Starting phenix.real_space_refine on Sun Sep 13 07:27:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jk3_22360/09_2026/7jk3_22360.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jk3_22360/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7jk3_22360/09_2026/7jk3_22360.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jk3_22360/09_2026/7jk3_22360.cif" model { file = "/net/cci-nas-00/data/ceres_data/7jk3_22360/09_2026/7jk3_22360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jk3_22360/09_2026/7jk3_22360.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jk3_22360/09_2026/7jk3_22360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jk3_22360/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 4.43, per 1000 atoms: 0.20 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: 1.74 Conformation dependent library (CDL) restraints added in 852.9 milliseconds 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: 2.61 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: 4.43 Time building geometry restraints manager: 2.37 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: 30087 3.96 - 7.92: 144 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: 11445 17.95 - 35.91: 1245 35.91 - 53.86: 441 53.86 - 71.82: 109 71.82 - 89.77: 26 Dihedral angle restraints: 13266 sinusoidal: 5853 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 13263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2456 0.044 - 0.089: 801 0.089 - 0.133: 192 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.020 Find NCS groups from input model: 0.120 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 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= 0.339 Angle : 0.886 19.789 30258 Z= 0.600 Chirality : 0.047 0.222 3492 Planarity : 0.007 0.076 3603 Dihedral : 17.657 89.771 8426 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/Z covalent geometry : bond 0.00480 / 0.34 (22172) covalent geometry : angle 0.88583 / 0.60 (30258) hydrogen bonds : bond 0.13487 / 8.91 ( 1075) hydrogen bonds : angle 6.01061 / 4.11 ( 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 : 0.850 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: 0.1728 time to fit residues: 55.9382 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 : 0.854 ------------------------------------------------------------------------------- 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... B 330 ASN B 348 ASN B 374 HIS B 498 ASN B 577 GLN C 578 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 HIS D 138 HIS D 455 GLN E 414 ASN E 433 GLN A 621 GLN A 718 ASN A 747 HIS A 749 GLN 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.068480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.048309 restraints weight = 73949.644| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.59 r_work: 0.2686 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22172 Z= 0.151 Angle : 0.588 10.483 30258 Z= 0.310 Chirality : 0.040 0.200 3492 Planarity : 0.005 0.055 3603 Dihedral : 17.134 86.700 3454 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.86 % Allowed : 9.74 % Favored : 89.40 % 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: -1.63 (0.15), residues: 2478 helix: -0.51 (0.13), residues: 1473 sheet: -1.44 (0.31), residues: 227 loop : -1.84 (0.19), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 322 TYR 0.012 0.001 TYR C 255 PHE 0.011 0.001 PHE C 668 TRP 0.010 0.001 TRP E 276 HIS 0.006 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (22172) covalent geometry : angle 0.58761 / 0.31 (30258) hydrogen bonds : bond 0.04326 / 2.93 ( 1075) hydrogen bonds : angle 4.09860 / 2.82 ( 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 157 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9508 (m-40) cc_final: 0.9151 (m110) REVERT: B 420 GLU cc_start: 0.9485 (mm-30) cc_final: 0.9234 (tp30) REVERT: B 540 TYR cc_start: 0.8427 (t80) cc_final: 0.7766 (t80) REVERT: B 562 CYS cc_start: 0.9271 (m) cc_final: 0.8839 (p) REVERT: C 324 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8706 (tm-30) REVERT: C 454 LEU cc_start: 0.7682 (tp) cc_final: 0.7414 (tt) REVERT: C 699 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8263 (mt-10) REVERT: D 153 CYS cc_start: 0.9074 (m) cc_final: 0.8818 (m) REVERT: D 347 GLU cc_start: 0.8999 (mp0) cc_final: 0.8608 (mp0) REVERT: D 440 MET cc_start: 0.8952 (mmp) cc_final: 0.8695 (mmm) REVERT: E 1 MET cc_start: 0.7885 (ppp) cc_final: 0.7589 (ppp) REVERT: E 212 LYS cc_start: 0.8896 (tppt) cc_final: 0.8580 (tppt) REVERT: E 249 LEU cc_start: 0.9326 (mt) cc_final: 0.8970 (tt) REVERT: F 224 ASP cc_start: 0.9493 (t0) cc_final: 0.9276 (t70) REVERT: A 622 ASN cc_start: 0.9423 (t0) cc_final: 0.9095 (t0) REVERT: A 631 GLU cc_start: 0.8864 (pp20) cc_final: 0.8463 (pm20) REVERT: G 491 GLU cc_start: 0.8501 (tt0) cc_final: 0.7898 (pt0) REVERT: G 592 CYS cc_start: 0.9130 (m) cc_final: 0.8639 (m) outliers start: 19 outliers final: 11 residues processed: 151 average time/residue: 0.1575 time to fit residues: 38.2971 Evaluate side-chains 135 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU 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 241 LEU 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 382 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: 2.9990 chunk 34 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 368 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 ASN A 809 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.068482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.048061 restraints weight = 74197.954| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.58 r_work: 0.2676 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22172 Z= 0.139 Angle : 0.540 8.431 30258 Z= 0.284 Chirality : 0.039 0.227 3492 Planarity : 0.004 0.051 3603 Dihedral : 16.978 86.627 3454 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.13 % Allowed : 10.46 % Favored : 88.41 % 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: -0.52 (0.16), residues: 2478 helix: 0.41 (0.14), residues: 1467 sheet: -1.17 (0.32), residues: 227 loop : -1.38 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 284 TYR 0.013 0.001 TYR C 255 PHE 0.009 0.001 PHE D 121 TRP 0.010 0.001 TRP E 276 HIS 0.003 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (22172) covalent geometry : angle 0.53952 / 0.28 (30258) hydrogen bonds : bond 0.03934 / 2.68 ( 1075) hydrogen bonds : angle 3.76126 / 2.59 ( 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 155 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9511 (m-40) cc_final: 0.9181 (m110) REVERT: B 420 GLU cc_start: 0.9503 (mm-30) cc_final: 0.9241 (tp30) REVERT: B 562 CYS cc_start: 0.9223 (m) cc_final: 0.8764 (p) REVERT: C 324 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8723 (tm-30) REVERT: C 383 ASP cc_start: 0.9327 (m-30) cc_final: 0.8943 (p0) REVERT: C 454 LEU cc_start: 0.7567 (tp) cc_final: 0.7176 (tt) REVERT: C 699 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8266 (mt-10) REVERT: D 153 CYS cc_start: 0.9161 (m) cc_final: 0.8929 (m) REVERT: D 347 GLU cc_start: 0.9048 (mp0) cc_final: 0.8629 (mp0) REVERT: D 426 MET cc_start: 0.8868 (mmm) cc_final: 0.8608 (mmp) REVERT: E 1 MET cc_start: 0.7873 (ppp) cc_final: 0.7464 (ppp) REVERT: E 249 LEU cc_start: 0.9335 (mt) cc_final: 0.8959 (tt) REVERT: E 254 CYS cc_start: 0.8076 (m) cc_final: 0.7682 (t) REVERT: F 224 ASP cc_start: 0.9490 (t0) cc_final: 0.9278 (t70) REVERT: A 622 ASN cc_start: 0.9441 (t0) cc_final: 0.9158 (t0) REVERT: A 631 GLU cc_start: 0.8835 (pp20) cc_final: 0.8424 (pm20) REVERT: G 491 GLU cc_start: 0.8565 (tt0) cc_final: 0.7930 (pt0) REVERT: G 592 CYS cc_start: 0.9016 (m) cc_final: 0.8595 (m) outliers start: 25 outliers final: 14 residues processed: 146 average time/residue: 0.1466 time to fit residues: 35.1131 Evaluate side-chains 136 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 373 LYS Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 241 LEU 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 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: 5.9990 chunk 203 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 chunk 173 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 HIS C 715 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 = 0.3380 r_free = 0.3380 target = 0.067357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.046959 restraints weight = 74414.871| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.55 r_work: 0.2651 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22172 