Starting phenix.real_space_refine on Sat Sep 12 10:44:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jk6_22363/09_2026/7jk6_22363.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jk6_22363/09_2026/7jk6_22363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jk6_22363/09_2026/7jk6_22363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jk6_22363/09_2026/7jk6_22363.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jk6_22363/09_2026/7jk6_22363.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jk6_22363/09_2026/7jk6_22363.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jk6_22363/09_2026/7jk6_22363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jk6_22363/09_2026/7jk6_22363.map" } resolution = 4.0 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= 0.001 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 9 5.49 5 Mg 3 5.21 5 S 82 5.16 5 C 9657 2.51 5 N 2638 2.21 5 O 2772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s 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: 15161 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3528 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 11, 'TRANS': 426} Chain breaks: 3 Chain: "E" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2974 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 11, 'TRANS': 362} Chain breaks: 5 Chain: "A" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2919 Classifications: {'peptide': 373} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 357} Chain breaks: 1 Chain: "B" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1328 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 1 Chain: "C" Number of atoms: 4173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4173 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 20, 'TRANS': 499} Chain breaks: 6 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: "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} Time building chain proxies: 3.05, per 1000 atoms: 0.20 Number of scatterers: 15161 At special positions: 0 Unit cell: (110.94, 149.64, 116.1, 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 82 16.00 P 9 15.00 Mg 3 11.99 O 2772 8.00 N 2638 7.00 C 9657 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 661.9 milliseconds 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3614 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 9 sheets defined 66.6% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'D' and resid 2 through 21 removed outlier: 3.607A pdb=" N ARG D 6 " --> pdb=" O PRO D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 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 Processing helix chain 'D' and resid 120 through 134 Processing helix chain 'D' and resid 148 through 153 removed outlier: 3.631A pdb=" N PHE D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 157 removed outlier: 6.237A pdb=" N ASN D 157 " --> pdb=" O ALA D 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 154 through 157' Processing helix chain 'D' and resid 158 through 167 Processing helix chain 'D' and resid 185 through 189 Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 211 through 224 removed outlier: 3.510A pdb=" N TYR D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 244 removed outlier: 3.986A pdb=" N ILE D 244 " --> pdb=" O ASN D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 removed outlier: 4.260A pdb=" N ARG D 253 " --> pdb=" O TYR D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 261 removed outlier: 3.983A pdb=" N GLU D 260 " --> pdb=" O ASP D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 281 removed outlier: 3.654A pdb=" N THR D 281 " --> pdb=" O LYS D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 295 Processing helix chain 'D' and resid 297 through 310 removed outlier: 3.577A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 333 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: 3.746A pdb=" N PHE D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 403 removed outlier: 3.504A pdb=" N VAL D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 443 removed outlier: 3.694A pdb=" N ILE D 436 " --> pdb=" O THR D 432 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN D 441 " --> pdb=" O HIS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 456 removed outlier: 3.590A pdb=" N GLN D 455 " --> pdb=" O ALA D 451 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 456 " --> pdb=" O GLN D 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 Proline residue: E 10 - end of helix Processing helix chain 'E' and resid 15 through 26 Processing helix chain 'E' and resid 47 through 62 Processing helix chain 'E' and resid 76 through 89 removed outlier: 3.774A pdb=" N MET E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 removed outlier: 3.821A pdb=" N ALA E 95 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU E 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 96' Processing helix chain 'E' and resid 100 through 110 Processing helix chain 'E' and resid 114 through 118 removed outlier: 3.846A pdb=" N GLU E 117 " --> pdb=" O THR E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 134 removed outlier: 4.018A pdb=" N ARG E 132 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET E 134 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 143 removed outlier: 3.695A pdb=" N VAL E 141 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'E' and resid 162 through 167 removed outlier: 3.996A pdb=" N TYR E 167 " --> pdb=" O GLU E 164 " (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 219 Processing helix chain 'E' and resid 222 through 238 Processing helix chain 'E' and resid 243 through 259 removed outlier: 3.888A pdb=" N LYS E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 289 Proline residue: E 282 - end of helix removed outlier: 3.626A pdb=" N SER E 285 " --> pdb=" O GLY E 281 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR E 288 " --> pdb=" O ARG E 284 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN E 289 " --> pdb=" O SER E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 337 Processing helix chain 'E' and resid 381 through 394 removed outlier: 3.955A pdb=" N GLU E 394 " --> pdb=" O TYR E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 413 removed outlier: 3.863A pdb=" N LEU E 404 " --> pdb=" O THR E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 449 removed outlier: 3.688A pdb=" N VAL E 441 " --> pdb=" O GLY E 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 549 removed outlier: 3.508A pdb=" N SER A 548 " --> pdb=" O LYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 571 through 589 Processing helix chain 'A' and resid 603 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 642 through 652 removed outlier: 3.734A pdb=" N TYR A 648 " --> pdb=" O TYR A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 671 removed outlier: 3.834A pdb=" N THR A 671 " --> pdb=" O LYS