Starting phenix.real_space_refine on Tue Jun 10 23:34:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ktp_23025/06_2025/7ktp_23025.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ktp_23025/06_2025/7ktp_23025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ktp_23025/06_2025/7ktp_23025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ktp_23025/06_2025/7ktp_23025.map" model { file = "/net/cci-nas-00/data/ceres_data/7ktp_23025/06_2025/7ktp_23025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ktp_23025/06_2025/7ktp_23025.cif" } resolution = 4.8 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: 5 Type Number sf(0) Gaussians Zn 7 6.06 5 S 88 5.16 5 C 7585 2.51 5 N 2129 2.21 5 O 2199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12008 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3098 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 19, 'TRANS': 375} Chain breaks: 4 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2917 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 352} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 2932 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 15, 'TRANS': 381} Chain breaks: 9 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 502 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 7, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 227 Chain: "D" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3054 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 22, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' ZN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 939 SG CYS A 302 30.674 93.245 115.304 0.99110.70 S ATOM 985 SG CYS A 307 27.984 95.013 113.853 0.87115.67 S ATOM 1591 SG CYS A 531 18.407 73.629 116.676 1.00169.00 S ATOM 1684 SG CYS A 544 20.797 75.718 113.378 1.00139.90 S ATOM 1734 SG CYS A 550 21.476 75.101 118.290 1.00148.49 S ATOM 1591 SG CYS A 531 18.407 73.629 116.676 1.00169.00 S ATOM 1684 SG CYS A 544 20.797 75.718 113.378 1.00139.90 S ATOM 1534 SG CYS A 524 17.395 79.645 115.870 1.00134.37 S ATOM 1719 SG CYS A 548 20.534 78.895 117.300 1.00137.34 S ATOM 1819 SG CYS A 561 38.830 72.036 108.448 1.00170.41 S ATOM 1973 SG CYS A 581 38.994 75.630 106.850 1.00146.47 S ATOM 2031 SG CYS A 589 42.140 74.320 110.087 1.00177.73 S ATOM 1819 SG CYS A 561 38.830 72.036 108.448 1.00170.41 S ATOM 1867 SG CYS A 567 40.775 73.315 104.723 1.00172.65 S ATOM 1906 SG CYS A 572 37.313 70.956 104.487 1.00183.12 S ATOM 1867 SG CYS A 567 40.775 73.315 104.723 1.00172.65 S Time building chain proxies: 7.61, per 1000 atoms: 0.63 Number of scatterers: 12008 At special positions: 0 Unit cell: (86.4, 166.05, 167.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 7 29.99 S 88 16.00 O 2199 8.00 N 2129 7.00 C 7585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 302 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 307 " pdb="ZN ZN A 801 " - pdb=" ND1 HIS A 310 " pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb="ZN ZN A 804 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 544 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 531 " pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 548 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 524 " pdb=" ZN A 806 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 561 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 567 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 572 " pdb=" ZN A 807 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 567 " 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 23 sheets defined 20.8% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 34 through 62 removed outlier: 3.903A pdb=" N LYS A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 315 through 319 removed outlier: 3.970A pdb=" N VAL A 318 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR A 319 " --> pdb=" O PRO A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 319' Processing helix chain 'A' and resid 435 through 450 Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 464 through 474 removed outlier: 3.613A pdb=" N LYS A 474 " --> pdb=" O GLN A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 removed outlier: 3.721A pdb=" N MET A 539 " --> pdb=" O CYS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 4.051A pdb=" N ALA A 577 " --> pdb=" O PRO A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 683 through 688 removed outlier: 3.519A pdb=" N ALA A 688 " --> pdb=" O ILE A 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 279 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.621A pdb=" N LYS B 342 " --> pdb=" O ASP B 339 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 343 " --> pdb=" O ILE B 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 339 through 343' Processing helix chain 'C' and resid 79 through 107 removed outlier: 3.749A pdb=" N HIS C 83 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Proline residue: C 93 - end of helix removed outlier: 3.718A pdb=" N THR C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 126 through 131 removed outlier: 