_start: 0.7996 (m) cc_final: 0.7643 (t) REVERT: A 622 ASN cc_start: 0.9415 (t0) cc_final: 0.9211 (t0) REVERT: A 628 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7621 (tm-30) REVERT: A 631 GLU cc_start: 0.8837 (pp20) cc_final: 0.8244 (pm20) REVERT: A 635 MET cc_start: 0.9383 (tpp) cc_final: 0.8986 (mmm) REVERT: G 491 GLU cc_start: 0.8564 (tt0) cc_final: 0.7919 (pt0) REVERT: G 592 CYS cc_start: 0.8856 (m) cc_final: 0.8579 (m) outliers start: 34 outliers final: 20 residues processed: 160 average time/residue: 0.1330 time to fit residues: 34.9458 Evaluate side-chains 144 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 382 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 0.0070 chunk 70 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 241 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 225 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.068078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.047576 restraints weight = 74138.467| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.61 r_work: 0.2661 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22172 Z= 0.105 Angle : 0.504 12.227 30258 Z= 0.255 Chirality : 0.037 0.302 3492 Planarity : 0.003 0.044 3603 Dihedral : 16.940 89.102 3578 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.49 % Allowed : 12.53 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.17), residues: 2478 helix: 1.66 (0.14), residues: 1472 sheet: -0.46 (0.34), residues: 228 loop : -0.63 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 231 TYR 0.013 0.001 TYR A 915 PHE 0.027 0.001 PHE C 290 TRP 0.018 0.001 TRP E 276 HIS 0.007 0.000 HIS C 652 Details of bonding type rmsd covalent geometry : bond 0.00229 (22172) covalent geometry : angle 0.50375 (30258) hydrogen bonds : bond 0.03204 ( 1075) hydrogen bonds : angle 3.26668 ( 3059) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9506 (m-40) cc_final: 0.9188 (m110) REVERT: B 420 GLU cc_start: 0.9602 (mm-30) cc_final: 0.9285 (tp30) REVERT: B 432 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8958 (pp) REVERT: B 540 TYR cc_start: 0.8231 (t80) cc_final: 0.7759 (t80) REVERT: B 562 CYS cc_start: 0.9216 (m) cc_final: 0.8677 (p) REVERT: C 324 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8708 (tm-30) REVERT: C 353 MET cc_start: 0.9138 (mmt) cc_final: 0.8745 (mmm) REVERT: C 435 ASN cc_start: 0.9477 (t0) cc_final: 0.9122 (m110) REVERT: C 699 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8275 (mt-10) REVERT: C 721 TRP cc_start: 0.8434 (p-90) cc_final: 0.8119 (p-90) REVERT: D 131 CYS cc_start: 0.9633 (t) cc_final: 0.9365 (t) REVERT: D 347 GLU cc_start: 0.9128 (mp0) cc_final: 0.8685 (mp0) REVERT: D 362 ASP cc_start: 0.9180 (t0) cc_final: 0.8963 (m-30) REVERT: D 389 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8616 (mt-10) REVERT: E 249 LEU cc_start: 0.9282 (mt) cc_final: 0.8961 (tt) REVERT: E 254 CYS cc_start: 0.7968 (m) cc_final: 0.7652 (t) REVERT: A 622 ASN cc_start: 0.9430 (t0) cc_final: 0.9226 (t0) REVERT: A 631 GLU cc_start: 0.8842 (pp20) cc_final: 0.8278 (pm20) REVERT: A 635 MET cc_start: 0.9362 (tpp) cc_final: 0.9053 (mmm) REVERT: G 322 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8488 (mtm-85) REVERT: G 420 MET cc_start: 0.8920 (pmm) cc_final: 0.8701 (pmm) REVERT: G 491 GLU cc_start: 0.8547 (tt0) cc_final: 0.7914 (pt0) REVERT: G 592 CYS cc_start: 0.8882 (m) cc_final: 0.8621 (m) outliers start: 33 outliers final: 23 residues processed: 151 average time/residue: 0.1280 time to fit residues: 31.9903 Evaluate side-chains 147 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 382 CYS Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 433 MET Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 109 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 249 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 227 optimal weight: 0.9990 chunk 62 optimal weight: 0.2980 chunk 99 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.068195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.047760 restraints weight = 73881.279| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.61 r_work: 0.2664 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22172 