Starting phenix.real_space_refine on Fri Jun 13 19:47:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jk6_22363/06_2025/7jk6_22363.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jk6_22363/06_2025/7jk6_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_22363/06_2025/7jk6_22363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jk6_22363/06_2025/7jk6_22363.map" model { file = "/net/cci-nas-00/data/ceres_data/7jk6_22363/06_2025/7jk6_22363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jk6_22363/06_2025/7jk6_22363.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.92, per 1000 atoms: 0.59 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: 3.82 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.85 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: 4.70 Time building geometry restraints manager: 4.42 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: 1.140 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: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 35.720 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.260 ------------------------------------------------------------------------------- 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 : 5.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.036 0.004 TRP B 475 HIS 0.012 0.002 HIS E 412 PHE 0.030 0.004 PHE E 450 TYR 0.029 0.004 TYR C 255 ARG 0.008 0.001 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.15005 ( 835) hydrogen bonds : angle 6.38914 ( 2433) covalent geometry : bond 0.00777 (15433) covalent geometry : angle 1.26688 (20882) 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 : 1.521 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: 0.9550 (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: 0.8915 (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: 0.8464 (t80) REVERT: C 221 GLN cc_start: 0.9668 (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: 0.3220 time to fit residues: 149.4960 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 : 1.963 ------------------------------------------------------------------------------- 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 157 optimal weight: 0.9980 chunk 140 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 56 optimal weight: 0.0060 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 overall best weight: 1.6002 ------------------------------------------------------------------------------- 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 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 591 HIS C 615 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.061983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.048169 restraints weight = 85223.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.049875 restraints weight = 48696.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.051067 restraints weight = 32774.699| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15437 Z= 0.156 Angle : 0.721 9.760 20882 Z= 0.367 Chirality : 0.042 0.174 2416 Planarity : 0.005 0.061 2642 Dihedral : 8.064 72.594 2148 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.33 % Allowed : 12.14 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.19), residues: 1843 helix: -0.11 (0.14), residues: 1118 sheet: -2.28 (0.36), residues: 162 loop : 0.01 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 475 HIS 0.014 0.001 HIS B 429 PHE 0.018 0.002 PHE C 49 TYR 0.029 0.002 TYR B 356 ARG 0.010 0.001 ARG F 231 Details of bonding type rmsd hydrogen bonds : bond 0.04633 ( 835) hydrogen bonds : angle 5.07505 ( 2433) covalent geometry : bond 0.00337 (15433) covalent geometry : angle 0.72066 (20882) Misc. bond : bond 0.00224 ( 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 256 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 234 time to evaluate : 2.311 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: 0.8390 (m-80) cc_final: 0.7936 (m-80) REVERT: D 102 SER cc_start: 0.9170 (t) cc_final: 0.8863 (p) REVERT: D 146 LEU cc_start: 0.9080 (mt) cc_final: 0.8689 (mm) REVERT: D 148 GLU cc_start: 0.8530 (tt0) cc_final: 0.8316 (tt0) REVERT: D 324 MET cc_start: 0.9031 (mtp) cc_final: 0.8556 (ttm) REVERT: D 404 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8701 (tp30) REVERT: D 409 LEU cc_start: 0.9317 (tp) cc_final: 0.8982 (mp) REVERT: E 82 GLU cc_start: 0.9308 (mt-10) cc_final: 0.9103 (mm-30) REVERT: E 228 ASN cc_start: 0.9620 (t0) cc_final: 0.9296 (p0) REVERT: E 402 ASN cc_start: 0.9487 (m110) cc_final: 0.9151 (p0) REVERT: E 415 LEU cc_start: 0.8880 (mm) cc_final: 0.8640 (mm) REVERT: A 552 LEU cc_start: 0.9359 (tp) cc_final: 0.8954 (pp) REVERT: