Starting phenix.real_space_refine on Wed Mar 4 17:58:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jk6_22363/03_2026/7jk6_22363.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jk6_22363/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7jk6_22363/03_2026/7jk6_22363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jk6_22363/03_2026/7jk6_22363.map" model { file = "/net/cci-nas-00/data/ceres_data/7jk6_22363/03_2026/7jk6_22363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jk6_22363/03_2026/7jk6_22363.cif" } 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-dev-5986/lib/python3.9/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: 3.16, per 1000 atoms: 0.21 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: 1.13 Conformation dependent library (CDL) restraints added in 505.8 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: 0.37 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: 2.36 Time building geometry restraints manager: 1.50 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: 8401 17.95 - 35.90: 828 35.90 - 53.86: 152 53.86 - 71.81: 26 71.81 - 89.76: 16 Dihedral angle restraints: 9423 sinusoidal: 3888 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 9420 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: 1.670 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.260 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 14.917 89.759 5809 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 covalent geometry : bond 0.00777 (15433) covalent geometry : angle 1.26688 (20882) hydrogen bonds : bond 0.15005 ( 835) hydrogen bonds : angle 6.38914 ( 2433) Misc. bond : bond 0.78415 ( 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 : 0.446 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: 0.1356 time to fit residues: 62.8536 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 : 0.567 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 591 HIS C 615 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.061669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.047965 restraints weight = 86034.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.049657 restraints weight = 49012.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.050840 restraints weight = 33024.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.051669 restraints weight = 24673.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.052212 restraints weight = 19821.964| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15437 Z= 0.172 Angle : 0.732 9.327 20882 Z= 0.375 Chirality : 0.043 0.181 2416 Planarity : 0.005 0.061 2642 Dihedral : 8.077 72.826 2148 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.27 % Allowed : 12.32 % Favored : 86.41 % 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: -0.59 (0.19), residues: 1843 helix: -0.10 (0.14), residues: 1118 sheet: -2.29 (0.36), residues: 162 loop : 0.01 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 231 TYR 0.028 0.002 TYR B 356 PHE 0.018 0.002 PHE C 49 TRP 0.020 0.002 TRP B 475 HIS 0.008 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00350 (15433) covalent geometry : angle 0.73176 (20882) hydrogen bonds : bond 0.04759 ( 835) hydrogen bonds : angle 5.10682 ( 2433) Misc. bond : bond 0.00521 ( 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 249 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 0.644 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: D 23 TYR cc_start: 0.8333 (m-80) cc_final: 0.7909 (m-80) REVERT: D 102 SER cc_start: 0.9187 (t) cc_final: 0.8881 (p) REVERT: D 146 LEU cc_start: 0.9081 (mt) cc_final: 0.8671 (mm) REVERT: D 148 GLU cc_start: 0.8553 (tt0) cc_final: 0.8340 (tt0) REVERT: D 324 MET cc_start: 0.9013 (mtp) cc_final: 0.8521 (ttm) REVERT: D 404 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8672 (tp30) REVERT: D 409 LEU cc_start: 0.9262 (tp) cc_final: 0.8957 (mp) REVERT: E 228 ASN cc_start: 0.9605 (t0) cc_final: 0.9285 (p0) REVERT: E 402 ASN cc_start: 0.9479 (m110) cc_final: 0.9138 (p0) REVERT: E 415 LEU cc_start: 0.8954 (mm) cc_final: 0.8708 (mm) REVERT: A 552 LEU cc_start: 0.9331 (tp) cc_final: 0.8916 (pp) REVERT: A 622 ASN cc_start: 0.9214 (t0) cc_final: 0.8971 (p0) REVERT: A 630 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8754 (mp) REVERT: A 635 MET cc_start: 0.8826 (mmm) cc_final: 0.8040 (mmt) REVERT: A 639 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8833 (pt0) REVERT: A 701 LEU cc_start: 0.8976 (tp) cc_final: 0.8748 (pp) REVERT: A 720 MET cc_start: 0.9369 (tpt) cc_final: 0.9169 (tpp) REVERT: A 724 GLU cc_start: 0.8114 (mp0) cc_final: 0.7787 (mp0) REVERT: A 855 MET cc_start: 0.8936 (ppp) cc_final: 0.8723 (ppp) REVERT: B 339 TYR cc_start: 0.8668 (m-10) cc_final: 0.8441 (m-10) REVERT: B 343 TRP cc_start: 0.9457 (m-10) cc_final: 0.9216 (m-10) REVERT: B 420 GLU cc_start: 0.9035 (tp30) cc_final: 0.8831 (tp30) REVERT: B 488 TRP cc_start: 0.8512 (m100) cc_final: 0.8076 (m100) REVERT: C 51 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8862 (mp0) REVERT: C 128 MET cc_start: 0.8927 (mpp) cc_final: 0.8638 (mpp) REVERT: C 212 PHE