A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 691 removed outlier: 4.352A pdb=" N LEU A 689 " --> pdb=" O GLU A 685 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 703 Processing helix chain 'A' and resid 746 through 759 removed outlier: 3.748A pdb=" N VAL A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 778 removed outlier: 3.747A pdb=" N VAL A 769 " --> pdb=" O LYS A 765 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 800 removed outlier: 3.880A pdb=" N ALA A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 818 removed outlier: 3.588A pdb=" N VAL A 810 " --> pdb=" O THR A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 829 Processing helix chain 'A' and resid 830 through 848 removed outlier: 3.679A pdb=" N ALA A 841 " --> pdb=" O LEU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 869 Processing helix chain 'A' and resid 874 through 888 removed outlier: 4.294A pdb=" N ARG A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 918 removed outlier: 3.873A pdb=" N ILE A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 Processing helix chain 'B' and resid 339 through 349 removed outlier: 3.767A pdb=" N GLU B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 372 Processing helix chain 'B' and resid 389 through 401 Processing helix chain 'B' and resid 410 through 424 Processing helix chain 'B' and resid 444 through 456 Processing helix chain 'B' and resid 471 through 475 removed outlier: 3.598A pdb=" N LEU B 474 " --> pdb=" O THR B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 483 Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.623A pdb=" N VAL C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 89 removed outlier: 3.669A pdb=" N GLU C 51 " --> pdb=" O GLN C 47 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ARG C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N THR C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 109 removed outlier: 3.962A pdb=" N ASP C 109 " --> pdb=" O ASN C 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 106 through 109' Processing helix chain 'C' and resid 110 through 124 Processing helix chain 'C' and resid 133 through 137 Processing helix chain 'C' and resid 139 through 159 Processing helix chain 'C' and resid 179 through 183 removed outlier: 3.581A 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 211 through 215 removed outlier: 3.640A pdb=" N PHE C 215 " --> pdb=" O PHE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 230 removed outlier: 3.578A pdb=" N HIS C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 253 removed outlier: 3.780A 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 removed outlier: 3.578A pdb=" N PHE C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 335 removed outlier: 3.554A pdb=" N CYS C 335 " --> pdb=" O PHE C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 361 through 368 removed outlier: 3.971A pdb=" N TYR C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 380 Processing helix chain 'C' and resid 382 through 416 Proline residue: C 390 - end of helix Processing helix chain 'C' and resid 425 through 436 Processing helix chain 'C' and resid 441 through 453 Processing helix chain 'C' and resid 455 through 477 Processing helix chain 'C' and resid 484 through 508 Proline residue: C 493 - end of helix Processing helix chain 'C' and resid 563 through 576 Processing helix chain 'C' and resid 576 through 581 removed outlier: 3.501A pdb=" N LEU C 581 " --> pdb=" O VAL C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 587 Processing helix chain 'C' and resid 590 through 594 Processing helix chain 'C' and resid 598 through 607 removed outlier: 4.234A pdb=" N VAL C 602 " --> pdb=" O ASP C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 620 removed outlier: 3.509A pdb=" N ASN C 620 " --> pdb=" O THR C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'F' and resid 224 through 238 Processing sheet with id=AA1, first strand: chain 'D' and resid 50 through 54 removed outlier: 6.923A pdb=" N VAL D 142 " --> pdb=" O CYS D 176 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N LEU D 178 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE D 144 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL D 180 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU D 146 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 406 through 408 Processing sheet with id=AA3, first strand: chain 'E' and resid 65 through 70 removed outlier: 6.292A pdb=" N ARG E 65 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ALA E 124 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA E 67 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASP E 126 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU E 69 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER E 159 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY E 41 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA E 36 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU E 178 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR E 38 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU E 180 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE E 40 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 379 through 380 Processing sheet with id=AA5, first strand: chain 'A' and resid 628 through 633 removed outlier: 6.773A pdb=" N GLU A 628 " --> pdb=" O VAL A 680 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU A 682 " --> pdb=" O GLU A 628 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU A 630 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N ASP A 684 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE A 632 " --> pdb=" O ASP A 684 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR A 679 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL A 714 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 681 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE A 716 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL A 683 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N LEU A 740 " --> pdb=" O CYS A 593 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYR A 595 " --> pdb=" O LEU A 740 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 852 through 853 Processing sheet with id=AA7, first strand: chain 'B' and resid 485 through 488 removed outlier: 6.443A pdb=" N ASN B 352 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TRP B 488 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU B 354 " --> pdb=" O TRP B 488 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 378 " --> pdb=" O TYR C 14 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 102 removed outlier: 3.613A pdb=" N ARG C 262 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR C 98 " --> pdb=" O ARG C 262 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 127 through 131 removed outlier: 3.632A pdb=" N VAL C 237 " --> pdb=" O LEU C 205 " (cutoff:3.500A) 835 hydrogen bonds defined for protein. 