A 622 ASN cc_start: 0.9230 (t0) cc_final: 0.8993 (p0) REVERT: A 635 MET cc_start: 0.8818 (mmm) cc_final: 0.8041 (mmt) REVERT: A 639 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8790 (pt0) REVERT: A 701 LEU cc_start: 0.8981 (tp) cc_final: 0.8757 (pp) REVERT: A 720 MET cc_start: 0.9382 (tpt) cc_final: 0.9166 (tpp) REVERT: A 724 GLU cc_start: 0.8088 (mp0) cc_final: 0.7774 (mp0) REVERT: A 855 MET cc_start: 0.8980 (ppp) cc_final: 0.8769 (ppp) REVERT: B 339 TYR cc_start: 0.8669 (m-10) cc_final: 0.8444 (m-10) REVERT: B 343 TRP cc_start: 0.9459 (m-10) cc_final: 0.9229 (m-10) REVERT: B 488 TRP cc_start: 0.8537 (m100) cc_final: 0.8096 (m100) REVERT: C 51 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8833 (mp0) REVERT: C 128 MET cc_start: 0.8947 (mpp) cc_final: 0.8627 (mpp) REVERT: C 209 LEU cc_start: 0.9678 (mp) cc_final: 0.9452 (mm) REVERT: C 212 PHE cc_start: 0.8880 (t80) cc_final: 0.8330 (t80) REVERT: C 222 ASP cc_start: 0.9176 (m-30) cc_final: 0.8899 (p0) REVERT: C 336 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8451 (p) REVERT: C 340 LYS cc_start: 0.9078 (tttt) cc_final: 0.8780 (tptp) REVERT: C 384 TYR cc_start: 0.8783 (t80) cc_final: 0.8515 (t80) REVERT: C 429 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9017 (mp) REVERT: C 625 MET cc_start: 0.7476 (mmt) cc_final: 0.6414 (tpt) outliers start: 22 outliers final: 13 residues processed: 245 average time/residue: 0.2863 time to fit residues: 104.7929 Evaluate side-chains 199 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain 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 32 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN C 591 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.062018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.048117 restraints weight = 85366.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.049834 restraints weight = 49158.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.051027 restraints weight = 32985.190| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15437 Z= 0.134 Angle : 0.671 9.625 20882 Z= 0.335 Chirality : 0.041 0.241 2416 Planarity : 0.004 0.057 2642 Dihedral : 7.851 70.527 2146 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.04 % Favored : 96.91 % Rotamer: Outliers : 1.64 % Allowed : 14.81 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.19), residues: 1843 helix: 0.56 (0.15), residues: 1118 sheet: -1.98 (0.36), residues: 162 loop : -0.14 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 475 HIS 0.006 0.001 HIS E 412 PHE 0.036 0.001 PHE C 362 TYR 0.017 0.001 TYR D 239 ARG 0.005 0.000 ARG E 130 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 835) hydrogen bonds : angle 4.82351 ( 2433) covalent geometry : bond 0.00291 (15433) covalent geometry : angle 0.67133 (20882) Misc. bond : bond 0.00063 ( 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 229 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 79 PHE cc_start: 0.8296 (t80) cc_final: 0.7600 (t80) REVERT: D 102 SER cc_start: 0.9181 (t) cc_final: 0.8858 (p) REVERT: D 133 LYS cc_start: 0.9538 (tppt) cc_final: 0.9313 (tppt) REVERT: D 148 GLU cc_start: 0.8688 (tt0) cc_final: 0.8439 (tt0) REVERT: D 324 MET cc_start: 0.9007 (mtp) cc_final: 0.8780 (mmm) REVERT: D 404 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8697 (tp30) REVERT: D 409 LEU cc_start: 0.9288 (tp) cc_final: 0.8931 (mp) REVERT: E 82 GLU cc_start: 0.9317 (mt-10) cc_final: 0.8992 (mm-30) REVERT: E 228 ASN cc_start: 0.9597 (t0) cc_final: 0.9282 (p0) REVERT: E 402 ASN cc_start: 0.9510 (m110) cc_final: 0.9127 (p0) REVERT: E 415 LEU cc_start: 0.8866 (mm) cc_final: 0.8626 (mm) REVERT: A 552 LEU cc_start: 0.9366 (tp) cc_final: 0.8884 (pp) REVERT: A 635 MET cc_start: 0.8843 (mmm) cc_final: 0.8431 (mmt) REVERT: A 639 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8786 (pt0) REVERT: A 701 LEU cc_start: 0.8957 (tp) cc_final: 0.8742 (pp) REVERT: A 720 MET cc_start: 0.9360 (tpt) cc_final: 0.9151 (tpp) REVERT: A 767 GLU cc_start: 0.9312 (mm-30) cc_final: 0.9107 (tp30) REVERT: A 807 MET cc_start: 0.8833 (mmp) cc_final: 0.8462 (mmp) REVERT: B 343 TRP cc_start: 0.9457 (m-10) cc_final: 0.9190 (m-10) REVERT: B 393 MET cc_start: 0.8362 (mpp) cc_final: 0.8020 (mpp) REVERT: B 483 PHE cc_start: 0.7568 (m-10) cc_final: 0.7228 (m-10) REVERT: B 488 TRP cc_start: 0.8573 (m100) cc_final: 0.8154 (m100) REVERT: C 51 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8773 (mp0) REVERT: C 128 MET cc_start: 0.8934 (mpp) cc_final: 0.8692 (mpp) REVERT: C 185 MET cc_start: 0.9055 (mmm) cc_final: 0.8842 (mmm) REVERT: C 212 PHE cc_start: 0.8857 (t80) cc_final: 0.8178 (t80) REVERT: C 221 GLN cc_start: 0.9460 (OUTLIER) cc_final: 0.9188 (mp10) REVERT: C 222 ASP cc_start: 0.9157 (m-30) cc_final: 0.8944 (p0) REVERT: C 326 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7679 (t80) REVERT: C 388 LYS cc_start: 0.9285 (tptp) cc_final: 0.9039 (tptp) REVERT: C 429 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9033 (mp) REVERT: C 625 MET cc_start: 0.7476 (mmt) cc_final: 0.6440 (tpt) outliers start: 27 outliers final: 17 residues processed: 217 average time/residue: 0.2472 time to fit residues: 81.7465 Evaluate side-chains 192 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 138 VAL 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 390 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 326 PHE 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 52 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 81 optimal weight: 0.0270 chunk 159 optimal weight: 9.9990 overall best weight: 4.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 172 GLN E 68 HIS ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN C 312 HIS C 591 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.058629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.045536 restraints weight = 91467.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.047095 restraints weight = 51679.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.048214 restraints weight = 34823.192| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15437 Z= 0.241 Angle : 0.762 13.515 20882 Z= 0.380 Chirality : 0.043 0.251 2416 Planarity : 0.005 0.065 2642 Dihedral : 8.161 66.337 2146 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.77 % Favored : 97.12 % Rotamer: Outliers : 2.67 % Allowed : 15.84 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.19), residues: 1843 helix: 0.88 (0.15), residues: 1117 sheet: -1.92 (0.36), residues: 160 loop : -0.23 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 703 HIS 0.008 0.002 HIS D 255 PHE 0.036 0.002 PHE C 362 TYR 0.025 0.002 TYR A 579 ARG 0.007 0.001 ARG C 357 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 835) hydrogen bonds : angle 4.94485 ( 2433) covalent geometry : bond 0.00513 (15433) covalent geometry : angle 0.76151 (20882) Misc. bond : bond 0.00046 ( 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: 44 poor density : 173 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 324 MET cc_start: 0.9142 (mtp) cc_final: 0.8715 (ttm) REVERT: D 404 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8953 (tp30) REVERT: E 82 GLU cc_start: 0.9285 (mt-10) cc_final: 0.9031 (mm-30) REVERT: E 98 VAL cc_start: 0.9558 (OUTLIER) cc_final: 0.9265 (t) REVERT: E 134 MET cc_start: 0.7958 (ptm) cc_final: 0.7408 (ptm) REVERT: E 228 ASN cc_start: 0.9602 (t0) cc_final: 0.9318 (p0) REVERT: E 402 ASN cc_start: 0.9574 (m110) cc_final: 0.9141 (p0) REVERT: E 415 LEU cc_start: 0.8852 (mm) cc_final: 0.8601 (mm) REVERT: A 536 MET cc_start: 0.8439 (mmm) cc_final: 0.7926 (mmm) REVERT: A 552 LEU cc_start: 0.9302 (tp) cc_final: 0.8842 (pp) REVERT: A 639 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8740 (pt0) REVERT: A 701 LEU cc_start: 0.8917 (tp) cc_final: 0.8713 (pp) REVERT: A 720 MET cc_start: 0.9296 (tpt) cc_final: 0.9075 (tpp) REVERT: B 343 TRP cc_start: 0.9424 (m-10) cc_final: 0.9135 (m-10) REVERT: B 382 ASN cc_start: 0.7717 (m110) cc_final: 0.6947 (p0) REVERT: B 393 MET cc_start: 0.8422 (mpp) cc_final: 0.8115 (mpp) REVERT: B 476 ASP cc_start: 0.7586 (p0) cc_final: 0.7363 (p0) REVERT: B 488 TRP cc_start: 0.8480 (m100) cc_final: 0.8153 (m100) REVERT: C 51 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8758 (mp0) REVERT: C 128 MET cc_start: 0.8945 (mpp) cc_final: 0.8731 (mpp) REVERT: C 185 MET cc_start: 0.8937 (mmm) cc_final: 0.8725 (mmm) REVERT: C 221 GLN cc_start: 0.9584 (OUTLIER) cc_final: 0.9183 (mp10) REVERT: C 326 PHE cc_start: 0.8574 (m-80) cc_final: 0.8022 (t80) REVERT: C 429 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9071 (mp) REVERT: C 625 MET cc_start: 0.7415 (mmt) cc_final: 0.6531 (tpt) outliers start: 44 outliers final: 27 residues processed: 200 average time/residue: 0.2337 time to fit residues: 72.7135 Evaluate side-chains 186 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 699 ASN Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 502 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 53 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 109 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 172 GLN ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN C 591 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.059657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.046456 restraints weight = 89348.