cc_start: 0.8893 (t80) cc_final: 0.8362 (t80) REVERT: C 221 GLN cc_start: 0.9634 (mt0) cc_final: 0.9430 (mp10) REVERT: C 222 ASP cc_start: 0.9207 (m-30) cc_final: 0.8916 (p0) REVERT: C 336 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8424 (p) REVERT: C 340 LYS cc_start: 0.9104 (tttt) cc_final: 0.8794 (tptp) REVERT: C 384 TYR cc_start: 0.8782 (t80) cc_final: 0.8509 (t80) REVERT: C 388 LYS cc_start: 0.9269 (tptp) cc_final: 0.8888 (tptp) REVERT: C 429 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9026 (mp) REVERT: C 625 MET cc_start: 0.7482 (mmt) cc_final: 0.6306 (tpt) outliers start: 21 outliers final: 12 residues processed: 238 average time/residue: 0.1152 time to fit residues: 41.6271 Evaluate side-chains 198 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 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 A residue 630 LEU 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: 0.8980 chunk 61 optimal weight: 10.0000 chunk 107 optimal weight: 0.5980 chunk 143 optimal weight: 5.9990 chunk 54 optimal weight: 0.0020 chunk 106 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 163 ASN ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN B 429 HIS ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN C 325 HIS C 591 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.062576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.048571 restraints weight = 86100.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.050281 restraints weight = 49897.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.051462 restraints weight = 33613.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.052259 restraints weight = 25104.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.052901 restraints weight = 20235.032| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15437 Z= 0.131 Angle : 0.676 11.222 20882 Z= 0.335 Chirality : 0.041 0.224 2416 Planarity : 0.004 0.051 2642 Dihedral : 7.838 71.255 2146 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.96 % Rotamer: Outliers : 1.40 % Allowed : 14.62 % Favored : 83.98 % 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: -0.00 (0.19), residues: 1843 helix: 0.56 (0.15), residues: 1115 sheet: -2.04 (0.36), residues: 162 loop : -0.21 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 130 TYR 0.018 0.001 TYR D 239 PHE 0.022 0.001 PHE E 389 TRP 0.030 0.002 TRP B 475 HIS 0.011 0.001 HIS D 437 Details of bonding type rmsd covalent geometry : bond 0.00270 (15433) covalent geometry : angle 0.67635 (20882) hydrogen bonds : bond 0.04102 ( 835) hydrogen bonds : angle 4.79645 ( 2433) Misc. bond : bond 0.00088 ( 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 235 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 0.540 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 79 PHE cc_start: 0.8193 (t80) cc_final: 0.7494 (t80) REVERT: D 102 SER cc_start: 0.9184 (t) cc_final: 0.8853 (p) REVERT: D 146 LEU cc_start: 0.9020 (mt) cc_final: 0.8820 (mm) REVERT: D 148 GLU cc_start: 0.8718 (tt0) cc_final: 0.8477 (tt0) REVERT: D 324 MET cc_start: 0.8962 (mtp) cc_final: 0.8749 (mmm) REVERT: D 404 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8628 (tp30) REVERT: D 409 LEU cc_start: 0.9224 (tp) cc_final: 0.8906 (mp) REVERT: E 22 LEU cc_start: 0.9259 (mt) cc_final: 0.8813 (tp) REVERT: E 78 LYS cc_start: 0.9526 (mmtt) cc_final: 0.9177 (mmmt) REVERT: E 228 ASN cc_start: 0.9591 (t0) cc_final: 0.9273 (p0) REVERT: E 402 ASN cc_start: 0.9503 (m110) cc_final: 0.9107 (p0) REVERT: E 415 LEU cc_start: 0.8913 (mm) cc_final: 0.8664 (mm) REVERT: A 552 LEU cc_start: 0.9331 (tp) cc_final: 0.8848 (pp) REVERT: A 635 MET cc_start: 0.8772 (mmm) cc_final: 0.8351 (mmt) REVERT: A 639 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8814 (pt0) REVERT: A 689 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8621 (pp) REVERT: A 701 LEU cc_start: 0.8949 (tp) cc_final: 0.8736 (pp) REVERT: A 807 MET cc_start: 0.8885 (mmp) cc_final: 0.8561 (mmp) REVERT: B 343 TRP cc_start: 0.9444 (m-10) cc_final: 0.9161 (m-10) REVERT: B 393 MET cc_start: 0.8387 (mpp) cc_final: 0.8033 (mpp) REVERT: B 420 GLU cc_start: 0.9066 (tp30) cc_final: 0.8842 (tp30) REVERT: B 483 PHE cc_start: 0.7434 (m-10) cc_final: 0.7183 (m-10) REVERT: B 488 TRP cc_start: 0.8530 (m100) cc_final: 0.8109 (m100) REVERT: C 51 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8791 (mp0) REVERT: C 128 MET cc_start: 0.8886 (mpp) cc_final: 0.8669 (mpp) REVERT: C 212 PHE cc_start: 0.8859 (t80) cc_final: 0.8212 (t80) REVERT: C 221 GLN cc_start: 0.9615 (mt0) cc_final: 0.9375 (mp10) REVERT: C 326 PHE cc_start: 0.8174 (m-80) cc_final: 0.7677 (t80) REVERT: C 429 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9008 (mp) REVERT: C 625 MET cc_start: 0.7504 (mmt) cc_final: 0.6521 (tpt) outliers start: 23 outliers final: 13 residues processed: 226 average time/residue: 0.1100 time to fit residues: 38.4511 Evaluate side-chains 189 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain A residue 689 LEU 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 416 ASP Chi-restraints excluded: chain C residue 98 THR 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 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: 5.9990 chunk 181 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 67 optimal weight: 0.0770 chunk 167 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 182 optimal weight: 7.9990 overall best weight: 1.