Z= 0.178 Angle : 0.557 10.259 30258 Z= 0.286 Chirality : 0.040 0.377 3492 Planarity : 0.003 0.047 3603 Dihedral : 16.922 86.172 3454 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.13 % Allowed : 11.95 % Favored : 86.93 % 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: 0.23 (0.17), residues: 2478 helix: 1.01 (0.14), residues: 1480 sheet: -0.96 (0.33), residues: 228 loop : -1.07 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 675 TYR 0.021 0.001 TYR B 540 PHE 0.010 0.001 PHE E 237 TRP 0.012 0.001 TRP E 276 HIS 0.004 0.001 HIS D 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (22172) covalent geometry : angle 0.55700 / 0.29 (30258) hydrogen bonds : bond 0.03988 / 2.71 ( 1075) hydrogen bonds : angle 3.60745 / 2.49 ( 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 148 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9521 (m-40) cc_final: 0.9205 (m110) REVERT: B 420 GLU cc_start: 0.9529 (mm-30) cc_final: 0.9261 (tp30) REVERT: B 562 CYS cc_start: 0.9222 (m) cc_final: 0.8898 (m) REVERT: C 185 MET cc_start: 0.8226 (mmm) cc_final: 0.7970 (mmm) REVERT: C 324 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8772 (tm-30) REVERT: C 353 MET cc_start: 0.9107 (mmt) cc_final: 0.8743 (mmm) REVERT: C 454 LEU cc_start: 0.7447 (tp) cc_final: 0.7230 (tt) REVERT: C 699 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8275 (mt-10) REVERT: D 131 CYS cc_start: 0.9701 (t) cc_final: 0.9368 (t) REVERT: D 153 CYS cc_start: 0.9196 (m) cc_final: 0.8918 (m) REVERT: D 347 GLU cc_start: 0.9061 (mp0) cc_final: 0.8592 (mp0) REVERT: E 1 MET cc_start: 0.7957 (ppp) cc_final: 0.7527 (ppp) REVERT: E 249 LEU cc_start: 0.9322 (mt) cc_final: 0.8966 (tt) REVERT: E 254 CYS cc_start: 0.8082 (m) cc_final: 0.7689 (t) REVERT: F 224 ASP cc_start: 0.9493 (t0) cc_final: 0.9274 (t70) REVERT: A 622 ASN cc_start: 0.9428 (t0) cc_final: 0.9187 (t0) REVERT: A 628 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8025 (tm-30) REVERT: G 420 MET cc_start: 0.8955 (pmm) cc_final: 0.8723 (pmm) REVERT: G 491 GLU cc_start: 0.8515 (tt0) cc_final: 0.7892 (pt0) REVERT: G 592 CYS cc_start: 0.8960 (m) cc_final: 0.8661 (m) outliers start: 25 outliers final: 19 residues processed: 142 average time/residue: 0.1475 time to fit residues: 34.0364 Evaluate side-chains 135 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 652 HIS 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 810 VAL Chi-restraints excluded: chain A residue 868 MET 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 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: 4.9990 chunk 64 optimal weight: 3.9990 chunk 241 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 240 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 187 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 652 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.067386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.046143 restraints weight = 74139.100| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 3.65 r_work: 0.2620 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22172 Z= 0.173 Angle : 0.552 13.171 30258 Z= 0.281 Chirality : 0.040 0.311 3492 Planarity : 0.003 0.045 3603 Dihedral : 16.910 85.161 3454 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.67 % Allowed : 12.17 % Favored : 86.16 % 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: 0.54 (0.17), residues: 2478 helix: 1.26 (0.14), residues: 1481 sheet: -0.87 (0.33), residues: 228 loop : -0.94 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 374 TYR 0.014 0.001 TYR C 255 PHE 0.010 0.001 PHE E 237 TRP 0.012 0.001 TRP E 276 HIS 0.012 0.001 HIS C 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (22172) covalent geometry : angle 0.55225 / 0.28 (30258) hydrogen bonds : bond 0.03854 / 2.63 ( 1075) hydrogen bonds : angle 3.54834 / 2.46 ( 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 155 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9531 (m-40) cc_final: 0.9205 (m110) REVERT: B 393 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8950 (ptt) REVERT: B 420 GLU cc_start: 0.9556 (mm-30) cc_final: 0.9280 (tp30) REVERT: B 553 MET cc_start: 0.8804 (mmm) cc_final: 0.8312 (mmm) REVERT: B 562 CYS cc_start: 0.9184 (m) cc_final: 