4.005A pdb=" N LYS C 130 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR C 131 " --> pdb=" O ILE C 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 126 through 131' Processing helix chain 'C' and resid 136 through 145 removed outlier: 4.367A pdb=" N LYS C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 141 " --> pdb=" O MET C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 470 removed outlier: 3.560A pdb=" N LEU C 463 " --> pdb=" O LYS C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 602 removed outlier: 3.924A pdb=" N ARG C 593 " --> pdb=" O PRO C 589 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 600 " --> pdb=" O THR C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 624 Processing helix chain 'C' and resid 631 through 649 removed outlier: 4.162A pdb=" N MET C 637 " --> pdb=" O ASN C 633 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU C 641 " --> pdb=" O MET C 637 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLN C 645 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LYS C 646 " --> pdb=" O ASN C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 666 removed outlier: 3.645A pdb=" N PHE C 666 " --> pdb=" O SER C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 686 removed outlier: 3.516A pdb=" N ILE C 674 " --> pdb=" O SER C 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 28 Processing helix chain 'D' and resid 355 through 362 removed outlier: 3.893A pdb=" N ASP D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.101A pdb=" N TYR D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 85 Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 removed outlier: 5.856A pdb=" N SER A 115 " --> pdb=" O GLY A 682 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 122 removed outlier: 6.552A pdb=" N PHE A 121 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 615 through 619 Processing sheet with id=AA5, first strand: chain 'A' and resid 638 through 640 removed outlier: 6.985A pdb=" N PHE A 638 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA A 713 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 83 through 89 removed outlier: 6.172A pdb=" N CYS B 84 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP B 438 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN B 86 " --> pdb=" O ARG B 436 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 101 removed outlier: 4.284A pdb=" N GLY B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 116 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN B 100 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 114 " --> pdb=" O GLN B 100 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN B 136 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLU B 125 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU B 134 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 147 through 154 removed outlier: 4.537A pdb=" N THR B 149 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA B 166 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY B 167 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASN B 176 " --> pdb=" O CYS B 182 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N CYS B 182 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 193 through 198 removed outlier: 3.683A pdb=" N GLU B 195 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU B 215 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE B 228 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 217 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N GLN B 292 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL B 226 " --> pdb=" O GLN B 292 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 239 through 244 Processing sheet with id=AB2, first strand: chain 'B' and resid 312 through 315 removed outlier: 7.314A pdb=" N LYS B 332 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE B 352 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 368 through 369 Processing sheet with id=AB4, first strand: chain 'C' and resid 230 through 234 Processing sheet with id=AB5, first strand: chain 'C' and resid 203 through 211 removed outlier: 7.020A pdb=" N VAL C 186 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS C 210 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU C 184 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 440 through 441 removed outlier: 4.531A pdb=" N GLN C 440 " --> pdb=" O PHE C 432 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 432 " --> pdb=" O GLN C 440 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE C 429 " --> pdb=" O ILE C 487 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL C 489 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN C 431 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE C 491 " --> pdb=" O GLN C 431 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 486 " --> pdb=" O VAL C 479 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL C 479 " --> pdb=" O ARG C 486 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 525 through 527 removed outlier: 3.689A pdb=" N LEU