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 HIS C 312 HIS C 591 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.060378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.046850 restraints weight = 87869.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.048507 restraints weight = 49936.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.049667 restraints weight = 33336.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.050484 restraints weight = 24732.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.051027 restraints weight = 19805.787| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3227 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= 0.143 Angle : 0.655 9.805 20882 Z= 0.327 Chirality : 0.041 0.286 2416 Planarity : 0.004 0.047 2642 Dihedral : 7.743 68.880 2146 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.23 % Rotamer: Outliers : 1.70 % Allowed : 16.50 % Favored : 81.80 % 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: 0.40 (0.20), residues: 1843 helix: 0.93 (0.15), residues: 1121 sheet: -1.94 (0.36), residues: 152 loop : -0.22 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 130 TYR 0.024 0.002 TYR B 356 PHE 0.021 0.002 PHE D 149 TRP 0.033 0.002 TRP A 703 HIS 0.005 0.001 HIS D 255 Details of bonding type rmsd covalent geometry : bond 0.00308 (15433) covalent geometry : angle 0.65515 (20882) hydrogen bonds : bond 0.03790 ( 835) hydrogen bonds : angle 4.65084 ( 2433) Misc. bond : bond 0.00044 ( 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 217 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.591 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 79 PHE cc_start: 0.8347 (t80) cc_final: 0.7558 (t80) REVERT: D 102 SER cc_start: 0.9246 (t) cc_final: 0.8922 (p) REVERT: D 146 LEU cc_start: 0.8931 (mt) cc_final: 0.8699 (mm) REVERT: D 148 GLU cc_start: 0.8771 (tt0) cc_final: 0.8521 (tt0) REVERT: D 404 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8726 (tp30) REVERT: E 78 LYS cc_start: 0.9540 (mmtt) cc_final: 0.9235 (mmmt) REVERT: E 228 ASN cc_start: 0.9573 (t0) cc_final: 0.9244 (p0) REVERT: E 402 ASN cc_start: 0.9545 (m110) cc_final: 0.9060 (p0) REVERT: E 415 LEU cc_start: 0.8891 (mm) cc_final: 0.8633 (mm) REVERT: A 552 LEU cc_start: 0.9220 (tp) cc_final: 0.8811 (pp) REVERT: A 635 MET cc_start: 0.8846 (mmm) cc_final: 0.8472 (mmt) REVERT: A 855 MET cc_start: 0.8741 (ppp) cc_final: 0.8098 (ppp) REVERT: B 343 TRP cc_start: 0.9419 (m-10) cc_final: 0.9135 (m-10) REVERT: B 382 ASN cc_start: 0.7735 (m110) cc_final: 0.6949 (p0) REVERT: B 393 MET cc_start: 0.8423 (mpp) cc_final: 0.8179 (mpp) REVERT: B 420 GLU cc_start: 0.9098 (tp30) cc_final: 0.8867 (tp30) REVERT: B 483 PHE cc_start: 0.7716 (m-10) cc_final: 0.7435 (m-10) REVERT: B 488 TRP cc_start: 0.8523 (m100) cc_final: 0.8142 (m100) REVERT: C 51 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8785 (mp0) REVERT: C 185 MET cc_start: 0.8608 (mmm) cc_final: 0.8227 (tmm) REVERT: C 221 GLN cc_start: 0.9666 (mt0) cc_final: 0.9388 (mp10) REVERT: C 326 PHE cc_start: 0.8360 (m-80) cc_final: 0.7933 (t80) REVERT: C 388 LYS cc_start: 0.9305 (tptp) cc_final: 0.9028 (tptp) REVERT: C 429 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9041 (mp) REVERT: C 625 MET cc_start: 0.7437 (mmt) cc_final: 0.6414 (tpt) outliers start: 28 outliers final: 20 residues processed: 206 average time/residue: 0.1118 time to fit residues: 35.3942 Evaluate side-chains 186 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 341 CYS 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 689 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 861 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 83 optimal weight: 0.5980 chunk 172 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 165 optimal weight: 0.0060 chunk 142 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 124 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 = 0.3496 r_free = 0.3496 target = 0.061540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.047945 restraints weight = 88424.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.049606 restraints weight = 50820.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.050693 restraints weight = 34135.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.051549 restraints weight = 25719.