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.048030 restraints weight = 51548.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.049134 restraints weight = 34864.571| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3585 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= 0.130 Angle : 0.682 11.971 20882 Z= 0.336 Chirality : 0.042 0.335 2416 Planarity : 0.004 0.093 2642 Dihedral : 7.928 82.860 2146 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 1.76 % Allowed : 17.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.20), residues: 1843 helix: 1.08 (0.15), residues: 1125 sheet: -1.78 (0.36), residues: 160 loop : -0.13 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 475 HIS 0.011 0.001 HIS B 362 PHE 0.042 0.002 PHE C 362 TYR 0.013 0.001 TYR C 255 ARG 0.009 0.000 ARG F 231 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 835) hydrogen bonds : angle 4.70895 ( 2433) covalent geometry : bond 0.00284 (15433) covalent geometry : angle 0.68155 (20882) Misc. bond : bond 0.00045 ( 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 216 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 148 GLU cc_start: 0.8775 (tt0) cc_final: 0.8562 (pt0) REVERT: D 324 MET cc_start: 0.9071 (mtp) cc_final: 0.8651 (ttm) REVERT: D 404 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8821 (tp30) REVERT: E 78 LYS cc_start: 0.9392 (mmtt) cc_final: 0.8912 (tppt) REVERT: E 82 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8961 (mm-30) REVERT: E 228 ASN cc_start: 0.9570 (t0) cc_final: 0.9277 (p0) REVERT: E 402 ASN cc_start: 0.9570 (m110) cc_final: 0.9078 (p0) REVERT: A 552 LEU cc_start: 0.9225 (tp) cc_final: 0.8780 (pp) REVERT: A 635 MET cc_start: 0.8850 (mmt) cc_final: 0.8491 (mmt) REVERT: A 701 LEU cc_start: 0.8872 (tp) cc_final: 0.8643 (pp) REVERT: A 720 MET cc_start: 0.9269 (tpt) cc_final: 0.9047 (tpp) REVERT: A 767 GLU cc_start: 0.9282 (mm-30) cc_final: 0.9040 (tp30) REVERT: A 807 MET cc_start: 0.8834 (mmp) cc_final: 0.8504 (mmp) REVERT: B 382 ASN cc_start: 0.7802 (m110) cc_final: 0.7027 (p0) REVERT: B 393 MET cc_start: 0.8406 (mpp) cc_final: 0.7977 (mpp) REVERT: B 420 GLU cc_start: 0.9078 (tp30) cc_final: 0.8862 (tp30) REVERT: B 441 MET cc_start: 0.8171 (tpp) cc_final: 0.7819 (tpp) REVERT: B 488 TRP cc_start: 0.8506 (m100) cc_final: 0.7826 (m100) REVERT: C 51 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8776 (mp0) REVERT: C 185 MET cc_start: 0.8916 (mmm) cc_final: 0.8681 (mmm) REVERT: C 222 ASP cc_start: 0.9258 (m-30) cc_final: 0.8943 (p0) REVERT: C 223 LEU cc_start: 0.9830 (tt) cc_final: 0.9475 (mp) REVERT: C 326 PHE cc_start: 0.8511 (m-80) cc_final: 0.8005 (t80) REVERT: C 336 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8281 (p) REVERT: C 429 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9075 (mp) REVERT: C 504 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7937 (pp20) REVERT: C 625 MET cc_start: 0.7405 (mmt) cc_final: 0.6503 (tpt) outliers start: 29 outliers final: 18 residues processed: 206 average time/residue: 0.2671 time to fit residues: 85.1177 Evaluate side-chains 182 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain 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 170 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 441 VAL 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 B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 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 86 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 97 optimal weight: 0.0050 chunk 23 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- 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 352 ASN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.058684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.045586 restraints weight = 90304.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.047134 restraints weight = 52960.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.048176 restraints weight = 35769.553| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15437 Z= 0.175 Angle : 0.704 12.312 20882 Z= 0.345 Chirality : 0.042 0.283 2416 Planarity : 0.004 0.073 2642 Dihedral : 7.908 86.535 2146 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.96 % Rotamer: Outliers : 2.73 % Allowed : 18.20 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1843 helix: 1.14 (0.16), residues: 1130 sheet: -1.71 (0.37), residues: 160 loop : -0.17 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 475 HIS 0.009 0.001 HIS B 362 PHE 0.027 0.002 PHE D 149 TYR 0.018 0.001 TYR E 258 ARG 0.006 0.000 ARG A 692 