2433 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4802 1.34 - 1.46: 3285 1.46 - 1.58: 7212 1.58 - 1.71: 16 1.71 - 1.83: 118 Bond restraints: 15433 Sorted by residual: bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.06e+01 bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.87e+01 bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.81e+01 bond pdb=" C THR B 471 " pdb=" N PRO B 472 " ideal model delta sigma weight residual 1.334 1.388 -0.055 8.40e-03 1.42e+04 4.25e+01 bond pdb=" C5 ATP E 901 " pdb=" C6 ATP E 901 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.18e+01 ... (remaining 15428 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 20609 4.23 - 8.47: 245 8.47 - 12.70: 21 12.70 - 16.94: 3 16.94 - 21.17: 4 Bond angle restraints: 20882 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 139.87 118.70 21.17 1.00e+00 1.00e+00 4.48e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 120.99 18.88 1.00e+00 1.00e+00 3.56e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 119.69 17.14 1.00e+00 1.00e+00 2.94e+02 angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 122.88 16.99 1.00e+00 1.00e+00 2.89e+02 angle pdb=" PA ATP E 901 " pdb=" O3A ATP E 901 " pdb=" PB ATP E 901 " ideal model delta sigma weight residual 136.83 120.55 16.28 1.00e+00 1.00e+00 2.65e+02 ... (remaining 20877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8353 17.95 - 35.90: 800 35.90 - 53.86: 137 53.86 - 71.81: 25 71.81 - 89.76: 15 Dihedral angle restraints: 9330 sinusoidal: 3795 harmonic: 5535 Sorted by residual: dihedral pdb=" CA GLN C 347 " pdb=" C GLN C 347 " pdb=" N LEU C 348 " pdb=" CA LEU C 348 " ideal model delta harmonic sigma weight residual -180.00 -157.46 -22.54 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ASP C 337 " pdb=" C ASP C 337 " pdb=" N TYR C 338 " pdb=" CA TYR C 338 " ideal model delta harmonic sigma weight residual -180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA GLN D 158 " pdb=" C GLN D 158 " pdb=" N THR D 159 " pdb=" CA THR D 159 " ideal model delta harmonic sigma weight residual -180.00 -159.48 -20.52 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 9327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2113 0.102 - 0.204: 281 0.204 - 0.306: 18 0.306 - 0.407: 3 0.407 - 0.509: 1 Chirality restraints: 2416 Sorted by residual: chirality pdb=" CB THR C 336 " pdb=" CA THR C 336 " pdb=" OG1 THR C 336 " pdb=" CG2 THR C 336 " both_signs ideal model delta sigma weight residual False 2.55 2.04 0.51 2.00e-01 2.50e+01 6.48e+00 chirality pdb=" CB ILE E 123 " pdb=" CA ILE E 123 " pdb=" CG1 ILE E 123 " pdb=" CG2 ILE E 123 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.41e+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 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 2413 not shown) Planarity restraints: 2642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 324 " 0.021 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" CD GLU C 324 " -0.073 2.00e-02 2.50e+03 pdb=" OE1 GLU C 324 " 0.026 2.00e-02 2.50e+03 pdb=" OE2 GLU C 324 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 232 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C LEU E 232 " -0.070 2.00e-02 2.50e+03 pdb=" O LEU E 232 " 0.026 2.00e-02 2.50e+03 pdb=" N PHE E 233 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 747 " 0.019 2.00e-02 2.50e+03 3.87e-02 1.49e+01 pdb=" C HIS A 747 " -0.067 2.00e-02 2.50e+03 pdb=" O HIS A 747 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS A 748 " 0.023 2.00e-02 2.50e+03 ... (remaining 2639 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 82 2.55 - 3.14: 11269 3.14 - 3.73: 23759 3.73 - 4.31: 31565 4.31 - 4.90: 53330 Nonbonded interactions: 120005 Sorted by model distance: nonbonded pdb=" OG1 THR A 605 " pdb="MG MG A1002 " model vdw 1.967 2.170 nonbonded pdb=" O3G ATP E 901 " pdb="MG MG E 902 " model vdw 2.140 2.170 nonbonded pdb=" O3G ATP A1001 " pdb="MG MG A1002 " model vdw 2.164 2.170 nonbonded pdb=" OG1 THR D 63 " pdb="MG MG D 902 " model vdw 2.170 2.170 nonbonded pdb=" O2B ATP D 901 " pdb="MG MG D 902 " model vdw 2.179 2.170 ... (remaining 120000 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.800 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 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 : 0.015 0.877 15437 Z= 1.320 Angle : 1.267 21.170 20882 Z= 0.741 Chirality : 0.070 0.509 2416 Planarity : 0.008 0.087 2642 Dihedral : 14.680 89.759 5716 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.24 % Allowed : 5.95 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -2.89 (0.16), residues: 1843 helix: -2.46 (0.10), residues: 1099 sheet: -2.88 (0.33), residues: 168 loop : 0.20 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 20 TYR 0.029 0.004 TYR C 255 PHE 0.030 0.004 PHE E 450 TRP 0.036 0.004 TRP B 475 HIS 0.012 0.002 HIS E 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00777 / 0.39 (15433) covalent geometry : angle 1.26688 / 0.74 (20882) hydrogen bonds : bond 0.15005 / 10.02 ( 835) hydrogen bonds : angle 6.38914 / 4.44 ( 2433) Misc. bond : bond 0.78415 / 45.41 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 322 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 23 TYR cc_start: 0.8450 (m-80) cc_final: 0.7820 (m-80) REVERT: D 79 PHE cc_start: 0.8139 (t80) cc_final: 0.7580 (t80) REVERT: D 102 SER cc_start: 0.9213 (t) cc_final: 0.8949 (p) REVERT: D 146 LEU cc_start: 0.9126 (mt) cc_final: 0.8683 (mt) REVERT: D 147 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8506 (mp0) REVERT: D 151 LEU cc_start: 0.9591 (tt) cc_final: 0.9145 (tt) REVERT: D 341 CYS cc_start: 0.8707 (t) cc_final: 0.8413 (m) REVERT: D 409 LEU cc_start: 0.9153 (tp) cc_final: 0.8905 (mp) REVERT: E 82 GLU cc_start: 0.9314 (mt-10) cc_final: 0.8968 (mt-10) REVERT: E 164 GLU cc_start: 0.8902 (pt0) cc_final: 0.8489 (tm-30) REVERT: E 228 ASN cc_start: 0.9644 (t0) cc_final: 0.9270 (p0) REVERT: E 402 ASN cc_start: 0.9549 (m110) cc_final: 0.8881 (p0) REVERT: E 413 LEU cc_start: 0.8377 (mp) cc_final: 0.8039 (mp) REVERT: E 415 LEU cc_start: 0.8852 (mm) cc_final: 0.8626 (mm) REVERT: A 622 ASN cc_start: 0.9367 (t0) cc_final: 0.8916 (p0) REVERT: A 635 MET cc_start: 0.8918 (mmm) cc_final: 0.8098 (mmt) REVERT: A 720 MET cc_start: 0.9397 (tpt) cc_final: 0.9196 (tpp) REVERT: A 829 CYS cc_start: 0.8742 (m) cc_final: 0.8471 (m) REVERT: A 879 LEU cc_start: 0.9254 (mt) cc_final: 0.8887 (mt) REVERT: B 339 TYR cc_start: 0.8597 (m-10) cc_final: 0.8319 (m-80) REVERT: B 474 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8651 (pt) REVERT: B 488 TRP cc_start: 0.8221 (m100) cc_final: 0.7834 (m100) REVERT: C 51 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8889 (mp0) REVERT: C 189 LYS cc_start: 0.9729 (tttm) cc_final: 0.9524 (tptp) REVERT: C 212 PHE cc_start: 0.8799 (t80) cc_final: 0.8463 (t80) REVERT: C 221 GLN cc_start: 0.9667 (mt0) cc_final: 0.9361 (mp10) REVERT: C 384 TYR cc_start: 0.8916 (t80) cc_final: 0.8601 (t80) REVERT: C 625 MET cc_start: 0.7564 (mmt) cc_final: 0.6762 (tpt) outliers start: 4 outliers final: 2 residues processed: 324 average time/residue: 0.1389 time to fit residues: 64.9883 Evaluate side-chains 204 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 201 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 172 GLN D 243 ASN D 315 GLN E 107 GLN E 137 ASN E 278 HIS E 433 GLN ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 312 HIS C 591 HIS C 615 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.061616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.047922 restraints weight = 86127.