Starting phenix.real_space_refine on Fri Sep 27 07:45:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk6_22363/09_2024/7jk6_22363.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk6_22363/09_2024/7jk6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk6_22363/09_2024/7jk6_22363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk6_22363/09_2024/7jk6_22363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk6_22363/09_2024/7jk6_22363.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk6_22363/09_2024/7jk6_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 9.35, per 1000 atoms: 0.62 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: 3.46 Conformation dependent library (CDL) restraints added in 1.8 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: 1.58 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: 4.71 Time building geometry restraints manager: 4.02 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: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 34.090 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.990 ------------------------------------------------------------------------------- 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 : 0.008 0.101 15433 Z= 0.498 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 *********************** 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 fitting. rotamer outliers: 4 poor density : 322 time to evaluate : 1.801 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: 0.3050 time to fit residues: 139.7220 Evaluate side-chains 204 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 201 time to evaluate : 1.649 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 15433 Z= 0.216 Angle : 0.721 9.760 20882 Z= 0.367 Chirality : 0.042 0.174 2416 Planarity : 0.005 0.061 2642 Dihedral : 8.064 72.593 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 *********************** 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 fitting. rotamer outliers: 22 poor density : 234 time to evaluate : 2.003 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: 0.8554 (m-80) cc_final: 0.7974 (m-80) REVERT: D 77 LYS cc_start: 0.9460 (mttt) cc_final: 0.9249 (mmtt) REVERT: D 102 SER cc_start: 0.9186 (t) cc_final: 0.8886 (p) REVERT: D 146 LEU cc_start: 0.9048 (mt) cc_final: 0.8660 (mm) REVERT: D 148 GLU cc_start: 0.8500 (tt0) cc_final: 0.8258 (tt0) REVERT: D 324 MET cc_start: 0.9098 (mtp) cc_final: 0.8564 (ttm) REVERT: D 404 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8748 (tp30) REVERT: D 409 LEU cc_start: 0.9387 (tp) cc_final: 0.9009 (mp) REVERT: E 82 GLU cc_start: 0.9407 (mt-10) cc_final: 0.9144 (mm-30) REVERT: E 164 GLU cc_start: 0.8777 (pt0) cc_final: 0.8555 (tm-30) REVERT: E 228 ASN cc_start: 0.9667 (t0) cc_final: 0.9327 (p0) REVERT: E 402 ASN cc_start: 0.9466 (m110) cc_final: 0.9142 (p0) REVERT: E 415 LEU cc_start: 0.8699 (mm) cc_final: 0.8476 (mm) REVERT: A 552 LEU cc_start: 0.9370 (tp) cc_final: 0.8969 (pp) REVERT: A 622 ASN cc_start: 0.9290 (t0) cc_final: 0.9064 (p0) REVERT: A 635 MET cc_start: 0.8814 (mmm) cc_final: 0.8084 (mmt) REVERT: A 639 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8711 (pt0) REVERT: A 701 LEU cc_start: 0.8974 (tp) cc_final: 0.8749 (pp) REVERT: A 720 MET cc_start: 0.9393 (tpt) cc_final: 0.9168 (tpp) REVERT: A 724 GLU cc_start: 0.8069 (mp0) cc_final: 0.7766 (mp0) REVERT: A 855 MET cc_start: 0.9017 (ppp) cc_final: 0.8815 (ppp) REVERT: B 343 TRP cc_start: 0.9462 (m-10) cc_final: 0.9249 (m-10) REVERT: B 488 TRP cc_start: 0.8421 (m100) cc_final: 0.7981 (m100) REVERT: C 51 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8836 (mp0) REVERT: C 128 MET cc_start: 0.8941 (mpp) cc_final: 0.8601 (mpp) REVERT: C 209 LEU cc_start: 0.9655 (mp) cc_final: 0.9432 (mm) REVERT: C 212 PHE cc_start: 0.8896 (t80) cc_final: 0.8351 (t80) REVERT: C 221 GLN cc_start: 0.9689 (mt0) cc_final: 0.9479 (mp10) REVERT: C 222 ASP cc_start: 0.9262 (m-30) cc_final: 0.8946 (p0) REVERT: C 336 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8406 (p) REVERT: C 340 LYS cc_start: 0.9049 (tttt) cc_final: 0.8761 (tptp) REVERT: C 384 TYR cc_start: 0.8791 (t80) cc_final: 0.8538 (t80) REVERT: C 388 LYS cc_start: 0.9300 (tptp) cc_final: 0.9099 (tptp) REVERT: C 429 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8990 (mp) REVERT: C 625 MET