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 835) hydrogen bonds : angle 4.73757 ( 2433) covalent geometry : bond 0.00378 (15433) covalent geometry : angle 0.70391 (20882) Misc. bond : bond 0.00049 ( 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 211 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 324 MET cc_start: 0.9125 (mtp) cc_final: 0.8678 (ttm) REVERT: D 404 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8875 (tp30) REVERT: E 1 MET cc_start: 0.8916 (tpt) cc_final: 0.8511 (tpt) REVERT: E 82 GLU cc_start: 0.9324 (mt-10) cc_final: 0.9086 (mm-30) REVERT: E 98 VAL cc_start: 0.9518 (OUTLIER) cc_final: 0.9035 (t) REVERT: E 228 ASN cc_start: 0.9583 (t0) cc_final: 0.9301 (p0) REVERT: E 402 ASN cc_start: 0.9575 (m110) cc_final: 0.8717 (t0) REVERT: E 406 GLN cc_start: 0.8681 (mm110) cc_final: 0.8190 (mm110) REVERT: A 552 LEU cc_start: 0.9232 (tp) cc_final: 0.8790 (pp) REVERT: A 720 MET cc_start: 0.9234 (tpt) cc_final: 0.9001 (tpp) REVERT: B 382 ASN cc_start: 0.7834 (m110) cc_final: 0.6661 (p0) REVERT: B 388 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7512 (mt) REVERT: B 420 GLU cc_start: 0.9133 (tp30) cc_final: 0.8895 (tp30) REVERT: B 488 TRP cc_start: 0.8447 (m100) cc_final: 0.7726 (m100) REVERT: C 51 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8758 (mp0) REVERT: C 185 MET cc_start: 0.8930 (mmm) cc_final: 0.8583 (mmm) REVERT: C 222 ASP cc_start: 0.9279 (m-30) cc_final: 0.9006 (p0) REVERT: C 326 PHE cc_start: 0.8608 (m-80) cc_final: 0.8130 (t80) REVERT: C 336 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8221 (p) REVERT: C 424 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7610 (tptp) REVERT: C 429 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9042 (mp) REVERT: C 450 MET cc_start: 0.8843 (ptp) cc_final: 0.8511 (ptp) REVERT: C 625 MET cc_start: 0.7390 (mmt) cc_final: 0.6545 (tpt) outliers start: 45 outliers final: 26 residues processed: 200 average time/residue: 0.2650 time to fit residues: 82.9009 Evaluate side-chains 190 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain A residue 688 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 352 ASN 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 105 ILE 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 424 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 112 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 173 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 102 optimal weight: 0.2980 chunk 29 optimal weight: 0.6980 chunk 139 optimal weight: 9.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 202 GLN E 150 ASN ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 GLN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.059944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.046665 restraints weight = 88432.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.048272 restraints weight = 51349.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.049407 restraints weight = 34595.554| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15437 Z= 0.117 Angle : 0.691 14.773 20882 Z= 0.332 Chirality : 0.042 0.351 2416 Planarity : 0.004 0.061 2642 Dihedral : 7.692 83.904 2146 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 1.40 % Allowed : 19.54 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.20), residues: 1843 helix: 1.15 (0.16), residues: 1137 sheet: -1.57 (0.35), residues: 167 loop : -0.06 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 475 HIS 0.008 0.001 HIS B 362 PHE 0.056 0.002 PHE C 362 TYR 0.013 0.001 TYR C 255 ARG 0.005 0.000 ARG F 231 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 835) hydrogen bonds : angle 4.55064 ( 2433) covalent geometry : bond 0.00247 (15433) covalent geometry : angle 0.69067 (20882) Misc. bond : bond 0.00047 ( 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 200 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 1.902 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 324 MET cc_start: 0.9001 (mtp) cc_final: 0.8592 (ttm) REVERT: D 385 MET cc_start: 0.8580 (mmp) cc_final: 0.8287 (mmm) REVERT: D 404 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8726 (tp30) REVERT: E 1 MET cc_start: 0.8693 (tpt) cc_final: 0.8213 (tpt) REVERT: E 82 GLU cc_start: 0.9533 (mt-10) cc_final: 0.9095 (mm-30) REVERT: E 98 VAL cc_start: 0.9484 (OUTLIER) cc_final: 0.8969 (t) REVERT: E 228 ASN cc_start: 0.9530 (t0) cc_final: 0.9175 (m110) REVERT: E 402 ASN cc_start: 0.9559 (m110) cc_final: 0.8722 (t0) REVERT: E 406 GLN cc_start: 0.8661 (mm110) cc_final: 0.8221 (mm110) REVERT: A 552 LEU cc_start: 0.9189 (tp) cc_final: 0.8791 (pp) REVERT: A 635 MET cc_start: 0.8923 (mmt) cc_final: 0.8570 (mmt) REVERT: A 689 LEU cc_start: 0.9183 (mt) cc_final: 0.8756 (pp) REVERT: A 701 LEU cc_start: 0.8669 (tp) cc_final: 0.8448 (pp) REVERT: A 720 MET cc_start: 0.9225 (tpt) cc_final: 0.8993 (tpp) REVERT: A 807 MET cc_start: 0.8937 (mmp) cc_final: 0.8609 (mmp) REVERT: A 855 MET cc_start: 0.8654 (ppp) cc_final: 0.7981 (ppp) REVERT: B 382 ASN cc_start: 0.7894 (m110) cc_final: 0.6703 (p0) REVERT: B 388 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7439 (mt) REVERT: B 420 GLU cc_start: 0.9107 (tp30) cc_final: 0.8879 (tp30) REVERT: B 488 TRP cc_start: 0.8382 (m100) cc_final: 0.7654 (m100) REVERT: C 51 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8770 (mp0) REVERT: C 128 MET cc_start: 0.9008 (mpp) cc_final: 0.8727 (mpp) REVERT: C 185 MET cc_start: 0.8895 (mmm) cc_final: 0.8481 (mmm) REVERT: C 222 ASP cc_start: 0.9229 (m-30) cc_final: 0.9007 (p0) REVERT: C 223 LEU cc_start: 0.9833 (tt) cc_final: 0.9527 (mp) REVERT: C 326 PHE cc_start: 0.8625 (m-80) cc_final: 0.8172 (t80) REVERT: C 336 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8216 (p) REVERT: C 429 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9038 (mp) REVERT: C 625 MET cc_start: 0.7423 (mmt) cc_final: 0.6610 (tpt) outliers start: 23 outliers final: 15 residues processed: 196 average time/residue: 0.2473 time to fit residues: 74.7892 Evaluate side-chains 178 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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 351 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain A residue 699 ASN Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain F residue 232 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 51 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 124 ASN D 243 ASN ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN C 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.058341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.045258 restraints weight = 89803.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.046821 restraints weight = 51949.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.047869 restraints weight = 35008.455| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15437 Z= 0.184 Angle : 0.733 17.630 20882 Z= 0.356 Chirality : 0.043 0.346 2416 Planarity : 0.004 0.042 2642 Dihedral : 7.750 82.976 2146 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.15 % Favored : 96.80 % Rotamer: Outliers : 1.76 % Allowed : 19.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.20), residues: 1843 helix: 1.24 (0.16), residues: 1132 sheet: -1.57 (0.35), residues: 176 loop : -0.03 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 475 HIS 0.007 0.001 HIS B 362 PHE 0.025 0.002 PHE C 362 TYR 0.023 0.001 TYR B 356 ARG 0.009 0.001 ARG D 97 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 835) hydrogen bonds : angle 4.73043 ( 2433) covalent geometry : bond 0.00399 (15433) covalent geometry : angle 0.73324 (20882) Misc. bond : bond 0.00049 ( 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 186 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 1.868 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: D 324 MET cc_start: 0.9113 (mtp) cc_final: 0.8675 (ttm) REVERT: D 404 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8902 (tp30) REVERT: D 409 LEU cc_start: 0.9359 (tp) cc_final: 0.8745 (mp) REVERT: D 426 MET cc_start: 0.9153 (tpp) cc_final: 0.8776 (tpp) REVERT: E 1 MET cc_start: 0.8693 (tpt) cc_final: 0.8258 (tpt) REVERT: E 78 LYS cc_start: 0.9398 (mmtt) cc_final: 0.8987 (mmmt) REVERT: E 82 GLU cc_start: 0.9551 (mt-10) cc_final: 0.9319 (mt-10) REVERT: E 228 ASN cc_start: 0.9553 (t0) cc_final: 0.9200 (m110) REVERT: A 536 MET cc_start: 0.8356 (mmm) cc_final: 0.7988 (mmm) REVERT: A 552 LEU cc_start: 0.9220 (tp) cc_final: 0.8807 (pp) REVERT: A 635 MET cc_start: 0.8937 (mmt) cc_final: 0.8598 (mmt) REVERT: A 807 MET cc_start: 0.8939 (mmp) cc_final: 0.8540 (mmp) REVERT: A 855 MET cc_start: 0.8710 (ppp) cc_final: 0.8030 (ppp) REVERT: B 382 ASN cc_start: 0.7867 (m110) cc_final: 0.6656 (p0) REVERT: B 388 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7487 (mt) REVERT: B 420 GLU cc_start: 0.9137 (tp30) cc_final: 0.8898 (tp30) REVERT: B 488 TRP cc_start: 0.8412 (m100) cc_final: 0.7752 (m100) REVERT: C 51 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8784 (mp0) REVERT: C 185 MET cc_start: 0.8903 (mmm) cc_final: 0.8569 (mmm) REVERT: C 222 ASP cc_start: 0.9332 (m-30) cc_final: 0.9115 (p0) REVERT: C 223 LEU cc_start: 0.9824 (tt) cc_final: 0.9511 (mp) REVERT: C 326 PHE cc_start: 0.8717 (m-80) cc_final: 0.8259 (t80) REVERT: C 336 