0.8826 (m) REVERT: C 185 MET cc_start: 0.8324 (mmm) cc_final: 0.7875 (mmm) REVERT: C 324 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8792 (tm-30) REVERT: C 353 MET cc_start: 0.9157 (mmt) cc_final: 0.8823 (mmm) REVERT: C 699 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8324 (mt-10) REVERT: D 131 CYS cc_start: 0.9675 (t) cc_final: 0.9361 (t) REVERT: D 153 CYS cc_start: 0.9163 (m) cc_final: 0.8885 (m) REVERT: D 347 GLU cc_start: 0.9115 (mp0) cc_final: 0.8642 (mp0) REVERT: E 1 MET cc_start: 0.7993 (ppp) cc_final: 0.7533 (ppp) REVERT: E 249 LEU cc_start: 0.9300 (mt) cc_final: 0.8974 (tt) REVERT: E 254 CYS cc_start: 0.8042 (m) cc_final: 0.7643 (t) REVERT: E 276 TRP cc_start: 0.8291 (t-100) cc_final: 0.7902 (t-100) REVERT: F 224 ASP cc_start: 0.9483 (t0) cc_final: 0.9239 (t70) REVERT: F 232 MET cc_start: 0.8576 (mmp) cc_final: 0.8119 (mmp) REVERT: A 622 ASN cc_start: 0.9452 (t0) cc_final: 0.9238 (t0) REVERT: A 628 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7962 (tm-30) REVERT: G 420 MET cc_start: 0.8961 (pmm) cc_final: 0.8695 (pmm) REVERT: G 491 GLU cc_start: 0.8577 (tt0) cc_final: 0.7930 (pt0) REVERT: G 592 CYS cc_start: 0.8867 (m) cc_final: 0.8587 (m) outliers start: 37 outliers final: 20 residues processed: 148 average time/residue: 0.1470 time to fit residues: 35.2770 Evaluate side-chains 135 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 MET 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 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 439 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 348 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 18 optimal weight: 0.0870 chunk 241 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 225 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.068241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.047802 restraints weight = 73648.427| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.57 r_work: 0.2673 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.2069 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= 0.100 Angle : 0.506 10.488 30258 Z= 0.261 Chirality : 0.038 0.191 3492 Planarity : 0.003 0.046 3603 Dihedral : 16.854 84.166 3454 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.35 % Allowed : 12.53 % Favored : 86.11 % 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: 0.89 (0.17), residues: 2478 helix: 1.54 (0.14), residues: 1468 sheet: -0.72 (0.34), residues: 228 loop : -0.76 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 374 TYR 0.014 0.001 TYR A 915 PHE 0.010 0.001 PHE E 237 TRP 0.007 0.001 TRP A 658 HIS 0.003 0.001 HIS D 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (22172) covalent geometry : angle 0.50624 / 0.26 (30258) hydrogen bonds : bond 0.03437 / 2.38 ( 1075) hydrogen bonds : angle 3.37052 / 2.33 ( 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: 30 poor density : 131 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 285 HIS cc_start: 0.9356 (OUTLIER) cc_final: 0.9094 (m90) REVERT: B 330 ASN cc_start: 0.9505 (m-40) cc_final: 0.9185 (m110) REVERT: B 420 GLU cc_start: 0.9479 (mm-30) cc_final: 0.9254 (tp30) REVERT: B 432 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8996 (pp) REVERT: B 553 MET cc_start: 0.8854 (mmm) cc_final: 0.8521 (mmm) REVERT: B 562 CYS cc_start: 0.9207 (m) cc_final: 0.8864 (m) REVERT: C 185 MET cc_start: 0.8271 (mmm) cc_final: 0.7820 (mmm) REVERT: C 324 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8716 (tm-30) REVERT: C 353 MET cc_start: 0.9119 (mmt) cc_final: 0.8663 (mmm) REVERT: C 374 ARG cc_start: 0.8835 (ttp80) cc_final: 0.8601 (ttp-110) REVERT: C 383 ASP cc_start: 0.9282 (m-30) cc_final: 0.8926 (p0) REVERT: C 435 ASN cc_start: 0.9460 (t0) cc_final: 0.8962 (p0) REVERT: C 699 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8261 (mt-10) REVERT: D 131 CYS cc_start: 0.9652 (t) cc_final: 0.9351 (t) REVERT: D 153 CYS cc_start: 0.9125 (m) cc_final: 0.8873 (m) REVERT: D 347 GLU cc_start: 0.9080 (mp0) cc_final: 0.8615 (mm-30) REVERT: D 362 ASP cc_start: 0.9191 (t0) cc_final: 0.8962 (m-30) REVERT: E 1 MET cc_start: 0.7934 (ppp) cc_final: 0.7547 (ppp) REVERT: E 249 LEU cc_start: 0.9306 (mt) cc_final: 0.8978 (tt) REVERT: E 254 CYS cc_start: 0.8000 (m) cc_final: 0.7665 (t) REVERT: E 276 TRP cc_start: 0.8311 (t-100) cc_final: 0.7901 (t-100) REVERT: F 224 ASP cc_start: 0.9480 (t0) cc_final: 0.9230 (t0) REVERT: F 232 MET cc_start: 0.8533 (mmp) cc_final: 0.8237 (mmm) REVERT: A 622 ASN cc_start: 0.9398 (t0) cc_final: 0.9172 (t0) REVERT: A 628 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7662 (tm-30) REVERT: G 420 MET cc_start: 0.8961 (pmm) cc_final: 0.8682 (pmm) REVERT: G 491 GLU cc_start: 0.8538 (tt0) cc_final: 0.7905 (pt0) REVERT: G 592 CYS cc_start: 0.8907 (m) cc_final: 0.8613 (m) outliers start: 30 outliers final: 21 residues processed: 155 average time/residue: 0.1410 time to fit residues: 35.5051 Evaluate side-chains 144 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 HIS 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 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 393 LEU 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 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 G residue 340 LEU 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: 0.9990 chunk 38 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 249 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 227 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 223 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.068036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.046989 restraints weight = 73147.921| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.62 r_work: 0.2654 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22172 Z= 0.116 Angle : 0.519 10.027 30258 Z= 0.265 Chirality : 0.039 0.280 3492 Planarity : 0.003 0.044 3603 Dihedral : 16.798 83.195 3454 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.49 % Allowed : 12.85 % Favored : 85.66 % 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: 1.05 (0.17), residues: 2478 helix: 1.64 (0.14), residues: 1470 sheet: -0.60 (0.34), residues: 228 loop : -0.64 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 231 TYR 0.013 0.001 TYR A 915 PHE 0.009 0.001 PHE E 237 TRP 0.007 0.001 TRP C 57 HIS 0.003 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (22172) covalent geometry : angle 0.51916 / 0.26 (30258) hydrogen bonds : bond 0.03423 / 2.35 ( 1075) hydrogen bonds : angle 3.35317 / 2.32 ( 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 163 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 285 HIS cc_start: 0.9327 (OUTLIER) cc_final: 0.9069 (m90) REVERT: B 330 ASN cc_start: 0.9514 (m-40) cc_final: 0.9187 (m110) REVERT: B 420 GLU cc_start: 0.9569 (mm-30) cc_final: 0.9300 (tp30) REVERT: B 432 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8964 (pp) REVERT: B 553 MET cc_start: 0.8905 (mmm) cc_final: 0.8468 (mmm) REVERT: B 562 CYS cc_start: 0.9214 (m) cc_final: 0.8876 (m) REVERT: C 185 MET cc_start: 0.8354 (mmm) cc_final: 0.8095 (mmm) REVERT: C 324 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8727 (tm-30) REVERT: C 353 MET cc_start: 0.9113 (mmt) cc_final: 0.8790 (mmm) REVERT: C 383 ASP cc_start: 0.9253 (m-30) cc_final: 0.8949 (p0) REVERT: C 435 ASN cc_start: 0.9485 (t0) cc_final: 0.9129 (m110) REVERT: C 699 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8303 (mt-10) REVERT: D 131 CYS cc_start: 0.9632 (t) cc_final: 0.9340 (t) REVERT: D 153 CYS cc_start: 0.9176 (m) cc_final: 0.8912 (m) REVERT: D 347 GLU cc_start: 0.9112 (mp0) cc_final: 0.8638 (mm-30) REVERT: D 362 ASP cc_start: 0.9210 (t0) cc_final: 0.8966 (m-30) REVERT: E 1 MET cc_start: 0.7906 (ppp) cc_final: 0.7505 (ppp) REVERT: E 249 LEU cc_start: 0.9304 (mt) cc_final: 0.8991 (tt) REVERT: E 254 CYS cc_start: 0.7999 (m) cc_final: 0.7655 (t) REVERT: E 276 TRP cc_start: 0.8346 (t-100) cc_final: 0.7977 (t-100) REVERT: E 337 HIS cc_start: 0.8405 (t-90) cc_final: 0.8075 (t-90) REVERT: F 224 ASP cc_start: 0.9461 (t0) cc_final: 0.9221 (t0) REVERT: F 232 MET cc_start: 0.8611 (mmp) cc_final: 0.8253 (mmm) REVERT: A 622 ASN cc_start: 0.9417 (t0) cc_final: 0.9216 (t0) REVERT: G 420 MET cc_start: 0.8966 (pmm) cc_final: 0.8675 (pmm) REVERT: G 491 GLU cc_start: 0.8588 (tt0) cc_final: 0.7926 (pt0) REVERT: G 592 CYS cc_start: 0.8860 (m) cc_final: 0.8593 (m) outliers start: 33 outliers final: 25 residues processed: 155 average time/residue: 0.1491 time to fit residues: 37.4084 Evaluate side-chains 