cc_start: 0.7448 (mmt) cc_final: 0.6534 (tpt) outliers start: 22 outliers final: 13 residues processed: 245 average time/residue: 0.2680 time to fit residues: 97.2424 Evaluate side-chains 200 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 185 time to evaluate : 1.904 ------------------------------------------------------------------------------- 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 93 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 169 optimal weight: 0.5980 chunk 182 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 163 ASN ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN C 107 GLN C 312 HIS C 591 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15433 Z= 0.238 Angle : 0.684 8.876 20882 Z= 0.346 Chirality : 0.041 0.211 2416 Planarity : 0.004 0.051 2642 Dihedral : 7.972 69.142 2146 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.04 % Favored : 96.91 % Rotamer: Outliers : 2.18 % Allowed : 14.62 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.12 (0.19), residues: 1843 helix: 0.67 (0.15), residues: 1122 sheet: -2.02 (0.36), residues: 162 loop : -0.20 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 475 HIS 0.009 0.001 HIS D 437 PHE 0.038 0.002 PHE C 362 TYR 0.020 0.001 TYR E 258 ARG 0.006 0.000 ARG E 130 *********************** 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 230 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 194 time to evaluate : 1.718 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: 0.8485 (t80) cc_final: 0.7724 (t80) REVERT: D 102 SER cc_start: 0.9257 (t) cc_final: 0.8934 (p) REVERT: D 133 LYS cc_start: 0.9552 (tppt) cc_final: 0.9344 (tppt) REVERT: D 148 GLU cc_start: 0.8610 (tt0) cc_final: 0.8316 (tt0) REVERT: D 324 MET cc_start: 0.9172 (mtp) cc_final: 0.8674 (ttm) REVERT: D 404 GLU cc_start: 0.9338 (mm-30) cc_final: 0.8895 (tp30) REVERT: E 82 GLU cc_start: 0.9420 (mt-10) cc_final: 0.9050 (mm-30) REVERT: E 134 MET cc_start: 0.7817 (ptm) cc_final: 0.7490 (ptp) REVERT: E 228 ASN cc_start: 0.9683 (t0) cc_final: 0.9356 (p0) REVERT: E 402 ASN cc_start: 0.9502 (m110) cc_final: 0.9128 (p0) REVERT: E 415 LEU cc_start: 0.8698 (mm) cc_final: 0.8489 (mm) REVERT: A 552 LEU cc_start: 0.9407 (tp) cc_final: 0.8904 (pp) REVERT: A 635 MET cc_start: 0.8840 (mmm) cc_final: 0.8535 (mmt) REVERT: A 701 LEU cc_start: 0.8948 (tp) cc_final: 0.8734 (pp) REVERT: A 720 MET cc_start: 0.9341 (tpt) cc_final: 0.9103 (tpp) REVERT: A 767 GLU cc_start: 0.9407 (mm-30) cc_final: 0.9150 (tp30) REVERT: A 807 MET cc_start: 0.8828 (mmp) cc_final: 0.8427 (mmp) REVERT: A 855 MET cc_start: 0.8997 (ppp) cc_final: 0.8642 (ppp) REVERT: B 343 TRP cc_start: 0.9462 (m-10) cc_final: 0.9212 (m-10) REVERT: B 393 MET cc_start: 0.8336 (mpp) cc_final: 0.7986 (mpp) REVERT: B 488 TRP cc_start: 0.8461 (m100) cc_final: 0.8045 (m100) REVERT: C 51 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8800 (mp0) REVERT: C 128 MET cc_start: 0.8969 (mpp) cc_final: 0.8683 (mpp) REVERT: C 185 MET cc_start: 0.9014 (mmm) cc_final: 0.8789 (mmm) REVERT: C 221 GLN cc_start: 0.9682 (mt0) cc_final: 0.9432 (mp10) REVERT: C 222 ASP cc_start: 0.9320 (m-30) cc_final: 0.9064 (p0) REVERT: C 326 PHE cc_start: 0.8286 (m-80) cc_final: 0.7783 (t80) REVERT: C 404 ARG cc_start: 0.8422 (tpt90) cc_final: 0.8188 (tpt90) REVERT: C 429 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9006 (mp) REVERT: C 625 MET cc_start: 0.7473 (mmt) cc_final: 0.6599 (tpt) outliers start: 36 outliers final: 25 residues processed: 215 average time/residue: 0.2468 time to fit residues: 80.5153 Evaluate side-chains 190 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain E residue 88 LEU 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 180 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 914 HIS Chi-restraints excluded: chain B residue 372 VAL 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 365 TYR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain F residue 232 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 169 optimal weight: 20.0000 chunk 179 optimal weight: 0.3980 chunk 88 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15433 Z= 0.188 Angle : 0.668 13.853 20882 Z= 0.330 Chirality : 0.041 0.224 2416 Planarity : 0.004 0.051 2642 Dihedral : 7.928 68.194 2146 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.77 % Favored : 97.18 % Rotamer: Outliers : 1.58 % Allowed : 16.57 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.45 (0.20), residues: 1843 helix: 1.00 (0.15), residues: 1117 sheet: -1.89 (0.35), residues: 161 loop : -0.21 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 703 HIS 0.006 0.001 HIS E 412 PHE 0.038 0.002 PHE C 362 TYR 0.023 0.001 TYR B 356 ARG 0.005 0.000 ARG C 357 *********************** 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 215 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 1.736 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 77 LYS cc_start: 0.9457 (mttt) cc_final: 0.9245 (mmtt) REVERT: D 102 SER cc_start: 0.9229 (t) cc_final: 0.8915 (p) REVERT: D 148 GLU cc_start: 0.8689 (tt0) cc_final: 0.8409 (tt0) REVERT: D 322 GLU cc_start: 0.9048 (pm20) cc_final: 0.8824 (pm20) REVERT: D 404 GLU cc_start: 0.9330 (mm-30) cc_final: 0.8874 (tp30) REVERT: E 78 LYS cc_start: 0.9435 (mmtt) cc_final: 0.8957 (tppt) REVERT: E 82 GLU cc_start: 0.9385 (mt-10) cc_final: 0.9048 (mm-30) REVERT: E 98 VAL cc_start: 0.9543 (OUTLIER) cc_final: 0.8921 (t) REVERT: E 134 MET cc_start: 0.7862 (ptm) cc_final: 0.7588 (ptm) REVERT: E 228 ASN cc_start: 0.9670 (t0) cc_final: 0.9342 (p0) REVERT: E 402 ASN cc_start: 0.9524 (m110) cc_final: 0.9090 (p0) REVERT: E 413 LEU cc_start: 0.8242 (mt) cc_final: 0.8007 (mt) REVERT: E 415 LEU cc_start: 0.8638 (mm) cc_final: 0.8415 (mm) REVERT: A 552 LEU cc_start: 0.9251 (tp) cc_final: 0.8861 (pp) REVERT: A 635 MET cc_start: 0.8875 (mmm) cc_final: 0.8566 (mmt) REVERT: A 701 LEU cc_start: 0.8917 (tp) cc_final: 0.8711 (pp) REVERT: A 720 MET cc_start: 0.9308 (tpt) cc_final: 0.9088 (tpp) REVERT: B 382 ASN cc_start: 0.7784 (m110) cc_final: 0.7050 (p0) REVERT: B 393 MET cc_start: 0.8416 (mpp) cc_final: 0.8068 (mpp) REVERT: B 483 PHE cc_start: 0.7515 (m-10) cc_final: 0.7283 (m-10) REVERT: B 488 TRP cc_start: 0.8396 (m100) cc_final: 0.7860 (m100) REVERT: C 51 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8765 (mp0) REVERT: C 128 MET cc_start: 0.8954 (mpp) cc_final: 0.8735 (mpp) REVERT: C 185 MET cc_start: 0.9012 (mmm) cc_final: 0.8763 (mmm) REVERT: C 221 GLN cc_start: 0.9708 (mt0) cc_final: 0.9439 (mp10) REVERT: C 222 ASP cc_start: 0.9324 (m-30) cc_final: 0.9113 (p0) REVERT: C 326 PHE cc_start: 0.8318 (m-80) cc_final: 0.7855 (t80) REVERT: C 429 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9036 (mp) REVERT: C 625 MET cc_start: 0.7342 (mmt) cc_final: 0.6538 (tpt) outliers start: 26 outliers final: 16 residues processed: 205 average time/residue: 0.2559 time to fit residues: 79.6506 Evaluate side-chains 184 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 166 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 180 LEU 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 365 TYR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 429 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 133 optimal weight: 20.0000 chunk 74 optimal weight: 0.0060 chunk 153 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15433 Z= 0.160 Angle : 0.658 11.616 20882 Z= 0.319 Chirality : 0.041 0.305 2416 Planarity : 0.004 0.088 2642 Dihedral : 7.754 77.011 2146 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 1.82 % Allowed : 16.57 % Favored : 81.61 % 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: 0.55 (0.20), residues: 1843 helix: 1.08 (0.16), residues: 1126 sheet: -1.86 (0.34), residues: 161 loop : -0.20 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 475 HIS 0.006 0.001 HIS E 412 PHE 0.042 0.001 PHE C 362 TYR 0.012 0.001 TYR C 430 ARG 0.011 0.000 ARG F 231 *********************** 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 235 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 205 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 77 LYS cc_start: 0.9463 (mttt) cc_final: 0.9247 (mmtt) REVERT: D 79 PHE cc_start: 0.8480 (t80) cc_final: 0.7709 (t80) REVERT: D 102 SER cc_start: 0.9196 (t) cc_final: 0.8902 (p) REVERT: D 324 MET cc_start: 0.9126 (mmm) cc_final: 0.8786 (mmm) REVERT: D 404 GLU cc_start: 0.9303 (mm-30) cc_final: 0.8811 (tp30) REVERT: D 407 MET cc_start: 0.8511 (ptm) cc_final: 0.8172 (ppp) REVERT: E 22 LEU cc_start: 0.9243 (mt) cc_final: 0.8915 (tp) REVERT: E 78 LYS cc_start: 0.9439 (mmtt) cc_final: 0.8727 (tppt) REVERT: E 82 GLU cc_start: 0.9415 (mt-10) cc_final: 0.9040 (mm-30) REVERT: E 98 VAL cc_start: 0.9557 (OUTLIER) cc_final: 0.8594 (t) REVERT: E 106 GLU cc_start: 0.9500 (OUTLIER) cc_final: 0.9299 (mm-30) REVERT: E 134 MET cc_start: 0.7749 (ptm) cc_final: 0.7336 (ptm) REVERT: E 228 ASN cc_start: 0.9637 (t0) cc_final: 0.9253 (p0) REVERT: E 402 ASN cc_start: 0.9535 (m110) cc_final: 0.9045 (p0) REVERT: E 413 LEU cc_start: 0.8255 (mt) cc_final: 0.8044 (mt) REVERT: E 415 LEU cc_start: 0.8589 (mm) cc_final: 0.8381 (mm) REVERT: A 552 LEU cc_start: 0.9227 (tp) cc_final: 0.8924 (pp) REVERT: A 635 MET cc_start: 0.8905 (mmm) cc_final: 0.8596 (mmt) REVERT: A 689 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8781 (pp) REVERT: A 720 MET cc_start: 0.9283 (tpt) cc_final: 0.9052 (tpp) REVERT: A 767 GLU cc_start: 0.9409 (mm-30) cc_final: 0.9113 (tp30) REVERT: A 807 MET cc_start: 0.8979 (mmp) cc_final: 0.8582 (mmp) REVERT: B 382 ASN cc_start: 0.7759 (m110) cc_final: 0.6624 (p0) REVERT: B 483 PHE cc_start: 0.7387 (m-10) cc_final: 0.7169 (m-10) REVERT: B 488 TRP cc_start: 0.8432 (m100) cc_final: 0.7749 (m100) REVERT: C 51 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8778 (mp0) REVERT: C 185 MET cc_start: 0.9007 (mmm) cc_final: 0.8746 (mmm) REVERT: C 221 GLN cc_start: 0.9703 (mt0) cc_final: 0.9452 (mp10) REVERT: C 222 ASP cc_start: 0.9270 (m-30) cc_final: 0.9057 (p0) REVERT: C 326 PHE cc_start: 0.8326 (m-80) cc_final: 0.7892 (t80) REVERT: C 429 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9045 (mp) REVERT: C 450 MET cc_start: 0.8731 (ptp) cc_final: 0.8469 (ptp) REVERT: C 504 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7902 (pp20) REVERT: C 625 MET cc_start: 0.7379 (mmt) cc_final: 0.6610 (tpt) outliers start: 30 outliers final: 17 residues processed: 227 average time/residue: 0.2457 time to fit residues: 84.8895 Evaluate side-chains 196 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 174 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 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 60 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 179 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 chunk 83 optimal weight: 0.4980 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 150 ASN A 824 GLN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15433 Z= 0.230 Angle : 0.712 11.405 20882 Z= 0.344 Chirality : 0.042 0.311 2416 Planarity : 0.004 0.097 2642 Dihedral : 7.777 86.020 2146 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 2.37 % Allowed : 17.35 % Favored : 80.28 % 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: 0.69 (0.20), residues: 1843 helix: 1.17 (0.16), residues: 1130 sheet: -1.77 (0.35), residues: 160 loop : -0.13 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 475 HIS 0.006 0.001 HIS A 809 PHE 0.025 0.002 PHE E 389 TYR 0.023 0.001 TYR A 579 ARG 0.010 0.000 ARG F 231 *********************** 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 218 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 179 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 77 LYS cc_start: 0.9478 (mttt) cc_final: 0.9249 (mmtt) REVERT: D 148 GLU cc_start: 0.8650 (tt0) cc_final: 0.8334 (tt0) REVERT: D 324 MET cc_start: 0.9220 (mmm) cc_final: 0.8864 (mmm) REVERT: D 404 GLU cc_start: 0.9346 (mm-30) cc_final: 0.8949 (tp30) REVERT: D 407 MET cc_start: 0.8537 (ptm) cc_final: 0.8195 (ppp) REVERT: E 1 MET cc_start: 0.8883 (tpt) cc_final: 0.8467 (tpt) REVERT: E 78 LYS cc_start: 0.9462 (mmtt) cc_final: 0.8993 (mmmt) REVERT: E 82 GLU cc_start: 0.9606 (mt-10) cc_final: 0.9319 (mt-10) REVERT: E 98 VAL cc_start: 0.9528 (OUTLIER) cc_final: 0.9090 (p) REVERT: E 228 ASN cc_start: 0.9657 (t0) cc_final: 0.9263 (m110) REVERT: E 402 ASN cc_start: 0.9532 (m110) cc_final: 0.9020 (p0) REVERT: E 403 LEU cc_start: 0.8178 (mt) cc_final: 0.7820 (mp) REVERT: E 413 LEU cc_start: 0.8305 (mt) cc_final: 0.7933 (mt) REVERT: E 415 LEU cc_start: 0.8623 (mm) cc_final: 0.8408 (mm) REVERT: A 552 LEU cc_start: 0.9250 (tp) cc_final: 0.8811 (pp) REVERT: A 635 MET cc_start: 0.8936 (mmm) cc_final: 0.8650 (mmt) REVERT: A 720 MET cc_start: 0.9270 (tpt) cc_final: 0.9045 (tpp) REVERT: A 767 GLU cc_start: 0.9411 (mm-30) cc_final: 0.9157 (tp30) REVERT: A 855 MET cc_start: 0.8830 (ppp) cc_final: 0.8274 (ppp) REVERT: B 382 ASN cc_start: 0.7683 (m110) cc_final: 0.6889 (p0) REVERT: B 483 PHE cc_start: 0.7559 (m-10) cc_final: 0.7348 (m-10) REVERT: B 488 TRP cc_start: 0.8342 (m100) cc_final: 0.7727 (m100) REVERT: C 51 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8764 (mp0) REVERT: C 185 MET cc_start: 0.9007 (mmm) cc_final: 0.8636 (mmm) REVERT: C 221 GLN cc_start: 0.9711 (mt0) cc_final: 0.9378 (mp10) REVERT: C 326 PHE cc_start: 0.8426 (m-80) cc_final: 0.8042 (t80) REVERT: C 336 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8183 (p) REVERT: C 429 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9025 (mp) REVERT: C 625 MET cc_start: 0.7366 (mmt) cc_final: 0.6667 (tpt) outliers start: 39 outliers final: 28 residues processed: 204 average time/residue: 0.2316 time to fit residues: 72.7489 Evaluate side-chains 189 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 158 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LEU 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 351 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 153 LEU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 249 LEU 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 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 300 LEU 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 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 173 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 131 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 112 optimal weight: 0.2980 chunk 109 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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** A 902 GLN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN C 61 ASN C 585 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15433 Z= 0.160 Angle : 0.686 11.710 20882 Z= 0.330 Chirality : 0.042 0.338 2416 Planarity : 0.004 0.053 2642 Dihedral : 7.584 85.957 2146 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.23 % Rotamer: Outliers : 1.40 % Allowed : 18.45 % Favored : 80.16 % 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: 0.82 (0.20), residues: 1843 helix: 1.25 (0.16), residues: 1122 sheet: -1.62 (0.35), residues: 160 loop : -0.05 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 475 HIS 0.009 0.001 HIS B 362 PHE 0.057 0.001 PHE C 362 TYR 0.016 0.001 TYR E 291 ARG 0.013 0.000 ARG F 231 *********************** 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 209 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 186 time to evaluate : 1.708 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 77 LYS cc_start: 0.9492 (mttt) cc_final: 0.9260 (mmtt) REVERT: D 97 ARG cc_start: 0.8760 (tpt170) cc_final: 0.8534 (tpt90) REVERT: D 148 GLU cc_start: 0.8671 (tt0) cc_final: 0.8337 (tt0) REVERT: D 324 MET cc_start: 0.9183 (mmm) cc_final: 0.8831 (mmm) REVERT: D 404 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8829 (tp30) REVERT: D 407 MET cc_start: 0.8519 (ptm) cc_final: 0.8244 (ppp) REVERT: E 1 MET cc_start: 0.8659 (tpt) cc_final: 0.8216 (tpt) REVERT: E 22 LEU cc_start: 0.9232 (mt) cc_final: 0.8913 (tp) REVERT: E 78 LYS cc_start: 0.9482 (mmtt) cc_final: 0.8985 (mmmt) REVERT: E 82 GLU cc_start: 0.9586 (mt-10) cc_final: 0.9272 (mt-10) REVERT: E 98 VAL cc_start: 0.9408 (OUTLIER) cc_final: 0.8896 (p) REVERT: E 106 GLU cc_start: 0.9518 (OUTLIER) cc_final: 0.9309 (mm-30) REVERT: E 228 ASN cc_start: 0.9630 (t0) cc_final: 0.9227 (m110) REVERT: E 413 LEU cc_start: 0.8339 (mt) cc_final: 0.7982 (mt) REVERT: E 415 LEU cc_start: 0.8590 (mm) cc_final: 0.8381 (mm) REVERT: A 552 LEU cc_start: 0.9223 (tp) cc_final: 0.8830 (pp) REVERT: A 635 MET cc_start: 0.8962 (mmm) cc_final: 0.8665 (mmt) REVERT: A 689 LEU cc_start: 0.9240 (mt) cc_final: 0.8857 (pp) REVERT: A 767 GLU cc_start: 0.9378 (mm-30) cc_final: 0.9059 (tp30) REVERT: A 807 MET cc_start: 0.8942 (mmp) cc_final: 0.8502 (mmp) REVERT: B 343 TRP cc_start: 0.9413 (m-10) cc_final: 0.9105 (m-10) REVERT: B 382 ASN cc_start: 0.7677 (m110) cc_final: 0.6880 (p0) REVERT: B 476 ASP cc_start: 0.7399 (p0) cc_final: 0.7089 (p0) REVERT: B 483 PHE cc_start: 0.7290 (m-10) cc_final: 0.7084 (m-10) REVERT: B 488 TRP cc_start: 0.8330 (m100) cc_final: 0.7804 (m100) REVERT: C 51 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8753 (mp0) REVERT: C 185 MET cc_start: 0.8989 (mmm) cc_final: 0.8554 (mmm) REVERT: C 221 GLN cc_start: 0.9678 (mt0) cc_final: 0.9373 (mp10) REVERT: C 326 