D 34 " --> pdb=" O GLN D 403 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 565 through 566 removed outlier: 4.796A pdb=" N TYR C 565 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 47 through 49 removed outlier: 7.274A pdb=" N ASN D 77 " --> pdb=" O ASN D 122 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASN D 122 " --> pdb=" O ASN D 77 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU D 79 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYS D 120 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE D 81 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 130 through 132 Processing sheet with id=AC2, first strand: chain 'D' and resid 183 through 185 removed outlier: 3.590A pdb=" N SER D 197 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 230 through 235 removed outlier: 3.785A pdb=" N LYS D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 276 through 281 removed outlier: 3.956A pdb=" N THR D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS D 311 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 320 through 322 removed outlier: 7.042A pdb=" N SER D 336 " --> pdb=" O PHE D 321 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASP D 346 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU D 366 " --> pdb=" O ASP D 346 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1104 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: 3.72 Time building geometry restraints manager: 3.37 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: 3943 1.34 - 1.46: 2770 1.46 - 1.58: 5448 1.58 - 1.70: 0 1.70 - 1.82: 121 Bond restraints: 12282 Sorted by residual: bond pdb=" C THR D 28 " pdb=" N PRO D 29 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.25e+00 bond pdb=" C ASN D 282 " pdb=" N PRO D 283 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.36e+00 bond pdb=" CA ILE B 290 " pdb=" CB ILE B 290 " ideal model delta sigma weight residual 1.527 1.546 -0.019 1.31e-02 5.83e+03 2.07e+00 bond pdb=" CA ARG C 196 " pdb=" C ARG C 196 " ideal model delta sigma weight residual 1.522 1.542 -0.019 1.36e-02 5.41e+03 2.04e+00 bond pdb=" CB PHE D 223 " pdb=" CG PHE D 223 " ideal model delta sigma weight residual 1.502 1.534 -0.032 2.30e-02 1.89e+03 1.95e+00 ... (remaining 12277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 16184 1.79 - 3.57: 371 3.57 - 5.36: 63 5.36 - 7.15: 31 7.15 - 8.93: 3 Bond angle restraints: 16652 Sorted by residual: angle pdb=" N ILE C 627 " pdb=" CA ILE C 627 " pdb=" C ILE C 627 " ideal model delta sigma weight residual 112.96 109.09 3.87 1.00e+00 1.00e+00 1.50e+01 angle pdb=" N THR D 28 " pdb=" CA THR D 28 " pdb=" C THR D 28 " ideal model delta sigma weight residual 109.81 116.73 -6.92 2.21e+00 2.05e-01 9.81e+00 angle pdb=" CA THR D 28 " pdb=" C THR D 28 " pdb=" N PRO D 29 " ideal model delta sigma weight residual 118.44 123.03 -4.59 1.59e+00 3.96e-01 8.33e+00 angle pdb=" N ARG C 196 " pdb=" CA ARG C 196 " pdb=" C ARG C 196 " ideal model delta sigma weight residual 111.71 115.02 -3.31 1.15e+00 7.56e-01 8.31e+00 angle pdb=" CA GLU C 493 " pdb=" CB GLU C 493 " pdb=" CG GLU C 493 " ideal model delta sigma weight residual 114.10 119.61 -5.51 2.00e+00 2.50e-01 7.59e+00 ... (remaining 16647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 6839 17.15 - 34.30: 417 34.30 - 51.45: 58 51.45 - 68.60: 15 68.60 - 85.75: 11 Dihedral angle restraints: 7340 sinusoidal: 2812 harmonic: 4528 Sorted by residual: dihedral pdb=" CA THR D 297 " pdb=" C THR D 297 " pdb=" N VAL D 298 " pdb=" CA VAL D 298 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ASP C 588 " pdb=" C ASP C 588 " pdb=" N PRO C 589 " pdb=" CA PRO C 589 " ideal model delta harmonic sigma weight residual -180.00 -160.77 -19.23 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA TYR B 244 " pdb=" C TYR B 244 " pdb=" N ASP B 245 " pdb=" CA ASP B 245 " ideal model delta harmonic sigma weight residual 180.00 161.39 18.61 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 7337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1163 0.036 - 0.072: 460 0.072 - 0.108: 122 0.108 - 0.144: 75 0.144 - 0.180: 13 Chirality restraints: 1833 Sorted by residual: chirality pdb=" CA VAL D 298 " pdb=" N VAL D 298 " pdb=" C VAL D 298 " pdb=" CB VAL D 298 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" CA THR D 28 " pdb=" N THR D 28 " pdb=" C THR D 28 " pdb=" CB THR D 28 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CA ILE B 228 " pdb=" N ILE B 228 " pdb=" C ILE B 228 " pdb=" CB ILE B 228 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 1830 not shown) Planarity restraints: 2152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 28 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO D 29 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 29 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 29 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 195 " 0.009 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C LYS C 195 " -0.029 2.00e-02 2.50e+03 pdb=" O LYS C 195 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG C 196 