154 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 HIS 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 373 LYS Chi-restraints excluded: chain C residue 393 LEU 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 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 908 VAL 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: 6.9990 chunk 44 optimal weight: 0.7980 chunk 120 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 221 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 249 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 133 GLN C 580 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.068135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.047326 restraints weight = 73251.010| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.62 r_work: 0.2653 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.2258 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= 0.101 Angle : 0.514 9.771 30258 Z= 0.262 Chirality : 0.038 0.196 3492 Planarity : 0.003 0.043 3603 Dihedral : 16.750 82.174 3454 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.35 % Allowed : 13.53 % Favored : 85.12 % 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: 1.22 (0.17), residues: 2478 helix: 1.74 (0.14), residues: 1471 sheet: -0.46 (0.34), residues: 228 loop : -0.53 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 675 TYR 0.024 0.001 TYR B 540 PHE 0.034 0.001 PHE C 290 TRP 0.007 0.001 TRP A 658 HIS 0.003 0.000 HIS G 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (22172) covalent geometry : angle 0.51410 / 0.26 (30258) hydrogen bonds : bond 0.03295 / 2.28 ( 1075) hydrogen bonds : angle 3.30379 / 2.28 ( 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 162 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 285 HIS cc_start: 0.9377 (OUTLIER) cc_final: 0.9118 (m90) REVERT: B 330 ASN cc_start: 0.9505 (m-40) cc_final: 0.9177 (m110) REVERT: B 420 GLU cc_start: 0.9586 (mm-30) cc_final: 0.9328 (tp30) REVERT: B 432 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8966 (pp) REVERT: B 562 CYS cc_start: 0.9188 (m) cc_final: 0.8819 (m) REVERT: C 185 MET cc_start: 0.8324 (mmm) cc_final: 0.8043 (mmm) REVERT: C 324 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8715 (tm-30) REVERT: C 353 MET cc_start: 0.9125 (mmt) cc_final: 0.8823 (mmm) REVERT: C 383 ASP cc_start: 0.9276 (m-30) cc_final: 0.8975 (p0) REVERT: C 435 ASN cc_start: 0.9474 (t0) cc_final: 0.9108 (m110) REVERT: C 699 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8264 (mt-10) REVERT: D 116 LYS cc_start: 0.8967 (ttpt) cc_final: 0.8739 (tptt) REVERT: D 131 CYS cc_start: 0.9607 (t) cc_final: 0.9345 (t) REVERT: D 153 CYS cc_start: 0.9139 (m) cc_final: 0.8931 (m) REVERT: D 347 GLU cc_start: 0.9134 (mp0) cc_final: 0.8700 (mp0) REVERT: D 362 ASP cc_start: 0.9225 (t0) cc_final: 0.8984 (m-30) REVERT: E 1 MET cc_start: 0.7917 (ppp) cc_final: 0.7526 (ppp) REVERT: E 249 LEU cc_start: 0.9278 (mt) cc_final: 0.8965 (tt) REVERT: E 254 CYS cc_start: 0.7972 (m) cc_final: 0.7655 (t) REVERT: E 276 TRP cc_start: 0.8350 (t-100) cc_final: 0.8105 (t-100) REVERT: E 337 HIS cc_start: 0.8393 (t-90) cc_final: 0.8066 (t-90) REVERT: F 224 ASP cc_start: 0.9476 (t0) cc_final: 0.9222 (t0) REVERT: F 232 MET cc_start: 0.8623 (mmp) cc_final: 0.8181 (mmp) REVERT: A 855 MET cc_start: 0.9439 (mmp) cc_final: 0.9070 (mmp) REVERT: A 900 LEU cc_start: 0.9308 (mp) cc_final: 0.9102 (tt) REVERT: G 420 MET cc_start: 0.8951 (pmm) cc_final: 0.8644 (pmm) REVERT: G 491 GLU cc_start: 0.8539 (tt0) cc_final: 0.7910 (pt0) REVERT: G 592 CYS cc_start: 0.8859 (m) cc_final: 0.8590 (m) outliers start: 30 outliers final: 22 residues processed: 157 average time/residue: 0.1398 time to fit residues: 35.8652 Evaluate side-chains 152 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain B residue 432 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 393 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 597 SER 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 564 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 908 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 199 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 189 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 chunk 202 optimal weight: 0.0040 