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.052092 restraints weight = 20676.845| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15437 Z= 0.118 Angle : 0.672 14.766 20882 Z= 0.323 Chirality : 0.041 0.272 2416 Planarity : 0.004 0.040 2642 Dihedral : 7.635 70.472 2146 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.12 % Rotamer: Outliers : 1.82 % Allowed : 16.99 % Favored : 81.19 % 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: 0.58 (0.20), residues: 1843 helix: 1.09 (0.16), residues: 1124 sheet: -1.87 (0.35), residues: 151 loop : -0.19 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 693 TYR 0.012 0.001 TYR C 430 PHE 0.024 0.001 PHE A 854 TRP 0.024 0.002 TRP B 475 HIS 0.005 0.001 HIS A 914 Details of bonding type rmsd covalent geometry : bond 0.00255 (15433) covalent geometry : angle 0.67200 (20882) hydrogen bonds : bond 0.03604 ( 835) hydrogen bonds : angle 4.53614 ( 2433) Misc. bond : bond 0.00047 ( 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 228 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.430 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 79 PHE cc_start: 0.8280 (t80) cc_final: 0.7525 (t80) REVERT: D 102 SER cc_start: 0.9190 (t) cc_final: 0.8886 (p) REVERT: D 146 LEU cc_start: 0.8876 (mt) cc_final: 0.8641 (mm) REVERT: D 148 GLU cc_start: 0.8774 (tt0) cc_final: 0.8489 (tt0) REVERT: D 324 MET cc_start: 0.9002 (mmm) cc_final: 0.8705 (mmm) REVERT: D 404 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8637 (tp30) REVERT: E 22 LEU cc_start: 0.9291 (mt) cc_final: 0.8955 (tp) REVERT: E 78 LYS cc_start: 0.9541 (mmtt) cc_final: 0.9215 (mmmt) REVERT: E 228 ASN cc_start: 0.9545 (t0) cc_final: 0.9172 (p0) REVERT: E 402 ASN cc_start: 0.9562 (m110) cc_final: 0.8711 (t0) REVERT: E 406 GLN cc_start: 0.8542 (mm110) cc_final: 0.8106 (mm110) REVERT: A 552 LEU cc_start: 0.9187 (tp) cc_final: 0.8798 (pp) REVERT: A 635 MET cc_start: 0.8871 (mmm) cc_final: 0.8490 (mmt) REVERT: A 689 LEU cc_start: 0.9123 (mt) cc_final: 0.8704 (pp) REVERT: A 805 VAL cc_start: 0.7953 (OUTLIER) cc_final: 0.7732 (m) REVERT: A 807 MET cc_start: 0.8844 (mmp) cc_final: 0.8528 (mmp) REVERT: A 855 MET cc_start: 0.8616 (ppp) cc_final: 0.8047 (ppp) REVERT: B 382 ASN cc_start: 0.7721 (m110) cc_final: 0.6577 (p0) REVERT: B 388 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7370 (mt) REVERT: B 420 GLU cc_start: 0.9101 (tp30) cc_final: 0.8886 (tp30) REVERT: B 483 PHE cc_start: 0.7512 (m-10) cc_final: 0.7291 (m-10) REVERT: B 488 TRP cc_start: 0.8568 (m100) cc_final: 0.7876 (m100) REVERT: C 51 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8767 (mp0) REVERT: C 185 MET cc_start: 0.8659 (mmm) cc_final: 0.8266 (tmm) REVERT: C 221 GLN cc_start: 0.9668 (mt0) cc_final: 0.9392 (mp10) REVERT: C 326 PHE cc_start: 0.8338 (m-80) cc_final: 0.7929 (t80) REVERT: C 336 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8245 (p) REVERT: C 429 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9054 (mp) REVERT: C 450 MET cc_start: 0.8777 (ptp) cc_final: 0.8523 (ptp) REVERT: C 504 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7962 (pp20) REVERT: C 625 MET cc_start: 0.7430 (mmt) cc_final: 0.6449 (tpt) outliers start: 30 outliers final: 17 residues processed: 220 average time/residue: 0.1065 time to fit residues: 36.5591 Evaluate side-chains 188 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 351 ILE Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 805 VAL 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 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 366 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain F residue 232 MET 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: 20.0000 chunk 21 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 165 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 150 ASN ** A 747 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.061020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.047495 restraints weight = 89019.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.049146 restraints weight = 51198.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.050296 restraints weight = 34581.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.051120 restraints weight = 25888.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.051659 restraints weight = 20850.492| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15437 Z= 0.122 Angle : 0.676 12.439 20882 Z= 0.324 Chirality : 0.041 0.277 2416 Planarity : 0.004 0.038 2642 Dihedral : 7.525 77.879 2146 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.04 % Favored : 96.91 % Rotamer: Outliers : 1.82 % Allowed : 17.78 % Favored : 80.40 % 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: 0.73 (0.20), residues: 1843 helix: 1.21 (0.16), residues: 1113 sheet: -1.81 (0.35), residues: 151 loop : -0.11 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 692 TYR 0.022 0.001 TYR A 579 PHE 0.024 0.001 PHE D 149 TRP 0.023 0.001 TRP B 475 HIS 0.011 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00264 (15433) covalent geometry : angle 0.67580 (20882) hydrogen bonds : bond 0.03494 ( 835) hydrogen bonds : angle 4.50823 ( 2433) Misc. bond : bond 0.00029 ( 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 207 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.622 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: D 146 LEU cc_start: 0.8861 (mt) cc_final: 0.8624 (mm) REVERT: D 148 GLU cc_start: 0.8807 (tt0) cc_final: 0.8510 (tt0) REVERT: D 324 MET cc_start: 0.9049 (mmm) cc_final: 0.8748 (mmm) REVERT: D 404 