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 86 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO D 87 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 87 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 87 " 0.023 5.00e-02 4.00e+02 ... (remaining 2149 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1275 2.76 - 3.29: 11705 3.29 - 3.83: 18342 3.83 - 4.36: 21638 4.36 - 4.90: 38319 Nonbonded interactions: 91279 Sorted by model distance: nonbonded pdb=" OD1 ASP B 431 " pdb=" OG SER B 433 " model vdw 2.221 3.040 nonbonded pdb=" OG SER D 147 " pdb=" O HIS D 176 " model vdw 2.281 3.040 nonbonded pdb=" O LEU C 100 " pdb=" ND2 ASN C 104 " model vdw 2.291 3.120 nonbonded pdb=" O ARG C 427 " pdb=" N ALA C 485 " model vdw 2.309 3.120 nonbonded pdb=" O ALA A 591 " pdb=" NH2 ARG A 609 " model vdw 2.320 3.120 ... (remaining 91274 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=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 31.870 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 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: 37.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 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 : 0.010 0.399 12294 Z= 0.359 Angle : 0.725 8.935 16652 Z= 0.382 Chirality : 0.047 0.180 1833 Planarity : 0.004 0.047 2152 Dihedral : 11.993 85.753 4380 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -4.13 (0.17), residues: 1508 helix: -1.87 (0.23), residues: 267 sheet: -3.01 (0.23), residues: 324 loop : -3.04 (0.16), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 345 HIS 0.004 0.001 HIS B 213 PHE 0.022 0.001 PHE C 86 TYR 0.015 0.001 TYR B 244 ARG 0.003 0.000 ARG A 715 Details of bonding type rmsd hydrogen bonds : bond 0.13405 ( 389) hydrogen bonds : angle 6.83020 ( 1104) metal coordination : bond 0.27719 ( 12) covalent geometry : bond 0.00453 (12282) covalent geometry : angle 0.72525 (16652) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 1.304 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: A 58 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8472 (tp30) REVERT: A 115 SER cc_start: 0.8523 (m) cc_final: 0.8292 (t) REVERT: A 607 ILE cc_start: 0.8831 (mp) cc_final: 0.8549 (tt) REVERT: A 613 LYS cc_start: 0.7632 (mmtt) cc_final: 0.6512 (mmmm) REVERT: B 94 GLN cc_start: 0.8732 (tp-100) cc_final: 0.8513 (mp10) REVERT: B 104 HIS cc_start: 0.8659 (m-70) cc_final: 0.8389 (p-80) REVERT: B 122 THR cc_start: 0.8025 (p) cc_final: 0.6581 (p) REVERT: B 124 TYR cc_start: 0.7878 (m-80) cc_final: 0.7331 (m-10) REVERT: B 152 TRP cc_start: 0.8534 (m100) cc_final: 0.8331 (m100) REVERT: B 157 ASN cc_start: 0.9515 (m-40) cc_final: 0.9133 (p0) REVERT: B 182 CYS cc_start: 0.6684 (t) cc_final: 0.6334 (t) REVERT: B 196 LEU cc_start: 0.9096 (mt) cc_final: 0.8697 (mt) REVERT: B 197 LYS cc_start: 0.8114 (mmtm) cc_final: 0.7871 (mmtp) REVERT: B 217 LEU cc_start: 0.9330 (tp) cc_final: 0.9119 (tp) REVERT: B 225 LEU cc_start: 0.8970 (tt) cc_final: 0.8519 (pt) REVERT: B 228 ILE cc_start: 0.9400 (mt) cc_final: 0.9074 (mm) REVERT: B 240 LEU cc_start: 0.9182 (mt) cc_final: 0.8667 (tp) REVERT: B 252 MET cc_start: 0.9172 (mmm) cc_final: 0.8895 (mmm) REVERT: B 263 TRP cc_start: 0.7467 (m100) cc_final: 0.6914 (m100) REVERT: B 271 MET cc_start: 0.9385 (mmm) cc_final: 0.9129 (mmt) REVERT: B 291 SER cc_start: 0.9075 (t) cc_final: 0.8532 (p) REVERT: B 294 ILE cc_start: 0.8987 (mm) cc_final: 0.8355 (mm) REVERT: B 314 TRP cc_start: 0.8026 (m100) cc_final: 0.6473 (m100) REVERT: B 325 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8473 (mp0) REVERT: B 330 CYS cc_start: 0.8529 (t) cc_final: 0.7373 (p) REVERT: B 331 TRP cc_start: 0.8662 (p-90) cc_final: 0.7691 (p-90) REVERT: C 80 GLN cc_start: 0.5374 (pt0) cc_final: 0.4286 (tp40) REVERT: C 111 LEU cc_start: 0.9475 (mt) cc_final: 0.9041 (mp) REVERT: C 574 LEU cc_start: 0.8262 (tp) cc_final: 0.7976 (tp) REVERT: C 598 THR cc_start: 0.9570 (t) cc_final: 0.9345 (p) REVERT: C 615 LYS cc_start: 0.9203 (pttt) cc_final: 0.8987 (pttp) REVERT: C 659 HIS cc_start: 0.9007 (t70) cc_final: 0.8779 (t-90) REVERT: C 660 LEU cc_start: 0.9563 (mt) cc_final: 0.9211 (mt) REVERT: C 663 MET cc_start: 0.8496 (ptp) cc_final: 0.8192 (ptt) REVERT: D 13 GLU cc_start: 0.6601 (mt-10) cc_final: 0.6378 (mt-10) REVERT: D 28 THR cc_start: 0.9080 (t) cc_final: 0.8614 (p) REVERT: D 45 LEU cc_start: 0.7392 (mt) cc_final: 0.7162 (mm) REVERT: D 48 GLN cc_start: 0.8469 (tt0) cc_final: 0.8135 (pm20) REVERT: D 115 ILE cc_start: 0.6654 (mm) cc_final: 0.5289 (mm) REVERT: D 261 ASN cc_start: 0.8575 (t0) cc_final: 0.7655 (p0) REVERT: D 275 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8001 (mp0) REVERT: D 313 PHE cc_start: 0.8722 (m-80) cc_final: 0.7849 (m-10) REVERT: D 367 LEU cc_start: 0.9154 (tp) cc_final: 0.8695 (tt) REVERT: D 403 GLN cc_start: 0.8623 (tt0) cc_final: 0.8253 (tm-30) REVERT: D 404 MET cc_start: 0.8197 (ptp) cc_final: 0.7933 (ptp) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.2876 time to fit residues: 156.3622 Evaluate side-chains 224 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.0270 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 594 HIS A 690 HIS ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 235 HIS ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 527 HIS D 27 ASN D 267 HIS ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.087186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.066333 restraints weight = 58499.