Z= 0.106 Angle : 0.503 12.153 30258 Z= 0.254 Chirality : 0.037 0.205 3492 Planarity : 0.003 0.043 3603 Dihedral : 16.863 87.916 3578 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.58 % Allowed : 12.49 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.18), residues: 2478 helix: 1.81 (0.14), residues: 1472 sheet: -0.35 (0.34), residues: 228 loop : -0.55 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 231 TYR 0.014 0.001 TYR A 915 PHE 0.009 0.001 PHE E 237 TRP 0.016 0.001 TRP E 276 HIS 0.008 0.000 HIS C 652 Details of bonding type rmsd covalent geometry : bond 0.00235 (22172) covalent geometry : angle 0.50323 (30258) hydrogen bonds : bond 0.03142 ( 1075) hydrogen bonds : angle 3.21404 ( 3059) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9499 (m-40) cc_final: 0.9187 (m110) REVERT: B 432 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8939 (pp) REVERT: B 540 TYR cc_start: 0.8243 (t80) cc_final: 0.7913 (t80) REVERT: B 553 MET cc_start: 0.8468 (ttt) cc_final: 0.8120 (ttt) REVERT: B 562 CYS cc_start: 0.9200 (m) cc_final: 0.8651 (p) REVERT: C 324 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8681 (tm-30) REVERT: C 353 MET cc_start: 0.9150 (mmt) cc_final: 0.8791 (mmm) REVERT: C 435 ASN cc_start: 0.9482 (t0) cc_final: 0.9120 (m110) REVERT: C 699 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8271 (mt-10) REVERT: C 721 TRP cc_start: 0.8456 (p-90) cc_final: 0.8178 (p-90) REVERT: D 116 LYS cc_start: 0.8926 (ttpt) cc_final: 0.8709 (tptt) REVERT: D 131 CYS cc_start: 0.9610 (t) cc_final: 0.9360 (t) REVERT: D 347 GLU cc_start: 0.9134 (mp0) cc_final: 0.8657 (mp0) REVERT: D 362 ASP cc_start: 0.9185 (t0) cc_final: 0.8974 (m-30) REVERT: D 389 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8608 (mt-10) REVERT: E 249 LEU cc_start: 0.9240 (mt) cc_final: 0.8967 (tt) REVERT: E 254 CYS cc_start: 0.7910 (m) cc_final: 0.7630 (t) REVERT: A 631 GLU cc_start: 0.8828 (pp20) cc_final: 0.8322 (pm20) REVERT: A 635 MET cc_start: 0.9411 (tpp) cc_final: 0.9038 (mmm) REVERT: G 322 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8494 (mtm-85) REVERT: G 420 MET cc_start: 0.8884 (pmm) cc_final: 0.8667 (pmm) REVERT: G 491 GLU cc_start: 0.8564 (tt0) cc_final: 0.7920 (pt0) REVERT: G 592 CYS cc_start: 0.8885 (m) cc_final: 0.8625 (m) outliers start: 35 outliers final: 26 residues processed: 155 average time/residue: 0.1265 time to fit residues: 32.9435 Evaluate side-chains 152 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 32 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 242 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 221 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 249 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 580 HIS C 660 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.066778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.045745 restraints weight = 74665.951| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.62 r_work: 0.2617 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22172 Z= 0.190 Angle : 0.562 12.028 30258 Z= 0.283 Chirality : 0.039 0.280 3492 Planarity : 0.003 0.050 3603 Dihedral : 16.907 87.191 3578 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.53 % Allowed : 13.21 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.18), residues: 2478 helix: 1.91 (0.14), residues: 1470 sheet: -0.36 (0.34), residues: 228 loop : -0.45 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 231 TYR 0.015 0.001 TYR A 915 PHE 0.012 0.001 PHE E 237 TRP 0.013 0.001 TRP E 276 HIS 0.004 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00434 (22172) covalent geometry : angle 0.56199 (30258) hydrogen bonds : bond 0.03663 ( 1075) hydrogen bonds : angle 3.36129 ( 3059) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9517 (m-40) cc_final: 0.9183 (m110) REVERT: B 432 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9040 (pp) REVERT: B 553 MET cc_start: 0.8415 (ttt) cc_final: 0.8091 (ttt) REVERT: B 562 CYS cc_start: 0.9202 (m) cc_final: 0.8794 (m) REVERT: C 324 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8799 (tm-30) REVERT: C 353 MET cc_start: 0.9173 (mmt) cc_final: 0.8948 (mmm) REVERT: C 435 ASN cc_start: 