PHE cc_start: 0.8428 (m-80) cc_final: 0.8017 (t80) REVERT: C 336 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8187 (p) REVERT: C 429 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9020 (mp) REVERT: C 450 MET cc_start: 0.8952 (ptp) cc_final: 0.8664 (pmm) REVERT: C 625 MET cc_start: 0.7376 (mmt) cc_final: 0.6655 (tpt) outliers start: 23 outliers final: 11 residues processed: 203 average time/residue: 0.2791 time to fit residues: 87.6086 Evaluate side-chains 184 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 169 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 861 VAL 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 F residue 232 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 202 GLN D 243 ASN E 68 HIS B 352 ASN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN C 133 GLN C 591 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15433 Z= 0.323 Angle : 0.770 15.701 20882 Z= 0.380 Chirality : 0.043 0.316 2416 Planarity : 0.005 0.077 2642 Dihedral : 7.836 81.157 2146 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.42 % Favored : 96.53 % Rotamer: Outliers : 1.94 % Allowed : 19.30 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1135 sheet: -1.66 (0.36), residues: 166 loop : -0.17 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 475 HIS 0.011 0.002 HIS B 362 PHE 0.025 0.002 PHE C 362 TYR 0.027 0.002 TYR C 255 ARG 0.008 0.001 ARG F 231 *********************** 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 193 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 1.792 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 77 LYS cc_start: 0.9502 (mttt) cc_final: 0.9252 (mmtt) REVERT: D 148 GLU cc_start: 0.8631 (tt0) cc_final: 0.8332 (tt0) REVERT: D 324 MET cc_start: 0.9278 (mmm) cc_final: 0.8926 (mmm) REVERT: D 404 GLU cc_start: 0.9391 (mm-30) cc_final: 0.9075 (tp30) REVERT: E 1 MET cc_start: 0.8727 (tpt) cc_final: 0.8409 (tpt) REVERT: E 78 LYS cc_start: 0.9488 (mmtt) cc_final: 0.8996 (mmmt) REVERT: E 82 GLU cc_start: 0.9583 (mt-10) cc_final: 0.9300 (mt-10) REVERT: E 98 VAL cc_start: 0.9465 (OUTLIER) cc_final: 0.8997 (p) REVERT: E 228 ASN cc_start: 0.9691 (t0) cc_final: 0.9306 (m110) REVERT: E 413 LEU cc_start: 0.8383 (mt) cc_final: 0.8064 (mt) REVERT: A 552 LEU cc_start: 0.9292 (tp) cc_final: 0.8871 (pp) REVERT: A 635 MET cc_start: 0.8966 (mmm) cc_final: 0.8710 (mmt) REVERT: A 701 LEU cc_start: 0.8780 (tp) cc_final: 0.8535 (pp) REVERT: A 767 GLU cc_start: 0.9402 (mm-30) cc_final: 0.9143 (tp30) REVERT: A 855 MET cc_start: 0.8748 (ppp) cc_final: 0.8116 (ppp) REVERT: B 382 ASN cc_start: 0.7718 (m110) cc_final: 0.6926 (p0) REVERT: B 476 ASP cc_start: 0.7452 (p0) cc_final: 0.7136 (p0) REVERT: B 488 TRP cc_start: 0.8278 (m100) cc_final: 0.7684 (m100) REVERT: C 51 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8790 (mp0) REVERT: C 185 MET cc_start: 0.9013 (mmm) cc_final: 0.8652 (mmm) REVERT: C 221 GLN cc_start: 0.9728 (mt0) cc_final: 0.9350 (mp10) REVERT: C 326 PHE cc_start: 0.8535 (m-80) cc_final: 0.8170 (t80) REVERT: C 327 PHE cc_start: 0.7078 (m-80) cc_final: 0.6855 (m-80) REVERT: C 336 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8271 (p) REVERT: C 429 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9025 (mp) REVERT: C 625 MET cc_start: 0.7349 (mmt) cc_final: 0.6685 (tpt) outliers start: 32 outliers final: 24 residues processed: 181 average time/residue: 0.2577 time to fit residues: 73.4081 Evaluate side-chains 182 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 155 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LEU 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 351 ILE Chi-restraints excluded: chain E residue 88 LEU 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 E residue 249 LEU Chi-restraints excluded: chain E residue 403 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 352 ASN Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 300 LEU 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 502 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 163 optimal weight: 5.9990 chunk 171 optimal weight: 0.0670 chunk 156 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 158 optimal weight: 0.0570 chunk 166 optimal weight: 2.9990 overall best weight: 1.0238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 352 