chunk 83 optimal weight: 2.9990 chunk 158 optimal weight: 0.5980 chunk 172 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.068147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.047331 restraints weight = 73107.280| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.62 r_work: 0.2653 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22172 Z= 0.103 Angle : 0.516 10.830 30258 Z= 0.263 Chirality : 0.038 0.292 3492 Planarity : 0.003 0.043 3603 Dihedral : 16.700 81.088 3454 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.35 % Allowed : 13.53 % Favored : 85.12 % 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: 1.34 (0.18), residues: 2478 helix: 1.83 (0.14), residues: 1471 sheet: -0.38 (0.35), residues: 223 loop : -0.46 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 675 TYR 0.021 0.001 TYR B 540 PHE 0.009 0.001 PHE E 237 TRP 0.007 0.001 TRP A 658 HIS 0.005 0.001 HIS C 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (22172) covalent geometry : angle 0.51626 / 0.26 (30258) hydrogen bonds : bond 0.03241 / 2.25 ( 1075) hydrogen bonds : angle 3.26862 / 2.26 ( 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 157 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 285 HIS cc_start: 0.9403 (OUTLIER) cc_final: 0.9140 (m90) REVERT: B 330 ASN cc_start: 0.9512 (m-40) cc_final: 0.9176 (m-40) REVERT: B 432 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8958 (pp) REVERT: B 553 MET cc_start: 0.8880 (mmm) cc_final: 0.8286 (mmm) REVERT: B 562 CYS cc_start: 0.9175 (m) cc_final: 0.8806 (m) REVERT: C 185 MET cc_start: 0.8347 (mmm) cc_final: 0.8043 (mmm) REVERT: C 324 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8715 (tm-30) REVERT: C 353 MET cc_start: 0.9124 (mmt) cc_final: 0.8732 (mmm) REVERT: C 383 ASP cc_start: 0.9279 (m-30) cc_final: 0.8982 (p0) REVERT: C 435 ASN cc_start: 0.9471 (t0) cc_final: 0.9105 (m110) REVERT: C 699 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8266 (mt-10) REVERT: D 116 LYS cc_start: 0.8937 (ttpt) cc_final: 0.8713 (tptt) REVERT: D 131 CYS cc_start: 0.9593 (t) cc_final: 0.9344 (t) REVERT: D 153 CYS cc_start: 0.9132 (m) cc_final: 0.8923 (m) REVERT: D 347 GLU cc_start: 0.9153 (mp0) cc_final: 0.8716 (mp0) REVERT: D 362 ASP cc_start: 0.9235 (t0) cc_final: 0.8990 (m-30) REVERT: E 1 MET cc_start: 0.7922 (ppp) cc_final: 0.7542 (ppp) REVERT: E 249 LEU cc_start: 0.9256 (mt) cc_final: 0.8960 (tt) REVERT: E 254 CYS cc_start: 0.7916 (m) cc_final: 0.7646 (t) REVERT: E 337 HIS cc_start: 0.8398 (t-90) cc_final: 0.8073 (t-90) REVERT: F 224 ASP cc_start: 0.9480 (t0) cc_final: 0.9230 (t0) REVERT: F 232 MET cc_start: 0.8642 (mmp) cc_final: 0.7998 (mmp) REVERT: G 420 MET cc_start: 0.8942 (pmm) cc_final: 0.8628 (pmm) REVERT: G 491 GLU cc_start: 0.8547 (tt0) cc_final: 0.7915 (pt0) REVERT: G 592 CYS cc_start: 0.8848 (m) cc_final: 0.8577 (m) outliers start: 30 outliers final: 27 residues processed: 151 average time/residue: 0.1471 time to fit residues: 36.4741 Evaluate side-chains 154 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 HIS 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 393 LEU 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 597 SER 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 217 CYS Chi-restraints excluded: chain E residue 262 VAL 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 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: 3.9990 chunk 177 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 11 optimal weight: 0.3980 chunk 189 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 241 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 195 optimal weight: 0.3980 chunk 157 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.068417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.047683 restraints weight = 73299.452| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.62 r_work: 0.2666 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2425 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= 0.097 Angle : 0.513 9.750 30258 Z= 0.260 Chirality : 0.038 0.282 3492 Planarity : 0.003 0.043 3603 Dihedral : 16.641 79.586 3454 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.40 % Allowed : 13.62 % 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: 