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8205 (p) REVERT: C 429 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9057 (mp) REVERT: C 625 MET cc_start: 0.7403 (mmt) cc_final: 0.6623 (tpt) outliers start: 29 outliers final: 22 residues processed: 180 average time/residue: 0.2352 time to fit residues: 67.0063 Evaluate side-chains 179 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 351 ILE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 699 ASN Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 577 VAL 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 174 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 176 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 352 ASN ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.058717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.045588 restraints weight = 89488.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.047181 restraints weight = 51351.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.048273 restraints weight = 34452.448| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15437 Z= 0.153 Angle : 0.717 17.885 20882 Z= 0.344 Chirality : 0.042 0.356 2416 Planarity : 0.004 0.042 2642 Dihedral : 7.740 80.742 2146 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.04 % Favored : 96.91 % Rotamer: Outliers : 2.00 % Allowed : 19.90 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.20), residues: 1843 helix: 1.28 (0.16), residues: 1132 sheet: -1.48 (0.36), residues: 174 loop : -0.03 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 475 HIS 0.007 0.001 HIS C 256 PHE 0.071 0.002 PHE C 362 TYR 0.019 0.001 TYR C 255 ARG 0.007 0.000 ARG F 231 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 835) hydrogen bonds : angle 4.65681 ( 2433) covalent geometry : bond 0.00334 (15433) covalent geometry : angle 0.71724 (20882) Misc. bond : bond 0.00046 ( 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 194 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 2.052 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: D 324 MET cc_start: 0.9108 (mtp) cc_final: 0.8664 (ttm) REVERT: D 385 MET cc_start: 0.8675 (mmp) cc_final: 0.8248 (mmm) REVERT: D 404 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8887 (tp30) REVERT: D 409 LEU cc_start: 0.9385 (tp) cc_final: 0.8781 (mp) REVERT: D 426 MET cc_start: 0.9172 (tpp) cc_final: 0.8792 (tpp) REVERT: E 1 MET cc_start: 0.8530 (tpt) cc_final: 0.8135 (tpt) REVERT: E 78 LYS cc_start: 0.9409 (mmtt) cc_final: 0.9040 (mmmm) REVERT: E 82 GLU cc_start: 0.9548 (mt-10) cc_final: 0.9301 (mt-10) REVERT: E 228 ASN cc_start: 0.9531 (t0) cc_final: 0.9185 (m110) REVERT: A 536 MET cc_start: 0.8299 (mmm) cc_final: 0.8018 (mmm) REVERT: A 552 LEU cc_start: 0.9208 (tp) cc_final: 0.8789 (pp) REVERT: A 635 MET cc_start: 0.8940 (mmt) cc_final: 0.8565 (mmt) REVERT: A 807 MET cc_start: 0.8977 (mmp) cc_final: 0.8581 (mmp) REVERT: A 855 MET cc_start: 0.8736 (ppp) cc_final: 0.8019 (ppp) REVERT: B 382 ASN cc_start: 0.7881 (m110) cc_final: 0.6626 (p0) REVERT: B 388 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7495 (mt) REVERT: B 420 GLU cc_start: 0.9120 (tp30) cc_final: 0.8882 (tp30) REVERT: B 488 TRP cc_start: 0.8397 (m100) cc_final: 0.7656 (m100) REVERT: C 51 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8782 (mp0) REVERT: C 223 LEU cc_start: 0.9818 (tt) cc_final: 0.9528 (mp) REVERT: C 326 PHE cc_start: 0.8720 (m-80) cc_final: 0.8277 (t80) REVERT: C 327 PHE cc_start: 0.7349 (m-80) cc_final: 0.7093 (m-80) REVERT: C 336 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8255 (p) REVERT: C 429 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9081 (mp) REVERT: C 625 MET cc_start: 0.7408 (mmt) cc_final: 0.6667 (tpt) outliers start: 33 outliers final: 25 residues processed: 187 average time/residue: 0.2469 time to fit residues: 72.5506 Evaluate side-chains 182 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain E residue 75 TYR 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 E residue 441 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 699 ASN Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 577 VAL 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 3 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 243 ASN ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.059189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.045888 restraints weight = 91745.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.047474 restraints weight = 53136.