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8671 (tp30) REVERT: E 1 MET cc_start: 0.8673 (tpt) cc_final: 0.8326 (tpt) REVERT: E 22 LEU cc_start: 0.9279 (mt) cc_final: 0.8994 (tp) REVERT: E 78 LYS cc_start: 0.9535 (mmtt) cc_final: 0.9215 (mmmt) REVERT: E 228 ASN cc_start: 0.9533 (t0) cc_final: 0.9155 (m110) REVERT: E 402 ASN cc_start: 0.9510 (m110) cc_final: 0.8984 (p0) REVERT: A 552 LEU cc_start: 0.9168 (tp) cc_final: 0.8779 (pp) REVERT: A 635 MET cc_start: 0.8897 (mmm) cc_final: 0.8542 (mmt) REVERT: A 689 LEU cc_start: 0.9145 (mt) cc_final: 0.8721 (pp) REVERT: A 807 MET cc_start: 0.8904 (mmp) cc_final: 0.8573 (mmp) REVERT: A 855 MET cc_start: 0.8618 (ppp) cc_final: 0.8068 (ppp) REVERT: B 382 ASN cc_start: 0.7740 (m110) cc_final: 0.6501 (p0) REVERT: B 388 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7284 (mt) REVERT: B 420 GLU cc_start: 0.9090 (tp30) cc_final: 0.8838 (tp30) REVERT: B 483 PHE cc_start: 0.7513 (m-10) cc_final: 0.7271 (m-10) REVERT: B 488 TRP cc_start: 0.8466 (m100) cc_final: 0.7773 (m100) REVERT: C 51 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8758 (mp0) REVERT: C 221 GLN cc_start: 0.9675 (mt0) cc_final: 0.9397 (mp10) REVERT: C 326 PHE cc_start: 0.8411 (m-80) cc_final: 0.8037 (t80) REVERT: C 336 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8181 (p) REVERT: C 388 LYS cc_start: 0.9263 (tptp) cc_final: 0.9005 (tptp) REVERT: C 429 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9042 (mp) REVERT: C 504 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7894 (pp20) REVERT: C 625 MET cc_start: 0.7453 (mmt) cc_final: 0.6482 (tpt) outliers start: 30 outliers final: 18 residues processed: 197 average time/residue: 0.1077 time to fit residues: 33.2245 Evaluate side-chains 185 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 351 ILE Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain A residue 632 ILE 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 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 366 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain F residue 232 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 138 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 78 optimal weight: 20.0000 chunk 73 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN 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 = 0.061070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.047551 restraints weight = 88583.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.049188 restraints weight = 50975.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.050315 restraints weight = 34567.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.051067 restraints weight = 25949.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.051672 restraints weight = 21093.573| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15437 Z= 0.128 Angle : 0.682 12.268 20882 Z= 0.328 Chirality : 0.042 0.320 2416 Planarity : 0.004 0.062 2642 Dihedral : 7.522 84.841 2146 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.96 % Rotamer: Outliers : 1.94 % Allowed : 18.20 % 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: 0.81 (0.20), residues: 1843 helix: 1.27 (0.16), residues: 1125 sheet: -1.66 (0.35), residues: 161 loop : -0.08 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 130 TYR 0.012 0.001 TYR E 258 PHE 0.054 0.001 PHE C 362 TRP 0.023 0.001 TRP B 475 HIS 0.009 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00283 (15433) covalent geometry : angle 0.68201 (20882) hydrogen bonds : bond 0.03461 ( 835) hydrogen bonds : angle 4.51905 ( 2433) Misc. bond : bond 0.00028 ( 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 202 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.649 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 146 LEU cc_start: 0.8852 (mt) cc_final: 0.8617 (mm) REVERT: D 148 GLU cc_start: 0.8794 (tt0) cc_final: 0.8507 (tt0) REVERT: D 324 MET cc_start: 0.9063 (mmm) cc_final: 0.8754 (mmm) REVERT: D 404 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8689 (tp30) REVERT: E 1 MET cc_start: 0.8589 (tpt) cc_final: 0.8274 (tpt) REVERT: E 22 LEU cc_start: 0.9281 (mt) cc_final: 0.8966 (tp) REVERT: E 78 LYS cc_start: 0.9542 (mmtt) cc_final: 0.9269 (mmmm) REVERT: E 228 ASN cc_start: 0.9525 (t0) cc_final: 0.9152 (m110) REVERT: A 552 LEU cc_start: 0.9176 (tp) cc_final: 0.8787 (pp) REVERT: A 635 MET cc_start: 0.8934 (mmm) cc_final: 0.8572 (mmt) REVERT: A 689 LEU cc_start: 0.9136 (mt) cc_final: 0.8709 (pp) REVERT: A 701 LEU cc_start: 0.8755 (tp) cc_final: 0.8470 (pp) REVERT: A 855 MET cc_start: 0.8627 (ppp) cc_final: 0.8067 (ppp) REVERT: B 382 ASN cc_start: 0.7780 (m110) cc_final: 0.6573 (p0) REVERT: B 388 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7285 (mt) REVERT: B 420 GLU cc_start: 0.9100 (tp30) cc_final: 0.8846 (tp30) REVERT: B 483 PHE cc_start: 0.7505 (m-10) cc_final: 0.7282 (m-10) REVERT: B 488 TRP cc_start: 0.8477 (m100) cc_final: 0.7766 (m100) REVERT: C 51 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8774 (mp0) REVERT: C 221 GLN cc_start: 0.9674 (mt0) cc_final: 0.9401 (mp10) REVERT: C 326 PHE