ASN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15433 Z= 0.173 Angle : 0.708 14.070 20882 Z= 0.339 Chirality : 0.042 0.354 2416 Planarity : 0.004 0.053 2642 Dihedral : 7.661 81.721 2146 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.77 % Favored : 97.18 % Rotamer: Outliers : 1.21 % Allowed : 20.08 % Favored : 78.70 % 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: 0.85 (0.20), residues: 1843 helix: 1.33 (0.16), residues: 1118 sheet: -1.52 (0.36), residues: 164 loop : -0.15 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 475 HIS 0.009 0.001 HIS B 362 PHE 0.024 0.001 PHE C 362 TYR 0.026 0.001 TYR A 579 ARG 0.005 0.000 ARG F 231 *********************** 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 187 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 167 time to evaluate : 1.954 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 148 GLU cc_start: 0.8695 (tt0) cc_final: 0.8353 (tt0) REVERT: D 324 MET cc_start: 0.9191 (mmm) cc_final: 0.8845 (mmm) REVERT: D 385 MET cc_start: 0.8938 (mmp) cc_final: 0.8340 (mmm) REVERT: D 404 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8905 (tp30) REVERT: D 407 MET cc_start: 0.8455 (ptm) cc_final: 0.8188 (ppp) REVERT: D 409 LEU cc_start: 0.9380 (tp) cc_final: 0.8796 (mp) REVERT: D 426 MET cc_start: 0.9199 (tpp) cc_final: 0.8800 (tpp) REVERT: E 1 MET cc_start: 0.8578 (tpt) cc_final: 0.8189 (tpt) REVERT: E 78 LYS cc_start: 0.9469 (mmtt) cc_final: 0.8999 (mmmt) REVERT: E 82 GLU cc_start: 0.9553 (mt-10) cc_final: 0.9241 (mt-10) REVERT: E 98 VAL cc_start: 0.9358 (OUTLIER) cc_final: 0.8861 (p) REVERT: E 228 ASN cc_start: 0.9645 (t0) cc_final: 0.9256 (m110) REVERT: A 552 LEU cc_start: 0.9273 (tp) cc_final: 0.8876 (pp) REVERT: A 635 MET cc_start: 0.8977 (mmm) cc_final: 0.8618 (mmt) REVERT: A 701 LEU cc_start: 0.8729 (tp) cc_final: 0.8488 (pp) REVERT: A 767 GLU cc_start: 0.9361 (mm-30) cc_final: 0.9031 (tp30) REVERT: A 807 MET cc_start: 0.8916 (mmp) cc_final: 0.8472 (mmp) REVERT: A 855 MET cc_start: 0.8698 (ppp) cc_final: 0.8037 (ppp) REVERT: B 343 TRP cc_start: 0.9415 (m-10) cc_final: 0.9091 (m-10) REVERT: B 382 ASN cc_start: 0.7722 (m110) cc_final: 0.6976 (p0) REVERT: B 476 ASP cc_start: 0.7554 (p0) cc_final: 0.7195 (p0) REVERT: B 488 TRP cc_start: 0.8300 (m100) cc_final: 0.7802 (m100) REVERT: C 51 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8783 (mp0) REVERT: C 128 MET cc_start: 0.9038 (mpp) cc_final: 0.8801 (mpp) REVERT: C 185 MET cc_start: 0.8972 (mmm) cc_final: 0.8557 (mmm) REVERT: C 221 GLN cc_start: 0.9710 (mt0) cc_final: 0.9366 (mp10) REVERT: C 326 PHE cc_start: 0.8543 (m-80) cc_final: 0.8158 (t80) REVERT: C 327 PHE cc_start: 0.7038 (m-80) cc_final: 0.6806 (m-80) REVERT: C 334 LEU cc_start: 0.9486 (mt) cc_final: 0.9264 (mm) REVERT: C 336 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8167 (p) REVERT: C 429 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9037 (mp) REVERT: C 450 MET cc_start: 0.8985 (ptp) cc_final: 0.8742 (ptp) REVERT: C 625 MET cc_start: 0.7372 (mmt) cc_final: 0.6701 (tpt) outliers start: 20 outliers final: 13 residues processed: 180 average time/residue: 0.2712 time to fit residues: 75.8847 Evaluate side-chains 173 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 1.704 ------------------------------------------------------------------------------- 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 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 632 ILE Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 861 VAL 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 366 VAL Chi-restraints excluded: chain C residue 429 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 109 optimal weight: 0.9980 chunk 176 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 185 optimal weight: 0.4980 chunk 170 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 124 ASN B 352 ASN ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15433 Z= 0.170 Angle : 0.716 14.696 20882 Z= 0.340 Chirality : 0.042 0.323 2416 Planarity : 0.004 0.049 2642 Dihedral : 7.532 83.495 2146 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.96 % Rotamer: Outliers : 1.15 % Allowed : 20.33 % 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: 0.88 (0.20), residues: 1843 helix: 1.32 (0.16), residues: 1119 sheet: -1.50 (0.36), residues: 165 loop : -0.06 