0.9484 (t0) cc_final: 0.9207 (m-40) REVERT: C 699 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8329 (mt-10) REVERT: C 721 TRP cc_start: 0.8513 (p-90) cc_final: 0.8150 (p-90) REVERT: D 116 LYS cc_start: 0.8917 (ttpt) cc_final: 0.8705 (tptt) REVERT: D 131 CYS cc_start: 0.9609 (t) cc_final: 0.9369 (t) REVERT: D 311 HIS cc_start: 0.9300 (OUTLIER) cc_final: 0.8930 (t-90) REVERT: D 347 GLU cc_start: 0.9148 (mp0) cc_final: 0.8655 (mm-30) REVERT: D 362 ASP cc_start: 0.9186 (t0) cc_final: 0.8953 (m-30) REVERT: D 389 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8619 (mt-10) REVERT: E 129 GLU cc_start: 0.9258 (OUTLIER) cc_final: 0.8670 (pm20) REVERT: E 249 LEU cc_start: 0.9299 (mt) cc_final: 0.8983 (tt) REVERT: E 254 CYS cc_start: 0.8079 (m) cc_final: 0.7734 (t) REVERT: E 337 HIS cc_start: 0.8408 (t-90) cc_final: 0.8090 (t-90) REVERT: E 426 MET cc_start: 0.8290 (ptm) cc_final: 0.8077 (ptp) REVERT: F 232 MET cc_start: 0.8335 (mmp) cc_final: 0.7939 (mmp) REVERT: A 631 GLU cc_start: 0.8853 (pp20) cc_final: 0.8319 (pm20) REVERT: A 635 MET cc_start: 0.9493 (tpp) cc_final: 0.9169 (mmm) REVERT: G 322 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8491 (mtm-85) REVERT: G 420 MET cc_start: 0.8959 (pmm) cc_final: 0.8734 (pmm) REVERT: G 592 CYS cc_start: 0.8903 (m) cc_final: 0.8662 (m) outliers start: 34 outliers final: 25 residues processed: 146 average time/residue: 0.1306 time to fit residues: 31.8771 Evaluate side-chains 144 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 199 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 173 optimal weight: 9.9990 chunk 202 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.067095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.046119 restraints weight = 73996.003| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 3.61 r_work: 0.2631 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22172 Z= 0.149 Angle : 0.529 10.296 30258 Z= 0.267 Chirality : 0.038 0.305 3492 Planarity : 0.003 0.040 3603 Dihedral : 16.891 87.210 3578 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.49 % Allowed : 13.30 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.18), residues: 2478 helix: 1.97 (0.14), residues: 1475 sheet: -0.33 (0.34), residues: 228 loop : -0.37 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 231 TYR 0.014 0.001 TYR A 915 PHE 0.010 0.001 PHE E 237 TRP 0.013 0.001 TRP E 276 HIS 0.003 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00340 (22172) covalent geometry : angle 0.52915 (30258) hydrogen bonds : bond 0.03385 ( 1075) hydrogen bonds : angle 3.28706 ( 3059) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9513 (m-40) cc_final: 0.9182 (m110) REVERT: B 432 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9036 (pp) REVERT: B 553 MET cc_start: 0.8428 (ttt) cc_final: 0.8107 (ttt) REVERT: B 562 CYS cc_start: 0.9199 (m) cc_final: 0.8774 (m) REVERT: C 324 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8799 (tm-30) REVERT: C 435 ASN cc_start: 0.9488 (t0) cc_final: 0.9215 (m-40) REVERT: C 699 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8319 (mt-10) REVERT: C 721 TRP cc_start: 0.8532 (p-90) cc_final: 0.8216 (p-90) REVERT: D 131 CYS cc_start: 0.9606 (t) cc_final: 0.9377 (t) REVERT: D 311 HIS cc_start: 0.9286 (OUTLIER) cc_final: 0.8932 (t-90) REVERT: D 347 GLU cc_start: 0.9134 (mp0) cc_final: 0.8676 (mp0) REVERT: D 362 ASP cc_start: 0.9174 (t0) cc_final: 0.8961 (m-30) REVERT: D 389 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8618 (mt-10) REVERT: E 249 LEU cc_start: 0.9261 (mt) cc_final: 0.8996 (tt) REVERT: E 254 CYS cc_start: 0.8040 (m) cc_final: 0.7698 (t) REVERT: E 337 HIS cc_start: 0.8462 (t-90) cc_final: 0.8145 (t-90) REVERT: E 426 MET cc_start: 0.8379 (ptm) cc_final: 0.8161 (ptp) REVERT: A 631 GLU cc_start: 0.8850 (pp20) cc_final: 0.8340 (pm20) REVERT: A 635 MET cc_start: 0.9488 (tpp) cc_final: 0.9162 (mmm) REVERT: G 322 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8823 (mtm110) REVERT: G 420 MET cc_start: 0.8911 (pmm) cc_final: 0.8675 (pmm) REVERT: G 592 CYS cc_start: 0.8910 (m) cc_final: 0.8662 (m) outliers start: 33 outliers final: 28 residues processed: 140 average time/residue: 