cc_start: 0.8426 (m-80) cc_final: 0.8052 (t80) REVERT: C 336 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8127 (p) REVERT: C 388 LYS cc_start: 0.9261 (tptp) cc_final: 0.8998 (tptp) REVERT: C 429 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9028 (mp) REVERT: C 450 MET cc_start: 0.8976 (ptp) cc_final: 0.8677 (pmm) REVERT: C 504 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7878 (pp20) REVERT: C 625 MET cc_start: 0.7439 (mmt) cc_final: 0.6481 (tpt) outliers start: 32 outliers final: 22 residues processed: 190 average time/residue: 0.1116 time to fit residues: 32.6014 Evaluate side-chains 188 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 340 LEU Chi-restraints excluded: chain D residue 341 CYS 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 180 LEU Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain A residue 632 ILE 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 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 366 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 33 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN C 591 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.060993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.047390 restraints weight = 89744.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.049031 restraints weight = 52063.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.050154 restraints weight = 35220.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.050913 restraints weight = 26473.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.051500 restraints weight = 21436.937| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15437 Z= 0.128 Angle : 0.703 18.148 20882 Z= 0.335 Chirality : 0.041 0.302 2416 Planarity : 0.004 0.040 2642 Dihedral : 7.462 88.569 2146 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.88 % Favored : 97.07 % Rotamer: Outliers : 1.88 % Allowed : 18.81 % Favored : 79.31 % 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: 0.88 (0.20), residues: 1843 helix: 1.30 (0.16), residues: 1124 sheet: -1.53 (0.35), residues: 162 loop : -0.05 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 231 TYR 0.024 0.001 TYR A 579 PHE 0.023 0.001 PHE C 362 TRP 0.022 0.002 TRP B 475 HIS 0.009 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00283 (15433) covalent geometry : angle 0.70329 (20882) hydrogen bonds : bond 0.03399 ( 835) hydrogen bonds : angle 4.50292 ( 2433) Misc. bond : bond 0.00032 ( 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 200 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.523 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: D 146 LEU cc_start: 0.8843 (mt) cc_final: 0.8564 (mm) REVERT: D 148 GLU cc_start: 0.8790 (tt0) cc_final: 0.8500 (tt0) REVERT: D 324 MET cc_start: 0.9072 (mmm) cc_final: 0.8755 (mmm) REVERT: D 404 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8701 (tp30) REVERT: E 1 MET cc_start: 0.8459 (tpt) cc_final: 0.8142 (tpt) REVERT: E 22 LEU cc_start: 0.9305 (mt) cc_final: 0.8988 (tp) REVERT: E 39 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8825 (pp) REVERT: E 78 LYS cc_start: 0.9513 (mmtt) cc_final: 0.9246 (mmmt) REVERT: E 228 ASN cc_start: 0.9520 (t0) cc_final: 0.9065 (m110) REVERT: A 552 LEU cc_start: 0.9190 (tp) cc_final: 0.8797 (pp) REVERT: A 635 MET cc_start: 0.8905 (mmm) cc_final: 0.8551 (mmt) REVERT: A 689 LEU cc_start: 0.9149 (mt) cc_final: 0.8710 (pp) REVERT: A 701 LEU cc_start: 0.8724 (tp) cc_final: 0.8485 (pp) REVERT: A 807 MET cc_start: 0.8815 (mmp) cc_final: 0.8386 (mmp) REVERT: A 855 MET cc_start: 0.8619 (ppp) cc_final: 0.8049 (ppp) REVERT: B 382 ASN cc_start: 0.7842 (m110) cc_final: 0.7039 (p0) REVERT: B 420 GLU cc_start: 0.9106 (tp30) cc_final: 0.8844 (tp30) REVERT: B 483 PHE cc_start: 0.7505 (m-10) cc_final: 0.7292 (m-10) REVERT: B 488 TRP cc_start: 0.8472 (m100) cc_final: 0.7775 (m100) REVERT: C 51 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8795 (mp0) REVERT: C 221 GLN cc_start: 0.9677 (mt0) cc_final: 0.9370 (mp10) REVERT: C 326 PHE cc_start: 0.8457 (m-80) cc_final: 0.8118 (t80) REVERT: C 336 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8149 (p) REVERT: C 429 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9021 (mp) REVERT: C 450 MET cc_start: 0.8980 (ptp) cc_final: 0.8753 (ptp) REVERT: C 504 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7895 (pp20) REVERT: C 625 MET cc_start: 0.7423 (mmt) cc_final: 0.6557 (tpt) outliers start: 31 outliers final: 23 residues processed: 189 average time/residue: 0.1021 time to fit residues: 30.5539 Evaluate side-chains 185 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 341 CYS Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 39 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 180 LEU Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain A residue 632 ILE 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 A residue 914 HIS Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 212 PHE 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 366 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 141 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 22 optimal weight: 0.1980 chunk 179 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 107 GLN ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN C 68 GLN C 591 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.060965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.047427 restraints weight = 88845.