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.068061 restraints weight = 39671.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.069295 restraints weight = 29590.309| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12294 Z= 0.163 Angle : 0.616 6.493 16652 Z= 0.324 Chirality : 0.045 0.239 1833 Planarity : 0.004 0.065 2152 Dihedral : 4.433 24.854 1639 Min Nonbonded Distance : 1.609 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.24 % Allowed : 4.22 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.87 (0.19), residues: 1508 helix: -0.38 (0.28), residues: 290 sheet: -2.18 (0.24), residues: 351 loop : -2.39 (0.19), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 218 HIS 0.009 0.002 HIS A 313 PHE 0.019 0.002 PHE A 294 TYR 0.021 0.002 TYR A 659 ARG 0.007 0.001 ARG D 131 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 389) hydrogen bonds : angle 5.40005 ( 1104) metal coordination : bond 0.00977 ( 12) covalent geometry : bond 0.00343 (12282) covalent geometry : angle 0.61554 (16652) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 253 time to evaluate : 1.345 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: A 58 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8760 (tp30) REVERT: A 553 ASP cc_start: 0.8623 (t0) cc_final: 0.8377 (t0) REVERT: A 651 GLU cc_start: 0.9589 (mm-30) cc_final: 0.9223 (tp30) REVERT: A 681 LYS cc_start: 0.8526 (mttt) cc_final: 0.8313 (mtmm) REVERT: A 707 HIS cc_start: 0.7850 (m-70) cc_final: 0.7336 (m-70) REVERT: B 122 THR cc_start: 0.8029 (p) cc_final: 0.6731 (p) REVERT: B 124 TYR cc_start: 0.8369 (m-80) cc_final: 0.7734 (m-10) REVERT: B 152 TRP cc_start: 0.9046 (m100) cc_final: 0.8700 (m100) REVERT: B 157 ASN cc_start: 0.9558 (m-40) cc_final: 0.9190 (p0) REVERT: B 198 PHE cc_start: 0.8789 (m-80) cc_final: 0.8404 (m-80) REVERT: B 218 TRP cc_start: 0.9338 (m-90) cc_final: 0.8511 (m-90) REVERT: B 221 GLN cc_start: 0.9001 (mm110) cc_final: 0.8766 (mm-40) REVERT: B 225 LEU cc_start: 0.9298 (tt) cc_final: 0.8917 (pt) REVERT: B 228 ILE cc_start: 0.9254 (mt) cc_final: 0.9049 (mm) REVERT: B 252 MET cc_start: 0.9086 (mmm) cc_final: 0.8769 (mmm) REVERT: B 263 TRP cc_start: 0.7976 (m100) cc_final: 0.7141 (m100) REVERT: B 291 SER cc_start: 0.9273 (t) cc_final: 0.9053 (p) REVERT: B 294 ILE cc_start: 0.8777 (mm) cc_final: 0.8456 (mm) REVERT: B 314 TRP cc_start: 0.8475 (m100) cc_final: 0.7703 (m100) REVERT: B 331 TRP cc_start: 0.8948 (p-90) cc_final: 0.7852 (p-90) REVERT: B 362 ASP cc_start: 0.9247 (m-30) cc_final: 0.8974 (p0) REVERT: B 377 LEU cc_start: 0.8736 (tt) cc_final: 0.8011 (tp) REVERT: C 111 LEU cc_start: 0.9399 (mt) cc_final: 0.9101 (mp) REVERT: C 117 TYR cc_start: 0.7046 (p90) cc_final: 0.6805 (p90) REVERT: C 574 LEU cc_start: 0.8692 (tp) cc_final: 0.7519 (tp) REVERT: C 595 LYS cc_start: 0.9274 (mmmm) cc_final: 0.8920 (mmmm) REVERT: C 615 LYS cc_start: 0.9170 (pttt) cc_final: 0.8841 (pttp) REVERT: C 618 ASN cc_start: 0.8460 (m110) cc_final: 0.8190 (m110) REVERT: C 638 LEU cc_start: 0.9292 (mt) cc_final: 0.8678 (mt) REVERT: C 684 MET cc_start: 0.8458 (mpp) cc_final: 0.8087 (mpp) REVERT: D 28 THR cc_start: 0.9099 (t) cc_final: 0.8797 (t) REVERT: D 36 MET cc_start: 0.8692 (tpt) cc_final: 0.8330 (tmm) REVERT: D 253 MET cc_start: 0.4825 (mpp) cc_final: 0.4527 (mpp) REVERT: D 275 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8050 (mp0) REVERT: D 313 PHE cc_start: 0.8533 (m-80) cc_final: 0.7954 (m-10) REVERT: D 367 LEU cc_start: 0.9240 (tp) cc_final: 0.8833 (tt) REVERT: D 395 GLU cc_start: 0.9434 (pp20) cc_final: 0.9208 (pm20) REVERT: D 399 MET cc_start: 0.9361 (tmm) cc_final: 0.8373 (tmm) REVERT: D 403 GLN cc_start: 0.8487 (tt0) cc_final: 0.8146 (tm-30) REVERT: D 404 MET cc_start: 0.8906 (ptp) cc_final: 0.8507 (ptp) outliers start: 3 outliers final: 1 residues processed: 255 average time/residue: 0.2311 time to fit residues: 88.3858 Evaluate side-chains 176 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 28 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 132 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 636 ASN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN C 88 GLN C 527 HIS C 659 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.084695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.062982 restraints weight = 64395.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.064922 restraints weight = 41473.