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.049605 restraints weight = 48980.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.050797 restraints weight = 32983.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.051595 restraints weight = 24582.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.052224 restraints weight = 19750.077| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15437 Z= 0.162 Angle : 0.724 9.480 20882 Z= 0.369 Chirality : 0.042 0.173 2416 Planarity : 0.005 0.060 2642 Dihedral : 5.409 57.739 2055 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.52 % Allowed : 12.38 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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 (0.19), residues: 1843 helix: -0.04 (0.14), residues: 1117 sheet: -2.27 (0.36), residues: 162 loop : -0.00 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 231 TYR 0.030 0.002 TYR B 356 PHE 0.018 0.002 PHE C 49 TRP 0.017 0.002 TRP B 475 HIS 0.008 0.001 HIS C 591 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (15433) covalent geometry : angle 0.72444 / 0.37 (20882) hydrogen bonds : bond 0.04598 / 3.14 ( 835) hydrogen bonds : angle 5.08724 / 3.54 ( 2433) Misc. bond : bond 0.00263 / 0.13 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 233 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 23 TYR cc_start: 0.8409 (m-80) cc_final: 0.7965 (m-80) REVERT: D 102 SER cc_start: 0.9195 (t) cc_final: 0.8884 (p) REVERT: D 146 LEU cc_start: 0.9044 (mt) cc_final: 0.8643 (mm) REVERT: D 148 GLU cc_start: 0.8566 (tt0) cc_final: 0.8337 (tt0) REVERT: D 324 MET cc_start: 0.9020 (mtp) cc_final: 0.8540 (ttm) REVERT: D 404 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8711 (tp30) REVERT: D 409 LEU cc_start: 0.9280 (tp) cc_final: 0.8956 (mp) REVERT: E 82 GLU cc_start: 0.9302 (mt-10) cc_final: 0.9085 (mm-30) REVERT: E 228 ASN cc_start: 0.9627 (t0) cc_final: 0.9299 (p0) REVERT: E 402 ASN cc_start: 0.9486 (m110) cc_final: 0.9154 (p0) REVERT: E 415 LEU cc_start: 0.8935 (mm) cc_final: 0.8685 (mm) REVERT: A 552 LEU cc_start: 0.9333 (tp) cc_final: 0.8924 (pp) REVERT: A 622 ASN cc_start: 0.9223 (t0) cc_final: 0.8998 (p0) REVERT: A 635 MET cc_start: 0.8791 (mmm) cc_final: 0.8017 (mmt) REVERT: A 639 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8816 (pt0) REVERT: A 701 LEU cc_start: 0.8970 (tp) cc_final: 0.8746 (pp) REVERT: A 720 MET cc_start: 0.9382 (tpt) cc_final: 0.9176 (tpp) REVERT: A 724 GLU cc_start: 0.8085 (mp0) cc_final: 0.7758 (mp0) REVERT: A 855 MET cc_start: 0.8959 (ppp) cc_final: 0.8741 (ppp) REVERT: B 339 TYR cc_start: 0.8665 (m-10) cc_final: 0.8438 (m-10) REVERT: B 343 TRP cc_start: 0.9456 (m-10) cc_final: 0.9235 (m-10) REVERT: B 420 GLU cc_start: 0.9033 (tp30) cc_final: 0.8829 (tp30) REVERT: B 475 TRP cc_start: 0.8546 (m-90) cc_final: 0.8340 (m-90) REVERT: B 488 TRP cc_start: 0.8488 (m100) cc_final: 0.8065 (m100) REVERT: C 51 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8856 (mp0) REVERT: C 128 MET cc_start: 0.8956 (mpp) cc_final: 0.8631 (mpp) REVERT: C 212 PHE cc_start: 0.8898 (t80) cc_final: 0.8397 (t80) REVERT: C 221 GLN cc_start: 0.9643 (mt0) cc_final: 0.9421 (mp10) REVERT: C 222 ASP cc_start: 0.9216 (m-30) cc_final: 0.8919 (p0) REVERT: C 336 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8368 (p) REVERT: C 340 LYS cc_start: 0.9092 (tttt) cc_final: 0.8785 (tptp) REVERT: C 384 TYR cc_start: 0.8769 (t80) cc_final: 0.8488 (t80) REVERT: C 429 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9031 (mp) REVERT: C 625 MET cc_start: 0.7472 (mmt) cc_final: 0.6312 (tpt) outliers start: 25 outliers final: 14 residues processed: 245 average time/residue: 0.1184 time to fit residues: 43.7119 Evaluate side-chains 199 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain F residue 232 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 172 GLN ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN C 107 GLN C 591 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.060783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.046905 restraints weight = 87987.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.048571 restraints weight = 50437.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.049718 restraints weight = 34087.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.050469 restraints weight = 25561.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.051078 restraints weight = 20747.192| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15437 Z= 0.168 Angle : 0.695 9.143 20882 Z= 0.348 Chirality : 0.042 0.257 2416 Planarity : 0.004 0.063 2642 Dihedral : 5.044 49.428 2053 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.88 % Favored : 97.07 % Rotamer: Outliers : 2.06 % Allowed : 14.62 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.14 (0.19), residues: 1843 helix: 0.66 (0.15), residues: 1121 sheet: -1.95 (0.37), residues: 162 loop : -0.14 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 130 TYR 0.020 0.002 TYR E 258 PHE 0.026 0.002 PHE E 389 TRP 0.018 0.002 TRP A 703 HIS 0.006 0.001 HIS E 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (15433) covalent geometry : angle 0.69526 / 0.35 (20882) hydrogen bonds : bond 0.04140 / 2.81 ( 835) hydrogen bonds : angle 4.86785 / 3.37 ( 2433) Misc. bond : bond 0.00085 / 0.