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.049048 restraints weight = 51314.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.050164 restraints weight = 34931.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.050886 restraints weight = 26294.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.051490 restraints weight = 21434.317| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15437 Z= 0.124 Angle : 0.700 16.595 20882 Z= 0.333 Chirality : 0.041 0.362 2416 Planarity : 0.004 0.040 2642 Dihedral : 7.378 85.690 2146 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.23 % Rotamer: Outliers : 1.88 % Allowed : 18.93 % Favored : 79.19 % 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: 1.09 (0.20), residues: 1843 helix: 1.45 (0.16), residues: 1104 sheet: -1.29 (0.36), residues: 173 loop : 0.13 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 231 TYR 0.011 0.001 TYR C 430 PHE 0.067 0.001 PHE C 362 TRP 0.022 0.002 TRP B 475 HIS 0.008 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00276 (15433) covalent geometry : angle 0.69989 (20882) hydrogen bonds : bond 0.03345 ( 835) hydrogen bonds : angle 4.47046 ( 2433) Misc. bond : bond 0.00033 ( 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 193 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.530 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 146 LEU cc_start: 0.8820 (mt) cc_final: 0.8605 (mm) REVERT: D 148 GLU cc_start: 0.8751 (tt0) cc_final: 0.8469 (tt0) REVERT: D 324 MET cc_start: 0.9058 (mmm) cc_final: 0.8743 (mmm) REVERT: D 404 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8711 (tp30) REVERT: D 409 LEU cc_start: 0.9221 (tp) cc_final: 0.8516 (mp) REVERT: D 429 LEU cc_start: 0.8700 (tp) cc_final: 0.8153 (pt) REVERT: E 1 MET cc_start: 0.8357 (tpt) cc_final: 0.8034 (tpt) REVERT: E 78 LYS cc_start: 0.9523 (mmtt) cc_final: 0.9257 (mmmt) REVERT: E 224 ASP cc_start: 0.9110 (t0) cc_final: 0.8809 (t0) REVERT: E 228 ASN cc_start: 0.9507 (t0) cc_final: 0.9082 (m110) REVERT: A 552 LEU cc_start: 0.9189 (tp) cc_final: 0.8807 (pp) REVERT: A 635 MET cc_start: 0.8920 (mmm) cc_final: 0.8474 (mmt) REVERT: A 689 LEU cc_start: 0.9151 (mt) cc_final: 0.8714 (pp) REVERT: A 701 LEU cc_start: 0.8715 (tp) cc_final: 0.8492 (pp) REVERT: A 855 MET cc_start: 0.8622 (ppp) cc_final: 0.8019 (ppp) REVERT: B 343 TRP cc_start: 0.9428 (m-10) cc_final: 0.9106 (m-10) REVERT: B 382 ASN cc_start: 0.7855 (m110) cc_final: 0.6616 (p0) REVERT: B 388 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7391 (mt) REVERT: B 420 GLU cc_start: 0.9109 (tp30) cc_final: 0.8844 (tp30) REVERT: B 483 PHE cc_start: 0.7469 (m-10) cc_final: 0.7264 (m-10) REVERT: B 488 TRP cc_start: 0.8441 (m100) cc_final: 0.7911 (m100) REVERT: C 51 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8799 (mp0) REVERT: C 221 GLN cc_start: 0.9660 (mt0) cc_final: 0.9310 (mp10) REVERT: C 326 PHE cc_start: 0.8489 (m-80) cc_final: 0.8146 (t80) REVERT: C 336 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8183 (p) REVERT: C 429 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8990 (mp) REVERT: C 450 MET cc_start: 0.8977 (ptp) cc_final: 0.8731 (ptp) REVERT: C 504 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7925 (pp20) REVERT: C 625 MET cc_start: 0.7443 (mmt) cc_final: 0.6629 (tpt) outliers start: 31 outliers final: 23 residues processed: 181 average time/residue: 0.1050 time to fit residues: 30.1120 Evaluate side-chains 184 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 341 CYS 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 E residue 180 LEU Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain A residue 632 ILE 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 A residue 914 HIS Chi-restraints excluded: chain B residue 388 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 311 ILE Chi-restraints excluded: chain C residue 336 THR 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 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: 0.9980 chunk 119 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 151 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3488 r_free = 0.3488 target = 0.060901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.047531 restraints weight = 87683.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.049161 restraints weight = 51562.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.050292 restraints weight = 34969.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.051033 restraints weight = 26209.