1.46 (0.18), residues: 2478 helix: 1.92 (0.14), residues: 1474 sheet: -0.31 (0.35), residues: 223 loop : -0.43 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 675 TYR 0.020 0.001 TYR B 540 PHE 0.010 0.001 PHE D 118 TRP 0.041 0.001 TRP E 276 HIS 0.004 0.001 HIS E 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (22172) covalent geometry : angle 0.51269 / 0.26 (30258) hydrogen bonds : bond 0.03164 / 2.20 ( 1075) hydrogen bonds : angle 3.23268 / 2.23 ( 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 157 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.851 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 285 HIS cc_start: 0.9390 (OUTLIER) cc_final: 0.9130 (m90) REVERT: B 330 ASN cc_start: 0.9508 (m-40) cc_final: 0.9183 (m-40) REVERT: B 432 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8958 (pp) REVERT: B 553 MET cc_start: 0.8946 (mmm) cc_final: 0.8326 (mmm) REVERT: B 562 CYS cc_start: 0.9176 (m) cc_final: 0.8802 (m) REVERT: C 52 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8740 (mm-30) REVERT: C 185 MET cc_start: 0.8316 (mmm) cc_final: 0.8007 (mmm) REVERT: C 324 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8665 (tm-30) REVERT: C 353 MET cc_start: 0.9101 (mmt) cc_final: 0.8741 (mmm) REVERT: C 383 ASP cc_start: 0.9281 (m-30) cc_final: 0.8973 (p0) REVERT: C 699 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8247 (mt-10) REVERT: D 131 CYS cc_start: 0.9581 (t) cc_final: 0.9350 (t) REVERT: D 153 CYS cc_start: 0.9137 (m) cc_final: 0.8930 (m) REVERT: D 347 GLU cc_start: 0.9139 (mp0) cc_final: 0.8710 (mp0) REVERT: D 362 ASP cc_start: 0.9214 (t0) cc_final: 0.8987 (m-30) REVERT: E 1 MET cc_start: 0.7915 (ppp) cc_final: 0.7563 (ppp) REVERT: E 249 LEU cc_start: 0.9239 (mt) cc_final: 0.8971 (tt) REVERT: E 254 CYS cc_start: 0.7905 (m) cc_final: 0.7648 (t) REVERT: E 337 HIS cc_start: 0.8405 (t-90) cc_final: 0.8083 (t-90) REVERT: F 224 ASP cc_start: 0.9474 (t0) cc_final: 0.9225 (t0) REVERT: F 232 MET cc_start: 0.8622 (mmp) cc_final: 0.8386 (mmm) REVERT: G 420 MET cc_start: 0.8953 (pmm) cc_final: 0.8631 (pmm) REVERT: G 491 GLU cc_start: 0.8534 (tt0) cc_final: 0.7872 (pt0) REVERT: G 592 CYS cc_start: 0.8905 (m) cc_final: 0.8614 (m) outliers start: 31 outliers final: 25 residues processed: 152 average time/residue: 0.1455 time to fit residues: 36.4769 Evaluate side-chains 150 residues out of total 2219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 HIS Chi-restraints excluded: chain B residue 432 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 410 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 597 SER 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 217 CYS Chi-restraints excluded: chain E residue 262 VAL 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 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 245 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 0.4980 chunk 112 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 146 optimal weight: 0.0060 overall best weight: 3.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 230 HIS C 660 ASN G 573 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.067066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.046102 restraints weight = 74364.839| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 3.61 r_work: 0.2627 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22172 Z= 0.180 Angle : 0.564 11.353 30258 Z= 0.283 Chirality : 0.039 0.266 3492 Planarity : 0.003 0.040 3603 Dihedral : 16.656 78.496 3454 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.17 % Allowed : 13.93 % Favored : 84.90 % 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: 1.51 (0.18), residues: 2478 helix: 1.98 (0.14), residues: 1471 sheet: -0.41 (0.34), residues: 229 loop : -0.40 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 231 TYR 0.019 0.001 TYR B 540 PHE 0.011 0.001 PHE E 237 TRP 0.024 0.001 TRP E 276 HIS 0.004 0.001 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (22172) covalent geometry : angle 0.56372 / 0.28 (30258) hydrogen bonds : bond 0.03653 / 2.51 ( 1075) hydrogen bonds : angle 3.35874 / 2.32 ( 3059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4454.39 seconds wall clock time: 77 minutes 31.59 seconds (4651.59 seconds total)