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 79 PHE cc_start: 0.8235 (t80) cc_final: 0.7590 (t80) REVERT: D 102 SER cc_start: 0.9259 (t) cc_final: 0.8936 (p) REVERT: D 148 GLU cc_start: 0.8695 (tt0) cc_final: 0.8440 (tt0) REVERT: D 324 MET cc_start: 0.9048 (mtp) cc_final: 0.8620 (ttm) REVERT: D 404 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8767 (tp30) REVERT: E 82 GLU cc_start: 0.9292 (mt-10) cc_final: 0.9073 (mm-30) REVERT: E 228 ASN cc_start: 0.9601 (t0) cc_final: 0.9300 (p0) REVERT: E 402 ASN cc_start: 0.9517 (m110) cc_final: 0.9132 (p0) REVERT: E 415 LEU cc_start: 0.8940 (mm) cc_final: 0.8713 (mm) REVERT: A 552 LEU cc_start: 0.9363 (tp) cc_final: 0.8868 (pp) REVERT: A 635 MET cc_start: 0.8829 (mmm) cc_final: 0.8454 (mmt) REVERT: A 701 LEU cc_start: 0.8943 (tp) cc_final: 0.8732 (pp) REVERT: A 720 MET cc_start: 0.9326 (tpt) cc_final: 0.9103 (tpp) REVERT: A 807 MET cc_start: 0.8833 (mmp) cc_final: 0.8409 (mmp) REVERT: A 855 MET cc_start: 0.8905 (ppp) cc_final: 0.8546 (ppp) REVERT: B 343 TRP cc_start: 0.9461 (m-10) cc_final: 0.9205 (m-10) REVERT: B 345 CYS cc_start: 0.9189 (m) cc_final: 0.8974 (m) REVERT: B 388 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.6916 (mt) REVERT: B 420 GLU cc_start: 0.9056 (tp30) cc_final: 0.8829 (tp30) REVERT: B 488 TRP cc_start: 0.8557 (m100) cc_final: 0.8136 (m100) REVERT: C 51 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8802 (mp0) REVERT: C 128 MET cc_start: 0.8954 (mpp) cc_final: 0.8712 (mpp) REVERT: C 185 MET cc_start: 0.8972 (mmm) cc_final: 0.8751 (mmm) REVERT: C 221 GLN cc_start: 0.9626 (mt0) cc_final: 0.9380 (mp10) REVERT: C 326 PHE cc_start: 0.8378 (m-80) cc_final: 0.7820 (t80) REVERT: C 388 LYS cc_start: 0.9293 (tptp) cc_final: 0.9050 (tptp) REVERT: C 429 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9025 (mp) REVERT: C 450 MET cc_start: 0.8657 (ptp) cc_final: 0.8362 (ptp) REVERT: C 625 MET cc_start: 0.7517 (mmt) cc_final: 0.6462 (tpt) outliers start: 34 outliers final: 22 residues processed: 212 average time/residue: 0.1087 time to fit residues: 36.0491 Evaluate side-chains 185 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 699 ASN Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 914 HIS Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain F residue 232 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 122 optimal weight: 9.9990 chunk 181 optimal weight: 0.0770 chunk 7 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 182 optimal weight: 9.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 163 ASN ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.060635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.046870 restraints weight = 88236.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.048510 restraints weight = 51535.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.049639 restraints weight = 34747.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.050372 restraints weight = 26037.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.050978 restraints weight = 21199.972| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15437 Z= 0.146 Angle : 0.670 13.210 20882 Z= 0.330 Chirality : 0.041 0.250 2416 Planarity : 0.004 0.045 2642 Dihedral : 4.820 41.903 2053 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 1.82 % Allowed : 16.32 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.47 (0.20), residues: 1843 helix: 0.99 (0.15), residues: 1119 sheet: -1.82 (0.37), residues: 160 loop : -0.18 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 130 TYR 0.022 0.001 TYR B 356 PHE 0.028 0.002 PHE E 389 TRP 0.036 0.003 TRP A 703 HIS 0.006 0.001 HIS E 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (15433) covalent geometry : angle 0.67010 / 0.33 (20882) hydrogen bonds : bond 0.03816 / 2.61 ( 835) hydrogen bonds : angle 4.69949 / 3.26 ( 2433) Misc. bond : bond 0.00041 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 79 PHE cc_start: 0.8291 (t80) cc_final: 0.7589 (t80) REVERT: D 102 SER cc_start: 0.9208 (t) cc_final: 0.8898 (p) REVERT: D 148 GLU cc_start: 0.8768 (tt0) cc_final: 0.8523 (tt0) REVERT: D 404 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8771 (tp30) REVERT: E 82 GLU cc_start: 0.9507 (mt-10) cc_final: 0.9249 (mt-10) REVERT: E 228 ASN cc_start: 0.9601 (t0) cc_final: 0.9292 (p0) REVERT: E 402 ASN cc_start: 0.9552 (m110) cc_final: 0.9128 (p0) REVERT: E 413 LEU cc_start: 0.8303 (mt) cc_final: 0.8065 (mt) REVERT: E 415 LEU cc_start: 0.8870 (mm) cc_final: 0.8624 (mm) REVERT: A 552 LEU cc_start: 0.9238 (tp) cc_final: 0.8858 (pp) REVERT: A 635 MET cc_start: 0.8867 (mmm) cc_final: 0.8504 (mmt) REVERT: A 701 LEU cc_start: 0.8938 (tp) cc_final: 0.8733 (pp) REVERT: A 720 MET cc_start: 0.9311 (tpt) cc_final: 0.9091 (tpp) REVERT: B 388 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.6963 (mt) REVERT: B 420 GLU cc_start: 0.9062 (tp30) cc_final: 0.8829 (tp30) REVERT: B 483 PHE cc_start: 0.7661 (m-10) cc_final: 0.7417 (m-10) REVERT: B 488 TRP cc_start: 0.8491 (m100) cc_final: 0.7954 (m100) REVERT: C 51 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8763 (mp0) REVERT: C 185 MET cc_start: 0.8937 (mmm) cc_final: 0.8715 (mmm) REVERT: C 221 GLN cc_start: 0.9676 (mt0) cc_final: 0.9419 (mp10) REVERT: C 326 PHE cc_start: 0.8449 (m-80) cc_final: 0.7987 (t80) REVERT: C 429 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9033 (mp) REVERT: C 625 MET cc_start: 0.7427 (mmt) cc_final: 0.6502 (tpt) outliers start: 30 outliers final: 20 residues processed: 213 average time/residue: 0.1116 time to fit residues: 36.8534 Evaluate side-chains 189 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 699 ASN Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain F residue 233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 83 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 165 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 243 ASN E 150 ASN ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.059948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.046615 restraints weight = 87769.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.048224 restraints weight = 51622.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.049307 restraints weight = 34860.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.050118 restraints weight = 26236.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.050735 restraints weight = 21063.927| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15437 Z= 0.129 Angle : 0.671 11.271 20882 Z= 0.324 Chirality : 0.041 0.275 2416 Planarity : 0.004 0.100 2642 Dihedral : 4.705 42.715 2053 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.04 % Favored : 96.91 % Rotamer: Outliers : 2.12 % Allowed : 16.63 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.60 (0.20), residues: 1843 helix: 1.11 (0.16), residues: 1124 sheet: -1.79 (0.36), residues: 160 loop : -0.19 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 231 TYR 0.012 0.001 TYR E 258 PHE 0.024 0.001 PHE A 854 TRP 0.024 0.002 TRP B 475 HIS 0.005 0.001 HIS E 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (15433) covalent geometry : angle 0.67060 / 0.32 (20882) hydrogen bonds : bond 0.03638 / 2.48 ( 835) hydrogen bonds : angle 4.60329 / 3.17 ( 2433) Misc. bond : bond 0.00037 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 79 PHE cc_start: 0.8292 (t80) cc_final: 0.7514 (t80) REVERT: D 102 SER cc_start: 0.9214 (t) cc_final: 0.8897 (p) REVERT: D 149 PHE cc_start: 0.8365 (t80) cc_final: 0.8159 (t80) REVERT: D 324 MET cc_start: 0.9083 (mmm) cc_final: 0.8762 (mmm) REVERT: D 404 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8737 (tp30) REVERT: E 78 LYS cc_start: 0.9415 (mmtt) cc_final: 0.8954 (mmmt) REVERT: E 80 MET cc_start: 0.9564 (ttm) cc_final: 0.9343 (mtt) REVERT: E 82 GLU cc_start: 0.9559 (mt-10) cc_final: 0.9264 (mt-10) REVERT: E 228 ASN cc_start: 0.9559 (t0) cc_final: 0.9242 (p0) REVERT: E 402 ASN cc_start: 0.9572 (m110) cc_final: 