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.051668 restraints weight = 21276.280| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15437 Z= 0.117 Angle : 0.711 16.528 20882 Z= 0.334 Chirality : 0.041 0.368 2416 Planarity : 0.003 0.041 2642 Dihedral : 7.289 85.367 2146 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.88 % Favored : 97.07 % Rotamer: Outliers : 1.64 % Allowed : 19.60 % Favored : 78.76 % 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: 1.06 (0.20), residues: 1843 helix: 1.35 (0.16), residues: 1121 sheet: -1.18 (0.36), residues: 173 loop : 0.19 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 130 TYR 0.022 0.001 TYR B 356 PHE 0.025 0.001 PHE C 332 TRP 0.024 0.002 TRP B 475 HIS 0.007 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00257 (15433) covalent geometry : angle 0.71102 (20882) hydrogen bonds : bond 0.03283 ( 835) hydrogen bonds : angle 4.43168 ( 2433) Misc. bond : bond 0.00036 ( 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 : 0.564 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: D 148 GLU cc_start: 0.8769 (tt0) cc_final: 0.8452 (tt0) REVERT: D 324 MET cc_start: 0.9076 (mmm) cc_final: 0.8755 (mmm) REVERT: D 385 MET cc_start: 0.8628 (mmp) cc_final: 0.8176 (mmm) REVERT: D 404 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8706 (tp30) REVERT: D 409 LEU cc_start: 0.9256 (tp) cc_final: 0.8557 (mp) REVERT: D 429 LEU cc_start: 0.8690 (tp) cc_final: 0.8107 (pt) REVERT: E 1 MET cc_start: 0.8285 (tpt) cc_final: 0.7971 (tpt) REVERT: E 78 LYS cc_start: 0.9514 (mmtt) cc_final: 0.9240 (mmmt) REVERT: E 224 ASP cc_start: 0.9085 (t0) cc_final: 0.8764 (t0) REVERT: E 228 ASN cc_start: 0.9493 (t0) cc_final: 0.9062 (m110) REVERT: A 552 LEU cc_start: 0.9201 (tp) cc_final: 0.8835 (pp) REVERT: A 635 MET cc_start: 0.8813 (mmm) cc_final: 0.8495 (mmt) REVERT: A 689 LEU cc_start: 0.9181 (mt) cc_final: 0.8760 (pp) REVERT: A 701 LEU cc_start: 0.8705 (tp) cc_final: 0.8477 (pp) REVERT: A 807 MET cc_start: 0.8801 (mmp) cc_final: 0.8394 (mmp) REVERT: A 855 MET cc_start: 0.8600 (ppp) cc_final: 0.7983 (ppp) REVERT: B 343 TRP cc_start: 0.9420 (m-10) cc_final: 0.9108 (m-10) REVERT: B 382 ASN cc_start: 0.7843 (m110) cc_final: 0.6592 (p0) REVERT: B 388 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7390 (mt) REVERT: B 420 GLU cc_start: 0.9106 (tp30) cc_final: 0.8844 (tp30) REVERT: B 476 ASP cc_start: 0.7573 (p0) cc_final: 0.7261 (p0) REVERT: B 483 PHE cc_start: 0.7461 (m-10) cc_final: 0.7247 (m-10) REVERT: B 488 TRP cc_start: 0.8451 (m100) cc_final: 0.7865 (m100) REVERT: C 51 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8804 (mp0) REVERT: C 128 MET cc_start: 0.8996 (mpp) cc_final: 0.8755 (mpp) REVERT: C 221 GLN cc_start: 0.9664 (mt0) cc_final: 0.9318 (mp10) REVERT: C 326 PHE cc_start: 0.8475 (m-80) cc_final: 0.8132 (t80) REVERT: C 334 LEU cc_start: 0.9408 (mt) cc_final: 0.9115 (mm) REVERT: C 429 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9013 (mp) REVERT: C 450 MET cc_start: 0.8925 (ptp) cc_final: 0.8695 (ptp) REVERT: C 504 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7870 (pp20) REVERT: C 625 MET cc_start: 0.7405 (mmt) cc_final: 0.6588 (tpt) outliers start: 27 outliers final: 20 residues processed: 180 average time/residue: 0.1021 time to fit residues: 28.8665 Evaluate side-chains 182 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 341 CYS 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 E residue 180 LEU Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain A residue 632 ILE 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 A residue 914 HIS Chi-restraints excluded: chain B residue 388 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 474 LEU Chi-restraints excluded: chain C residue 504 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 164 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 406 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.060993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.047645 restraints weight = 87784.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.049248 restraints weight = 51668.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.050364 restraints weight = 35088.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.051147 restraints weight = 26359.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.051756 restraints weight = 21248.423| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15437 Z= 0.117 Angle : 0.712 15.740 20882 Z= 0.335 Chirality : 0.042 0.403 2416 Planarity : 0.004 0.052 2642 Dihedral : 7.238 85.572 2146 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.23 % Rotamer: Outliers : 1.58 % Allowed : 19.90 % Favored : 78.52 % 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: 1.09 (0.20), residues: 1843 helix: 1.38 (0.16), residues: 1121 sheet: -1.11 (0.37), residues: 173 loop : 0.18 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 130 TYR 0.009 0.001 TYR E 229 PHE 0.026 0.001 PHE C 332 TRP 0.025 0.002 TRP B 475 HIS 0.007 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00257 (15433) covalent geometry : angle 0.71208 (20882) hydrogen bonds : bond 0.03241 ( 835) hydrogen bonds : angle 4.41119 ( 2433) Misc. bond : bond 0.00037 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2665.08 seconds wall clock time: 46 minutes 48.37 seconds (2808.37 seconds total)