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.048575 restraints weight = 35419.980| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4435 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= 0.139 Angle : 0.716 18.568 20882 Z= 0.343 Chirality : 0.042 0.353 2416 Planarity : 0.004 0.042 2642 Dihedral : 7.662 81.379 2146 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 1.64 % Allowed : 20.02 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1843 helix: 1.27 (0.16), residues: 1140 sheet: -1.39 (0.36), residues: 174 loop : 0.04 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 475 HIS 0.006 0.001 HIS C 256 PHE 0.020 0.001 PHE C 362 TYR 0.023 0.001 TYR B 356 ARG 0.007 0.000 ARG F 231 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 835) hydrogen bonds : angle 4.60292 ( 2433) covalent geometry : bond 0.00306 (15433) covalent geometry : angle 0.71561 (20882) Misc. bond : bond 0.00050 ( 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 193 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 1.719 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 324 MET cc_start: 0.9090 (mtp) cc_final: 0.8652 (ttm) REVERT: D 385 MET cc_start: 0.8631 (mmp) cc_final: 0.8221 (mmm) REVERT: D 404 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8846 (tp30) REVERT: E 1 MET cc_start: 0.8456 (tpt) cc_final: 0.8063 (tpt) REVERT: E 130 ARG cc_start: 0.9396 (tpp80) cc_final: 0.9036 (mmp80) REVERT: E 228 ASN cc_start: 0.9541 (t0) cc_final: 0.9185 (m110) REVERT: A 536 MET cc_start: 0.8196 (mmm) cc_final: 0.7985 (mmm) REVERT: A 552 LEU cc_start: 0.9216 (tp) cc_final: 0.8822 (pp) REVERT: A 635 MET cc_start: 0.8887 (mmt) cc_final: 0.8569 (mmt) REVERT: A 807 MET cc_start: 0.8996 (mmp) cc_final: 0.8608 (mmp) REVERT: A 855 MET cc_start: 0.8743 (ppp) cc_final: 0.8023 (ppp) REVERT: B 343 TRP cc_start: 0.9440 (m-10) cc_final: 0.9113 (m-10) REVERT: B 352 ASN cc_start: 0.7790 (m110) cc_final: 0.7569 (m-40) REVERT: B 382 ASN cc_start: 0.7891 (m110) cc_final: 0.6639 (p0) REVERT: B 388 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7478 (mt) REVERT: B 420 GLU cc_start: 0.9125 (tp30) cc_final: 0.8884 (tp30) REVERT: B 488 TRP cc_start: 0.8416 (m100) cc_final: 0.7866 (m100) REVERT: C 51 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8771 (mp0) REVERT: C 185 MET cc_start: 0.8943 (tpp) cc_final: 0.8685 (mmm) REVERT: C 223 LEU cc_start: 0.9789 (tt) cc_final: 0.9561 (mp) REVERT: C 326 PHE cc_start: 0.8739 (m-80) cc_final: 0.8300 (t80) REVERT: C 327 PHE cc_start: 0.7292 (m-80) cc_final: 0.7036 (m-80) REVERT: C 336 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8240 (p) REVERT: C 429 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9073 (mp) REVERT: C 625 MET cc_start: 0.7411 (mmt) cc_final: 0.6651 (tpt) outliers start: 27 outliers final: 22 residues processed: 188 average time/residue: 0.2376 time to fit residues: 69.7152 Evaluate side-chains 186 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 88 LEU 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 E residue 204 LEU Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 699 ASN Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain F residue 232 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 171 optimal weight: 0.3980 chunk 129 optimal weight: 0.0270 chunk 50 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.2642 ------------------------------------------------------------------------------- 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 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.059852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.046474 restraints weight = 89688.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.048066 restraints weight = 51397.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.049137 restraints weight = 34838.460| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4517 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= 0.123 Angle : 0.721 17.961 20882 Z= 0.341 Chirality : 0.042 0.369 2416 Planarity : 0.004 0.044 2642 Dihedral : 7.548 82.686 2146 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 1.58 % Allowed : 20.57 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.20), residues: 1843 helix: 1.35 (0.16), residues: 1134 sheet: -1.32 (0.36), residues: 173 loop : 0.14 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 475 HIS 0.007 0.001 HIS C 250 PHE 0.024 0.001 PHE E 104 TYR 0.020 0.001 TYR C 255 ARG 0.008 0.000 ARG F 231 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 835) hydrogen bonds : angle 4.49927 ( 2433) covalent geometry : bond 0.00272 (15433) covalent geometry : angle 0.72136 (20882) Misc. bond : bond 0.00048 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5426.19 seconds wall clock time: 98 minutes 29.94 seconds (5909.94 seconds total)