0.9112 (p0) REVERT: E 413 LEU cc_start: 0.8288 (mt) cc_final: 0.8078 (mt) REVERT: E 415 LEU cc_start: 0.8817 (mm) cc_final: 0.8600 (mm) REVERT: A 552 LEU cc_start: 0.9205 (tp) cc_final: 0.8835 (pp) REVERT: A 635 MET cc_start: 0.8901 (mmm) cc_final: 0.8551 (mmt) REVERT: A 689 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8723 (pp) REVERT: A 720 MET cc_start: 0.9287 (tpt) cc_final: 0.9065 (tpp) REVERT: A 807 MET cc_start: 0.8896 (mmp) cc_final: 0.8564 (mmp) REVERT: B 388 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7106 (mt) REVERT: B 420 GLU cc_start: 0.9090 (tp30) cc_final: 0.8866 (tp30) REVERT: B 483 PHE cc_start: 0.7585 (m-10) cc_final: 0.7359 (m-10) REVERT: B 488 TRP cc_start: 0.8473 (m100) cc_final: 0.7835 (m100) REVERT: C 51 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8789 (mp0) REVERT: C 185 MET cc_start: 0.8945 (mmm) cc_final: 0.8721 (mmm) REVERT: C 221 GLN cc_start: 0.9715 (mt0) cc_final: 0.9422 (mp10) REVERT: C 326 PHE cc_start: 0.8490 (m-80) cc_final: 0.8042 (t80) REVERT: C 336 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8241 (p) REVERT: C 429 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9042 (mp) REVERT: C 504 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7887 (pp20) REVERT: C 625 MET cc_start: 0.7412 (mmt) cc_final: 0.6500 (tpt) outliers start: 35 outliers final: 21 residues processed: 203 average time/residue: 0.1079 time to fit residues: 34.4242 Evaluate side-chains 185 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 699 ASN Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 5 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 165 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 129 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.060004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.046740 restraints weight = 87426.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.048339 restraints weight = 51097.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.049451 restraints weight = 34562.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.050182 restraints weight = 25917.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.050771 restraints weight = 21001.149| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15437 Z= 0.119 Angle : 0.666 11.435 20882 Z= 0.318 Chirality : 0.041 0.261 2416 Planarity : 0.004 0.064 2642 Dihedral : 4.615 43.001 2053 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.09 % Favored : 96.85 % Rotamer: Outliers : 1.64 % Allowed : 17.72 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.74 (0.20), residues: 1843 helix: 1.23 (0.16), residues: 1126 sheet: -1.66 (0.35), residues: 171 loop : -0.11 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 231 TYR 0.018 0.001 TYR A 579 PHE 0.047 0.001 PHE C 362 TRP 0.024 0.002 TRP B 475 HIS 0.008 0.001 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (15433) covalent geometry : angle 0.66610 / 0.32 (20882) hydrogen bonds : bond 0.03439 / 2.35 ( 835) hydrogen bonds : angle 4.51421 / 3.11 ( 2433) Misc. bond : bond 0.00034 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 79 PHE cc_start: 0.8328 (t80) cc_final: 0.7551 (t80) REVERT: D 148 GLU cc_start: 0.8779 (tt0) cc_final: 0.8454 (tt0) REVERT: D 324 MET cc_start: 0.9074 (mmm) cc_final: 0.8771 (mmm) REVERT: D 404 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8719 (tp30) REVERT: E 1 MET cc_start: 0.8779 (tpt) cc_final: 0.8334 (tpt) REVERT: E 22 LEU cc_start: 0.9302 (mt) cc_final: 0.8999 (tp) REVERT: E 80 MET cc_start: 0.9527 (ttm) cc_final: 0.9313 (mtt) REVERT: E 82 GLU cc_start: 0.9551 (mt-10) cc_final: 0.9286 (mt-10) REVERT: E 134 MET cc_start: 0.7767 (ptm) cc_final: 0.7461 (ptp) REVERT: E 228 ASN cc_start: 0.9534 (t0) cc_final: 0.9166 (m110) REVERT: E 402 ASN cc_start: 0.9588 (m110) cc_final: 0.8738 (t0) REVERT: E 406 GLN cc_start: 0.8639 (mm110) cc_final: 0.8227 (mm110) REVERT: E 413 LEU cc_start: 0.8335 (mt) cc_final: 0.7950 (mt) REVERT: E 415 LEU cc_start: 0.8815 (mm) cc_final: 0.8579 (mm) REVERT: A 536 MET cc_start: 0.8403 (mmm) cc_final: 0.7841 (mmm) REVERT: A 552 LEU cc_start: 0.9202 (tp) cc_final: 0.8878 (pp) REVERT: A 635 MET cc_start: 0.8941 (mmm) cc_final: 0.8513 (mmt) REVERT: A 689 LEU cc_start: 0.9157 (mt) cc_final: 0.8733 (pp) REVERT: A 720 MET cc_start: 0.9285 (tpt) cc_final: 0.9059 (tpp) REVERT: A 855 MET cc_start: 0.8565 (ppp) cc_final: 0.7941 (ppp) REVERT: B 388 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7071 (mt) REVERT: B 420 GLU cc_start: 0.9090 (tp30) cc_final: 0.8832 (tp30) REVERT: B 483 PHE cc_start: 0.7530 (m-10) cc_final: 0.7318 (m-10) REVERT: B 488 TRP cc_start: 0.8464 (m100) cc_final: 0.7776 (m100) REVERT: C 51 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8768 (mp0) REVERT: C 185 MET cc_start: 0.8943 (mmm) cc_final: 0.8713 (mmm) REVERT: C 221 GLN cc_start: 0.9692 (mt0) cc_final: 0.9390 (mp10) REVERT: C 326 PHE cc_start: 0.8559 (m-80) cc_final: 0.8138 (t80) REVERT: C 429 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9024 (mp) REVERT: C 504 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7840 (pp20) REVERT: C 625 MET cc_start: 0.7420 (mmt) cc_final: 0.6552 (tpt) outliers start: 27 outliers final: 19 residues processed: 197 average time/residue: 0.1185 time to fit residues: 36.3364 Evaluate side-chains 178 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 233 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 138 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 124 ASN ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN C 61 ASN C 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.060366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.046866 restraints weight = 88536.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.048442 restraints weight = 51319.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.049476 restraints weight = 34979.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.050268 restraints weight = 26521.