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.066211 restraints weight = 29879.006| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12294 Z= 0.136 Angle : 0.564 6.952 16652 Z= 0.296 Chirality : 0.044 0.211 1833 Planarity : 0.004 0.050 2152 Dihedral : 4.269 18.786 1639 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.10 (0.20), residues: 1508 helix: 0.50 (0.31), residues: 274 sheet: -1.66 (0.25), residues: 359 loop : -1.96 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 49 HIS 0.005 0.001 HIS B 305 PHE 0.015 0.001 PHE A 294 TYR 0.021 0.002 TYR A 642 ARG 0.005 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 389) hydrogen bonds : angle 5.06572 ( 1104) metal coordination : bond 0.00257 ( 12) covalent geometry : bond 0.00290 (12282) covalent geometry : angle 0.56359 (16652) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 2.130 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: A 58 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8846 (tp30) REVERT: A 62 LYS cc_start: 0.9363 (ptpp) cc_final: 0.9117 (pttp) REVERT: A 553 ASP cc_start: 0.8624 (t0) cc_final: 0.8393 (t0) REVERT: A 611 LEU cc_start: 0.9434 (mm) cc_final: 0.9201 (mm) REVERT: A 612 LYS cc_start: 0.8238 (pptt) cc_final: 0.8032 (pptt) REVERT: A 651 GLU cc_start: 0.9535 (mm-30) cc_final: 0.9204 (tp30) REVERT: A 668 PHE cc_start: 0.8429 (t80) cc_final: 0.7767 (t80) REVERT: A 707 HIS cc_start: 0.8120 (m-70) cc_final: 0.7602 (m-70) REVERT: B 123 LEU cc_start: 0.9621 (mp) cc_final: 0.9381 (mp) REVERT: B 124 TYR cc_start: 0.8492 (m-80) cc_final: 0.8158 (m-80) REVERT: B 152 TRP cc_start: 0.9054 (m100) cc_final: 0.8626 (m100) REVERT: B 157 ASN cc_start: 0.9559 (m-40) cc_final: 0.9184 (p0) REVERT: B 180 MET cc_start: 0.7752 (mtp) cc_final: 0.7490 (mtp) REVERT: B 195 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8447 (tm-30) REVERT: B 198 PHE cc_start: 0.8836 (m-80) cc_final: 0.8595 (m-10) REVERT: B 218 TRP cc_start: 0.9242 (m-90) cc_final: 0.8268 (m-90) REVERT: B 226 VAL cc_start: 0.9797 (t) cc_final: 0.9594 (t) REVERT: B 228 ILE cc_start: 0.9296 (mt) cc_final: 0.9057 (mm) REVERT: B 291 SER cc_start: 0.9294 (t) cc_final: 0.8944 (p) REVERT: B 314 TRP cc_start: 0.8560 (m100) cc_final: 0.8200 (m100) REVERT: B 315 LEU cc_start: 0.9587 (tp) cc_final: 0.9186 (tp) REVERT: B 331 TRP cc_start: 0.8958 (p-90) cc_final: 0.7667 (p-90) REVERT: B 362 ASP cc_start: 0.9236 (m-30) cc_final: 0.8981 (p0) REVERT: B 366 MET cc_start: 0.6879 (mmp) cc_final: 0.6675 (mmm) REVERT: B 376 MET cc_start: 0.8763 (ppp) cc_final: 0.8393 (ppp) REVERT: B 377 LEU cc_start: 0.8536 (tt) cc_final: 0.8038 (tp) REVERT: C 111 LEU cc_start: 0.9424 (mt) cc_final: 0.9164 (mp) REVERT: C 117 TYR cc_start: 0.6928 (p90) cc_final: 0.6515 (p90) REVERT: C 469 LEU cc_start: 0.9240 (mt) cc_final: 0.9003 (mt) REVERT: C 569 ASP cc_start: 0.9224 (p0) cc_final: 0.8931 (p0) REVERT: C 570 THR cc_start: 0.8768 (p) cc_final: 0.8480 (p) REVERT: C 595 LYS cc_start: 0.9215 (mmmm) cc_final: 0.8858 (mmmm) REVERT: C 612 GLU cc_start: 0.8611 (mm-30) cc_final: 0.7517 (mm-30) REVERT: C 615 LYS cc_start: 0.9103 (pttt) cc_final: 0.8590 (pttp) REVERT: C 618 ASN cc_start: 0.8815 (m110) cc_final: 0.8490 (m110) REVERT: C 629 ASP cc_start: 0.9118 (m-30) cc_final: 0.8687 (m-30) REVERT: D 34 LEU cc_start: 0.9247 (mt) cc_final: 0.8801 (pp) REVERT: D 253 MET cc_start: 0.5043 (mpp) cc_final: 0.4672 (mpp) REVERT: D 275 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8151 (mp0) REVERT: D 322 GLN cc_start: 0.7293 (tp-100) cc_final: 0.5617 (mt0) REVERT: D 367 LEU cc_start: 0.9197 (tp) cc_final: 0.8789 (tt) REVERT: D 373 HIS cc_start: 0.8030 (m170) cc_final: 0.7480 (m170) REVERT: D 377 ILE cc_start: 0.7609 (mt) cc_final: 0.7381 (tt) REVERT: D 395 GLU cc_start: 0.9460 (pp20) cc_final: 0.9183 (pm20) REVERT: D 399 MET cc_start: 0.9465 (tmm) cc_final: 0.9033 (tmm) REVERT: D 403 GLN cc_start: 0.8507 (tt0) cc_final: 0.8269 (tm-30) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.2356 time to fit residues: 78.6954 Evaluate side-chains 172 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 131 optimal weight: 0.9980 chunk 73 optimal weight: 0.0980 chunk 136 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** D 305 ASN ** 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 = 0.3725 r_free = 0.3725 target = 0.085042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.063380 restraints weight = 63260.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.065307 restraints weight = 40747.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.066715 restraints weight = 29394.803| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12294 Z= 0.102 Angle : 0.514 6.817 16652 Z= 0.270 Chirality : 0.043 0.193 1833 Planarity : 0.003 0.041 2152 Dihedral : 4.081 18.682 1639 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.08 % Allowed : 2.71 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.20), residues: 1508 helix: 0.77 (0.31), residues: 276 sheet: -1.33 (0.25), residues: 378 loop : -1.65 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 218 HIS 0.004 0.001 HIS D 226 PHE 0.012 0.001 PHE C 86 TYR 0.013 0.001 TYR A 642 ARG 0.003 0.000 ARG A 579 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 389) hydrogen bonds : angle 4.82163 ( 1104) metal coordination : bond 0.00200 ( 12) covalent geometry : bond 0.00217 (12282) covalent