0.1390 time to fit residues: 32.3794 Evaluate side-chains 144 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 51 optimal weight: 5.9990 chunk 177 optimal weight: 0.0670 chunk 58 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 189 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 241 optimal weight: 7.9990 chunk 147 optimal weight: 0.4980 chunk 195 optimal weight: 0.5980 chunk 157 optimal weight: 0.4980 chunk 96 optimal weight: 0.1980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.068487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.048063 restraints weight = 74178.749| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.64 r_work: 0.2687 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22172 Z= 0.096 Angle : 0.514 8.994 30258 Z= 0.258 Chirality : 0.037 0.293 3492 Planarity : 0.003 0.057 3603 Dihedral : 16.715 87.186 3578 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.35 % Allowed : 13.48 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.18), residues: 2478 helix: 2.06 (0.14), residues: 1474 sheet: -0.12 (0.35), residues: 222 loop : -0.31 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 231 TYR 0.014 0.001 TYR A 915 PHE 0.014 0.001 PHE D 118 TRP 0.014 0.001 TRP E 276 HIS 0.003 0.000 HIS G 629 Details of bonding type rmsd covalent geometry : bond 0.00203 (22172) covalent geometry : angle 0.51353 (30258) hydrogen bonds : bond 0.02942 ( 1075) hydrogen bonds : angle 3.14642 ( 3059) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9491 (m-40) cc_final: 0.9162 (m-40) REVERT: B 432 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8953 (pp) REVERT: B 553 MET cc_start: 0.8367 (ttt) cc_final: 0.8135 (ttt) REVERT: B 562 CYS cc_start: 0.9210 (m) cc_final: 0.8780 (m) REVERT: C 52 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8726 (mm-30) REVERT: C 435 ASN cc_start: 0.9497 (t0) cc_final: 0.9121 (m110) REVERT: C 721 TRP cc_start: 0.8515 (p-90) cc_final: 0.8257 (p-90) REVERT: D 131 CYS cc_start: 0.9584 (t) cc_final: 0.9379 (t) REVERT: D 347 GLU cc_start: 0.9139 (mp0) cc_final: 0.8711 (mp0) REVERT: D 389 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8651 (mt-10) REVERT: E 129 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8609 (pm20) REVERT: E 249 LEU cc_start: 0.9219 (mt) cc_final: 0.8949 (tt) REVERT: E 254 CYS cc_start: 0.7882 (m) cc_final: 0.7645 (t) REVERT: E 426 MET cc_start: 0.8303 (ptm) cc_final: 0.8043 (ptp) REVERT: F 232 MET cc_start: 0.8197 (mmp) cc_final: 0.7565 (mmp) REVERT: A 631 GLU cc_start: 0.8802 (pp20) cc_final: 0.8327 (pm20) REVERT: A 635 MET cc_start: 0.9420 (tpp) cc_final: 0.9043 (mmm) REVERT: G 322 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8492 (mtm-85) REVERT: G 420 MET cc_start: 0.8875 (pmm) cc_final: 0.8629 (pmm) REVERT: G 592 CYS cc_start: 0.8931 (m) cc_final: 0.8660 (m) outliers start: 30 outliers final: 26 residues processed: 147 average time/residue: 0.1318 time to fit residues: 32.2962 Evaluate side-chains 147 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 245 optimal weight: 10.0000 chunk 239 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.066616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.045701 restraints weight = 74276.978| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 3.59 r_work: 0.2621 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22172 Z= 0.186 Angle : 0.571 10.450 30258 Z= 0.285 Chirality : 0.039 0.316 3492 Planarity : 0.003 0.043 3603 Dihedral : 16.750 88.957 3578 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.44 % Allowed : 13.57 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.18), residues: 2478 helix: 2.07 (0.14), residues: 1477 sheet: -0.22 (0.34), residues: 229 loop : -0.27 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 231 TYR 0.017 0.001 TYR A 915 PHE 0.013 0.001 PHE E 237 TRP 0.010 0.001 TRP E 276 HIS 0.004 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00427 (22172) covalent geometry : angle 0.57070 (30258) hydrogen bonds : bond 0.03735 ( 1075) hydrogen bonds : angle 3.30920 ( 3059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4558.71 seconds wall clock time: 78 minutes 53.05 seconds (4733.05 seconds total)