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.050856 restraints weight = 21442.786| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15437 Z= 0.131 Angle : 0.664 11.144 20882 Z= 0.322 Chirality : 0.041 0.291 2416 Planarity : 0.004 0.038 2642 Dihedral : 4.564 42.631 2053 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.04 % Favored : 96.91 % Rotamer: Outliers : 1.88 % Allowed : 18.26 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.20), residues: 1843 helix: 1.29 (0.16), residues: 1132 sheet: -1.55 (0.36), residues: 170 loop : 0.01 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 231 TYR 0.013 0.001 TYR E 258 PHE 0.030 0.001 PHE D 149 TRP 0.023 0.002 TRP B 475 HIS 0.009 0.001 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (15433) covalent geometry : angle 0.66364 / 0.32 (20882) hydrogen bonds : bond 0.03358 / 2.28 ( 835) hydrogen bonds : angle 4.51460 / 3.10 ( 2433) Misc. bond : bond 0.00035 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 148 GLU cc_start: 0.8780 (tt0) cc_final: 0.8482 (tt0) REVERT: D 324 MET cc_start: 0.9089 (mmm) cc_final: 0.8779 (mmm) REVERT: D 404 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8756 (tp30) REVERT: E 1 MET cc_start: 0.8705 (tpt) cc_final: 0.8302 (tpt) REVERT: E 82 GLU cc_start: 0.9533 (mt-10) cc_final: 0.9261 (mt-10) REVERT: E 228 ASN cc_start: 0.9540 (t0) cc_final: 0.9168 (m110) REVERT: E 402 ASN cc_start: 0.9558 (m110) cc_final: 0.9046 (p0) REVERT: E 413 LEU cc_start: 0.8373 (mt) cc_final: 0.8000 (mt) REVERT: E 415 LEU cc_start: 0.8843 (mm) cc_final: 0.8602 (mm) REVERT: A 552 LEU cc_start: 0.9210 (tp) cc_final: 0.8891 (pp) REVERT: A 635 MET cc_start: 0.8849 (mmm) cc_final: 0.8554 (mmt) REVERT: A 720 MET cc_start: 0.9258 (tpt) cc_final: 0.9030 (tpp) REVERT: A 807 MET cc_start: 0.8823 (mmp) cc_final: 0.8445 (mmp) REVERT: A 855 MET cc_start: 0.8587 (ppp) cc_final: 0.8010 (ppp) REVERT: B 420 GLU cc_start: 0.9094 (tp30) cc_final: 0.8834 (tp30) REVERT: B 476 ASP cc_start: 0.7587 (p0) cc_final: 0.7251 (p0) REVERT: B 488 TRP cc_start: 0.8445 (m100) cc_final: 0.7727 (m100) REVERT: C 51 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8756 (mp0) REVERT: C 221 GLN cc_start: 0.9686 (mt0) cc_final: 0.9383 (mp10) REVERT: C 326 PHE cc_start: 0.8559 (m-80) cc_final: 0.8132 (t80) REVERT: C 336 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.8164 (p) REVERT: C 429 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9021 (mp) REVERT: C 504 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7938 (pp20) REVERT: C 625 MET cc_start: 0.7431 (mmt) cc_final: 0.6596 (tpt) outliers start: 31 outliers final: 23 residues processed: 183 average time/residue: 0.1161 time to fit residues: 33.4336 Evaluate side-chains 183 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain A residue 699 ASN Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 33 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 GLN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.059997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.046682 restraints weight = 89504.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.048317 restraints weight = 51675.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.049428 restraints weight = 34539.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.050223 restraints weight = 25840.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.050815 restraints weight = 20778.124| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15437 Z= 0.120 Angle : 0.668 11.473 20882 Z= 0.321 Chirality : 0.041 0.261 2416 Planarity : 0.004 0.039 2642 Dihedral : 4.547 43.371 2053 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.09 % Favored : 96.85 % Rotamer: Outliers : 1.58 % Allowed : 18.75 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.92 (0.20), residues: 1843 helix: 1.33 (0.16), residues: 1126 sheet: -1.46 (0.36), residues: 170 loop : 0.00 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 231 TYR 0.020 0.001 TYR B 356 PHE 0.064 0.002 PHE C 362 TRP 0.024 0.002 TRP B 475 HIS 0.008 0.001 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (15433) covalent geometry : angle 0.66817 / 0.32 (20882) hydrogen bonds : bond 0.03359 / 2.30 ( 835) hydrogen bonds : angle 4.46909 / 3.07 ( 2433) Misc. bond : bond 0.00034 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 148 GLU cc_start: 0.8772 (tt0) cc_final: 0.8444 (tt0) REVERT: D 324 MET cc_start: 0.9108 (mmm) cc_final: 0.8789 (mmm) REVERT: D 404 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8732 (tp30) REVERT: E 1 MET cc_start: 0.8635 (tpt) cc_final: 0.8235 (tpt) REVERT: E 78 LYS cc_start: 0.9512 (mmtt) cc_final: 0.9017 (mmmm) REVERT: E 80 MET cc_start: 0.9589 (ttm) cc_final: 0.9327 (mtt) REVERT: E 82 GLU cc_start: 0.9545 (mt-10) cc_final: 0.9217 (mt-10) REVERT: E 228 ASN cc_start: 0.9508 (t0) cc_final: 0.9148 (m110) REVERT: E 413 LEU cc_start: 0.8364 (mt) cc_final: 0.8018 (mt) REVERT: E 415 LEU cc_start: 0.8824 (mm) cc_final: 0.8610 (mm) REVERT: A 552 LEU cc_start: 0.9176 (tp) cc_final: 0.8889 (pp) REVERT: A 635 MET cc_start: 0.8869 (mmm) cc_final: 0.8594 (mmt) REVERT: A 701 LEU cc_start: 0.8715 (tp) cc_final: 0.8463 (pp) REVERT: A 807 MET cc_start: 0.8838 (mmp) cc_final: 0.8457 (mmp) REVERT: A 855 MET cc_start: 0.8546 (ppp) cc_final: 0.7896 (ppp) REVERT: B 343 TRP cc_start: 0.9414 (m-10) cc_final: 0.9096 (m-10) REVERT: B 420 GLU cc_start: 0.9097 (tp30) cc_final: 0.8839 (tp30) REVERT: B 441 MET cc_start: 0.8286 (tpp) cc_final: 0.7984 (tpp) REVERT: B 476 ASP cc_start: 0.7562 (p0) cc_final: 0.7300 (p0) REVERT: B 488 TRP cc_start: 0.8391 (m100) cc_final: 0.7920 (m100) REVERT: C 51 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8783 (mp0) REVERT: C 128 MET cc_start: 0.9025 (mpp) cc_final: 0.8762 (mpp) REVERT: C 221 GLN cc_start: 0.9708 (mt0) cc_final: 0.9366 (mp10) REVERT: C 326 PHE cc_start: 0.8617 (m-80) cc_final: 0.8225 (t80) REVERT: C 336 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8169 (p) REVERT: C 429 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9031 (mp) REVERT: C 504 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7843 (pp20) REVERT: C 625 MET cc_start: 0.7432 (mmt) cc_final: 0.6608 (tpt) outliers start: 26 outliers final: 20 residues processed: 190 average time/residue: 0.1133 time to fit residues: 34.2154 Evaluate side-chains 184 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 699 ASN Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain F residue 233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 0.0980 chunk 174 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 179 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.061334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.047565 restraints weight = 88631.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.049240 restraints weight = 51017.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.050324 restraints weight = 34257.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.051130 restraints weight = 25786.