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 475 HIS 0.009 0.001 HIS B 362 PHE 0.076 0.001 PHE C 362 TYR 0.022 0.001 TYR C 255 ARG 0.007 0.000 ARG F 231 ********************** 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 187 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 1.819 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: 0.8684 (tt0) cc_final: 0.8319 (tt0) REVERT: D 324 MET cc_start: 0.9195 (mmm) cc_final: 0.8843 (mmm) REVERT: D 404 GLU cc_start: 0.9333 (mm-30) cc_final: 0.8892 (tp30) REVERT: D 409 LEU cc_start: 0.9392 (tp) cc_final: 0.8810 (mp) REVERT: D 426 MET cc_start: 0.9218 (tpp) cc_final: 0.8805 (tpp) REVERT: E 1 MET cc_start: 0.8490 (tpt) cc_final: 0.8092 (tpt) REVERT: E 78 LYS cc_start: 0.9479 (mmtt) cc_final: 0.8888 (mmmt) REVERT: E 82 GLU cc_start: 0.9553 (mt-10) cc_final: 0.9093 (mp0) REVERT: E 98 VAL cc_start: 0.9299 (OUTLIER) cc_final: 0.8769 (p) REVERT: E 106 GLU cc_start: 0.9524 (OUTLIER) cc_final: 0.9315 (mm-30) REVERT: E 130 ARG cc_start: 0.9517 (tpp80) cc_final: 0.9111 (mmp80) REVERT: E 228 ASN cc_start: 0.9634 (t0) cc_final: 0.9245 (m110) REVERT: A 552 LEU cc_start: 0.9241 (tp) cc_final: 0.8880 (pp) REVERT: A 635 MET cc_start: 0.8881 (mmm) cc_final: 0.8615 (mmt) REVERT: A 689 LEU cc_start: 0.9293 (mt) cc_final: 0.8894 (pp) REVERT: A 701 LEU cc_start: 0.8734 (tp) cc_final: 0.8503 (pp) REVERT: A 767 GLU cc_start: 0.9351 (mm-30) cc_final: 0.9029 (tp30) REVERT: A 807 MET cc_start: 0.8917 (mmp) cc_final: 0.8473 (mmp) REVERT: A 855 MET cc_start: 0.8683 (ppp) cc_final: 0.8014 (ppp) REVERT: B 343 TRP cc_start: 0.9411 (m-10) cc_final: 0.9093 (m-10) REVERT: B 382 ASN cc_start: 0.7717 (m110) cc_final: 0.6945 (p0) REVERT: B 476 ASP cc_start: 0.7392 (p0) cc_final: 0.7143 (p0) REVERT: B 488 TRP cc_start: 0.8352 (m100) cc_final: 0.7794 (m100) REVERT: C 51 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8783 (mp0) REVERT: C 128 MET cc_start: 0.9018 (mpp) cc_final: 0.8799 (mpp) REVERT: C 221 GLN cc_start: 0.9698 (mt0) cc_final: 0.9357 (mp10) REVERT: C 326 PHE cc_start: 0.8547 (m-80) cc_final: 0.8159 (t80) REVERT: C 327 PHE cc_start: 0.7055 (m-80) cc_final: 0.6818 (m-80) REVERT: C 334 LEU cc_start: 0.9484 (mt) cc_final: 0.9259 (mm) REVERT: C 336 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8083 (p) REVERT: C 429 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9045 (mp) REVERT: C 450 MET cc_start: 0.8998 (ptp) cc_final: 0.8750 (ptp) REVERT: C 625 MET cc_start: 0.7359 (mmt) cc_final: 0.6710 (tpt) outliers start: 19 outliers final: 13 residues processed: 181 average time/residue: 0.2600 time to fit residues: 72.7726 Evaluate side-chains 180 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 163 time to evaluate : 1.773 ------------------------------------------------------------------------------- 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 E residue 98 VAL Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain A residue 632 ILE 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 C residue 98 THR Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 429 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 7.9990 chunk 157 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN ** B 366 GLN ** 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 = 0.3454 r_free = 0.3454 target = 0.059702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.046558 restraints weight = 88551.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.048175 restraints weight = 50427.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.049289 restraints weight = 33725.755| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.216 15433 Z= 0.293 Angle : 0.893 59.193 20882 Z= 0.479 Chirality : 0.043 0.395 2416 Planarity : 0.004 0.049 2642 Dihedral : 7.530 83.541 2146 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 1.09 % Allowed : 20.51 % Favored : 78.40 % 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: 0.87 (0.20), residues: 1843 helix: 1.31 (0.16), residues: 1119 sheet: -1.51 (0.36), residues: 165 loop : -0.07 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 475 HIS 0.009 0.001 HIS B 362 PHE 0.055 0.001 PHE C 362 TYR 0.021 0.001 TYR C 255 ARG 0.006 0.000 ARG F 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2873.84 seconds wall clock time: 52 minutes 42.22 seconds (3162.22 seconds total)