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.051638 restraints weight = 20808.145| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15437 Z= 0.113 Angle : 0.672 10.752 20882 Z= 0.321 Chirality : 0.041 0.287 2416 Planarity : 0.004 0.057 2642 Dihedral : 4.509 43.271 2053 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.96 % Rotamer: Outliers : 1.52 % Allowed : 19.11 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.93 (0.20), residues: 1843 helix: 1.31 (0.16), residues: 1137 sheet: -1.39 (0.36), residues: 170 loop : 0.03 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 231 TYR 0.011 0.001 TYR C 430 PHE 0.025 0.001 PHE C 332 TRP 0.030 0.002 TRP B 475 HIS 0.007 0.001 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (15433) covalent geometry : angle 0.67242 / 0.32 (20882) hydrogen bonds : bond 0.03233 / 2.19 ( 835) hydrogen bonds : angle 4.39654 / 3.02 ( 2433) Misc. bond : bond 0.00031 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 148 GLU cc_start: 0.8732 (tt0) cc_final: 0.8410 (tt0) REVERT: D 324 MET cc_start: 0.9087 (mmm) cc_final: 0.8771 (mmm) REVERT: D 404 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8682 (tp30) REVERT: D 409 LEU cc_start: 0.9220 (tp) cc_final: 0.8476 (mp) REVERT: D 429 LEU cc_start: 0.8664 (tp) cc_final: 0.8073 (pt) REVERT: E 1 MET cc_start: 0.8523 (tpt) cc_final: 0.8102 (tpt) REVERT: E 82 GLU cc_start: 0.9510 (mt-10) cc_final: 0.9211 (mt-10) REVERT: E 228 ASN cc_start: 0.9527 (t0) cc_final: 0.9159 (m110) REVERT: A 536 MET cc_start: 0.8328 (mmm) cc_final: 0.8122 (mmt) REVERT: A 552 LEU cc_start: 0.9227 (tp) cc_final: 0.8975 (pp) REVERT: A 635 MET cc_start: 0.8868 (mmm) cc_final: 0.8567 (mmt) REVERT: A 689 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8768 (pp) REVERT: A 701 LEU cc_start: 0.8695 (tp) cc_final: 0.8463 (pp) REVERT: A 807 MET cc_start: 0.8872 (mmp) cc_final: 0.8508 (mmp) REVERT: A 855 MET cc_start: 0.8554 (ppp) cc_final: 0.7903 (ppp) REVERT: B 343 TRP cc_start: 0.9411 (m-10) cc_final: 0.9091 (m-10) REVERT: B 420 GLU cc_start: 0.9097 (tp30) cc_final: 0.8839 (tp30) REVERT: B 476 ASP cc_start: 0.7498 (p0) cc_final: 0.7190 (p0) REVERT: B 488 TRP cc_start: 0.8382 (m100) cc_final: 0.7850 (m100) REVERT: C 51 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8769 (mp0) REVERT: C 128 MET cc_start: 0.9013 (mpp) cc_final: 0.8775 (mpp) REVERT: C 221 GLN cc_start: 0.9670 (mt0) cc_final: 0.9323 (mp10) REVERT: C 326 PHE cc_start: 0.8573 (m-80) cc_final: 0.8177 (t80) REVERT: C 336 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8168 (p) REVERT: C 429 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9022 (mp) REVERT: C 504 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7911 (pp20) REVERT: C 625 MET cc_start: 0.7427 (mmt) cc_final: 0.6622 (tpt) outliers start: 25 outliers final: 16 residues processed: 192 average time/residue: 0.1149 time to fit residues: 34.8584 Evaluate side-chains 185 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 699 ASN Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain F residue 232 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 52 optimal weight: 0.3980 chunk 151 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 699 ASN ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.059379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.046288 restraints weight = 89117.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.047880 restraints weight = 52394.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.048970 restraints weight = 34986.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.049707 restraints weight = 26366.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.050249 restraints weight = 21423.741| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15437 Z= 0.147 Angle : 0.716 15.223 20882 Z= 0.342 Chirality : 0.042 0.340 2416 Planarity : 0.004 0.037 2642 Dihedral : 4.507 42.398 2053 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 1.64 % Allowed : 19.78 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.99 (0.20), residues: 1843 helix: 1.38 (0.16), residues: 1134 sheet: -1.53 (0.35), residues: 176 loop : 0.06 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 231 TYR 0.023 0.001 TYR B 356 PHE 0.042 0.002 PHE C 362 TRP 0.040 0.003 TRP A 703 HIS 0.008 0.001 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (15433) covalent geometry : angle 0.71584 / 0.34 (20882) hydrogen bonds : bond 0.03310 / 2.22 ( 835) hydrogen bonds : angle 4.46930 / 3.07 ( 2433) Misc. bond : bond 0.00038 / 0.02 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 148 GLU cc_start: 0.8737 (tt0) cc_final: 0.8407 (tt0) REVERT: D 324 MET cc_start: 0.9139 (mmm) cc_final: 0.8819 (mmm) REVERT: D 385 MET cc_start: 0.8656 (mmp) cc_final: 0.8261 (mmm) REVERT: D 404 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8803 (tp30) REVERT: D 409 LEU cc_start: 0.9256 (tp) cc_final: 0.8559 (mp) REVERT: D 429 LEU cc_start: 0.8707 (tp) cc_final: 0.8112 (pt) REVERT: E 1 MET cc_start: 0.8550 (tpt) cc_final: 0.8132 (tpt) REVERT: E 78 LYS cc_start: 0.9480 (mmtt) cc_final: 0.9252 (mmmt) REVERT: E 228 ASN cc_start: 0.9512 (t0) cc_final: 0.9163 (m110) REVERT: A 552 LEU cc_start: 0.9239 (tp) cc_final: 0.8988 (pp) REVERT: A 635 MET cc_start: 0.8895 (mmm) cc_final: 0.8624 (mmt) REVERT: A 701 LEU cc_start: 0.8652 (tp) cc_final: 0.8433 (pp) REVERT: B 420 GLU cc_start: 0.9097 (tp30) cc_final: 0.8836 (tp30) REVERT: B 476 ASP cc_start: 0.7492 (p0) cc_final: 0.7163 (p0) REVERT: B 488 TRP cc_start: 0.8408 (m100) cc_final: 0.7669 (m100) REVERT: C 51 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8786 (mp0) REVERT: C 128 MET cc_start: 0.9019 (mpp) cc_final: 0.8782 (mpp) REVERT: C 221 GLN cc_start: 0.9689 (mt0) cc_final: 0.9330 (mp10) REVERT: C 326 PHE cc_start: 0.8612 (m-80) cc_final: 0.8225 (t80) REVERT: C 336 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8197 (p) REVERT: C 429 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9043 (mp) REVERT: C 625 MET cc_start: 0.7415 (mmt) cc_final: 0.6599 (tpt) outliers start: 27 outliers final: 20 residues processed: 181 average time/residue: 0.1136 time to fit residues: 32.5407 Evaluate side-chains 182 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain F residue 232 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 164 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 74 optimal weight: 0.0370 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.059780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.046466 restraints weight = 90106.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.048084 restraints weight = 52491.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.049182 restraints weight = 34860.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.049871 restraints weight = 26117.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.050464 restraints weight = 21296.877| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.213 15437 Z= 0.245 Angle : 0.886 59.191 20882 Z= 0.477 Chirality : 0.041 0.359 2416 Planarity : 0.004 0.037 2642 Dihedral : 4.510 42.399 2053 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 1.70 % Allowed : 19.72 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.99 (0.20), residues: 1843 helix: 1.39 (0.16), residues: 1134 sheet: -1.52 (0.35), residues: 176 loop : 0.05 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 231 TYR 0.015 0.001 TYR B 356 PHE 0.034 0.001 PHE C 362 TRP 0.035 0.003 TRP A 703 HIS 0.007 0.001 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.24 (15433) covalent geometry : angle 0.88631 / 0.48 (20882) hydrogen bonds : bond 0.03310 / 2.22 ( 835) hydrogen bonds : angle 4.47119 / 3.07 ( 2433) Misc. bond : bond 0.00038 / 0.02 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2754.66 seconds wall clock time: 48 minutes 37.13 seconds (2917.13 seconds total)