geometry : angle 0.51383 (16652) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 1.504 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: A 58 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8753 (tp30) REVERT: A 62 LYS cc_start: 0.9462 (ptpp) cc_final: 0.9250 (pttp) REVERT: A 97 MET cc_start: 0.8422 (tpt) cc_final: 0.8045 (tpt) REVERT: A 553 ASP cc_start: 0.8662 (t0) cc_final: 0.8409 (t0) REVERT: A 611 LEU cc_start: 0.9463 (mm) cc_final: 0.9250 (mm) REVERT: A 651 GLU cc_start: 0.9592 (mm-30) cc_final: 0.9044 (tp30) REVERT: A 707 HIS cc_start: 0.8248 (m-70) cc_final: 0.7724 (m-70) REVERT: B 115 THR cc_start: 0.9181 (p) cc_final: 0.8823 (t) REVERT: B 152 TRP cc_start: 0.8973 (m100) cc_final: 0.8671 (m100) REVERT: B 157 ASN cc_start: 0.9605 (m-40) cc_final: 0.9188 (p0) REVERT: B 180 MET cc_start: 0.7555 (mtp) cc_final: 0.7260 (mtp) REVERT: B 195 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8351 (tm-30) REVERT: B 218 TRP cc_start: 0.9149 (m-90) cc_final: 0.8455 (m-90) REVERT: B 291 SER cc_start: 0.9210 (t) cc_final: 0.8812 (p) REVERT: B 292 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8337 (mm-40) REVERT: B 315 LEU cc_start: 0.9563 (tp) cc_final: 0.9267 (tp) REVERT: B 331 TRP cc_start: 0.8975 (p-90) cc_final: 0.7625 (p-90) REVERT: B 362 ASP cc_start: 0.9245 (m-30) cc_final: 0.8986 (p0) REVERT: B 367 ARG cc_start: 0.7723 (ttm-80) cc_final: 0.7014 (ttm-80) REVERT: B 376 MET cc_start: 0.8840 (ppp) cc_final: 0.8422 (ppp) REVERT: B 377 LEU cc_start: 0.8565 (tt) cc_final: 0.8041 (tp) REVERT: B 415 GLN cc_start: 0.5790 (mt0) cc_final: 0.5325 (mt0) REVERT: C 80 GLN cc_start: 0.4255 (tp-100) cc_final: 0.4027 (tp-100) REVERT: C 117 TYR cc_start: 0.6636 (p90) cc_final: 0.6007 (p90) REVERT: C 137 MET cc_start: 0.6517 (mmp) cc_final: 0.6197 (mtp) REVERT: C 469 LEU cc_start: 0.9213 (mt) cc_final: 0.8964 (mt) REVERT: C 569 ASP cc_start: 0.9244 (p0) cc_final: 0.8826 (p0) REVERT: C 570 THR cc_start: 0.8429 (p) cc_final: 0.8094 (p) REVERT: C 595 LYS cc_start: 0.9187 (mmmm) cc_final: 0.8830 (mmmm) REVERT: C 612 GLU cc_start: 0.8596 (mm-30) cc_final: 0.7440 (mm-30) REVERT: C 615 LYS cc_start: 0.9152 (pttt) cc_final: 0.8620 (pttp) REVERT: C 618 ASN cc_start: 0.8916 (m110) cc_final: 0.8706 (m-40) REVERT: C 629 ASP cc_start: 0.9115 (m-30) cc_final: 0.8902 (m-30) REVERT: D 20 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8554 (mt-10) REVERT: D 34 LEU cc_start: 0.9335 (mt) cc_final: 0.8849 (pp) REVERT: D 253 MET cc_start: 0.4778 (mpp) cc_final: 0.4473 (mpp) REVERT: D 275 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8218 (mp0) REVERT: D 322 GLN cc_start: 0.7449 (tp-100) cc_final: 0.5747 (mt0) REVERT: D 367 LEU cc_start: 0.9162 (tp) cc_final: 0.8883 (tt) REVERT: D 399 MET cc_start: 0.9485 (tmm) cc_final: 0.9052 (tmm) REVERT: D 403 GLN cc_start: 0.8758 (tt0) cc_final: 0.8497 (tm-30) outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.2021 time to fit residues: 68.5191 Evaluate side-chains 164 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 GLN A 542 ASN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 HIS ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN C 618 ASN D 192 HIS ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.081690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.060316 restraints weight = 65559.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.062206 restraints weight = 42223.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.063571 restraints weight = 30495.762| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.6268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12294 Z= 0.145 Angle : 0.575 7.080 16652 Z= 0.305 Chirality : 0.045 0.210 1833 Planarity : 0.004 0.054 2152 Dihedral : 4.488 21.418 1639 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.08 % Allowed : 2.07 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.21), residues: 1508 helix: 0.77 (0.31), residues: 283 sheet: -1.12 (0.26), residues: 374 loop : -1.52 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 325 HIS 0.022 0.001 HIS B 92 PHE 0.015 0.002 PHE A 687 TYR 0.023 0.002 TYR B 124 ARG 0.005 0.001 ARG A 579 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 389) hydrogen bonds : angle 5.00387 ( 1104) metal coordination : bond 0.00286 ( 12) covalent geometry : bond 0.00310 (12282) covalent geometry : angle 0.57510 (16652) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 1.470 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: A 58 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8878 (tp30) REVERT: A 97 MET cc_start: 0.8491 (tpt) cc_final: 0.8282 (tpt) REVERT: A 553 ASP cc_start: 0.8712 (t0) cc_final: 0.8456 (t0) REVERT: A 612 LYS cc_start: 0.8105 (pptt) cc_final: 0.7726 (pptt) REVERT: A 651 GLU cc_start: 0.9585 (mm-30) cc_final: 0.9100 (tp30) REVERT: A 668 PHE cc_start: 0.8212 (t80) cc_final: 0.7698 (t80) REVERT: A 702 MET cc_start: 0.8139 (ptt) cc_final: 0.7939 (ptt) REVERT: A 707 HIS cc_start: 0.8282 (m-70) cc_final: 0.7748 (m-70) REVERT: B 115 THR cc_start: 0.9148 (p) cc_final: 0.8643 (p) REVERT: B 123 LEU cc_start: 0.9763 (mt) cc_final: 0.9478 (mm) REVERT: B 157 ASN cc_start: 0.9668 (m-40) cc_final: 0.9257 (p0) REVERT: B 218 TRP cc_start: 0.9160 (m-90) cc_final: 0.8514 (m-90) REVERT: B 256 MET cc_start: 0.9152 (mmt) cc_final: 0.8939 (mmt) REVERT: B 291 SER cc_start: 0.9011 (t) cc_final: 0.8561 (p) REVERT: B 292 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8294 (mm-40) REVERT: B 315 LEU cc_start: 0.9586 (tp) cc_final: 0.9214 (tp) REVERT: B 366 MET cc_start: 0.6804 (mmp) cc_final: 0.6238 (mmm) REVERT: B 376 MET cc_start: 0.9079 (ppp) cc_final: 0.8521 (ppp) REVERT: B 377 LEU cc_start: 0.8750 (tt) cc_final: 0.8195 (tp) REVERT: C 80 GLN cc_start: 0.4581 (tp-100) cc_final: 0.4257 (tp-100) REVERT: C 117 TYR cc_start: 0.7307 (p90) cc_final: 0.6407 (p90) REVERT: C 137 MET cc_start: 0.6422 (mmp) cc_final: 0.6198 (mtp) REVERT: C 469 LEU cc_start: 0.9252 (mt) cc_final: 0.9021 (mt) REVERT: C 569 ASP cc_start: 0.9191 (p0) cc_final: 0.8783 (p0) REVERT: C 595 LYS cc_start: 0.9236 (mmmm) cc_final: 0.8858 (mmmm) REVERT: C 622 MET cc_start: 0.9454 (mmp) cc_final: 0.9107 (mmp) REVERT: C 629 ASP cc_start: 0.9227 (m-30) cc_final: 0.8949 (m-30) REVERT: D 20 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8640 (mt-10) REVERT: D 34 LEU cc_start: 0.9493 (mt) cc_final: 0.8986 (pp) REVERT: D 36 MET cc_start: 0.8530 (tpt) cc_final: 0.8319 (tpt) REVERT: D 250 GLN cc_start: 0.7934 (mp10) cc_final: 0.7722 (mp10) REVERT: D 252 LEU cc_start: 0.9282 (mp) cc_final: 0.9068 (mp) REVERT: D 253 MET cc_start: 0.5157 (mpp) cc_final: 0.4731 (mpp) REVERT: D 275 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7653 (mp0) REVERT: D 322 GLN cc_start: 0.7520 (tp-100) cc_final: 0.5947 (mt0) REVERT: D 361 ASP cc_start: 0.7124 (m-30) cc_final: 0.6908 (t0) REVERT: D 367 LEU cc_start: 0.9157 (tp) cc_final: 0.8683 (tt) REVERT: D 399 MET cc_start: 0.9415 (tmm) cc_final: 0.8854 (tmm) REVERT: D 403 GLN cc_start: 0.8812 (tt0) cc_final: 0.8580 (tm-30) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.1922 time to fit residues: 57.2406 Evaluate side-chains 152 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 129 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 122 optimal weight: 0.0470 chunk 62 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 127 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 overall best weight: 1.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 HIS C 88 GLN C 112 HIS D 272 HIS D 305 ASN ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.078550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.057959 restraints weight = 64510.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.059756 restraints weight = 41874.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.061006 restraints weight = 30381.064| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.7150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12294 Z= 0.184 Angle : 0.615 7.497 16652 Z= 0.326 Chirality : 0.045 0.170 1833 Planarity : 0.004 0.049 2152 Dihedral : 4.767 19.967 1639 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.21), residues: 1508 helix: 0.41 (0.31), residues: 286 sheet: -1.03 (0.26), residues: 384 loop : -1.40 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 388 HIS 0.019 0.001 HIS B 92 PHE 0.020 0.002 PHE A 294 TYR 0.023 0.002 TYR A 659 ARG 0.005 0.001 ARG B 367 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 389) hydrogen bonds : angle 5.15563 ( 1104) metal coordination : bond 0.00439 ( 12) covalent geometry : bond 0.00384 (12282) covalent geometry : angle 0.61526 (16652) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 GLN cc_start: 0.9537 (mm110) cc_final: 0.9196 (mm110) REVERT: A 553 ASP cc_start: 0.8688 (t0) cc_final: 0.8419 (t0) REVERT: A 651 GLU cc_start: 0.9551 (mm-30) cc_final: 0.9236 (tp30) REVERT: A 655 ARG cc_start: 0.8938 (mmt90) cc_final: 0.8168 (tpt170) REVERT: A 707 HIS cc_start: 0.8463 (m-70) cc_final: 0.8050 (m-70) REVERT: B 115 THR cc_start: 0.9237 (p) cc_final: 0.8626 (t) REVERT: B 123 LEU cc_start: 0.9794 (mt) cc_final: 0.9570 (mm) REVERT: B 152 TRP cc_start: 0.9137 (m100) cc_final: 0.8370 (m100) REVERT: B 157 ASN cc_start: 0.9686 (m-40) cc_final: 0.9222 (p0) REVERT: B 195 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8367 (tm-30) REVERT: B 291 SER cc_start: 0.8940 (t) cc_final: 0.8598 (t) REVERT: B 310 ASP cc_start: 0.7161 (m-30) cc_final: 0.6759 (m-30) REVERT: B 315 LEU cc_start: 0.9620 (tp) cc_final: 0.9263 (tp) REVERT: B 366 MET cc_start: 0.6603 (mmp) cc_final: 0.6214 (mmp) REVERT: B 376 MET cc_start: 0.9192 (ppp) cc_final: 0.8538 (ppp) REVERT: B 377 LEU cc_start: 0.8837 (tt) cc_final: 0.8224 (tp) REVERT: C 117 TYR cc_start: 0.7111 (p90) cc_final: 0.6282 (p90) REVERT: C 137 MET cc_start: 0.6533 (mmp) cc_final: 0.6150 (mtp) REVERT: C 569 ASP cc_start: 0.9117 (p0) cc_final: 0.8738 (p0) REVERT: C 595 LYS cc_start: 0.9132 (mmmm) cc_final: 0.8802 (mmmm) REVERT: C 612 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8429 (tp30) REVERT: C 622 MET cc_start: 0.9406 (mmp) cc_final: 0.9099 (mmp) REVERT: C 629 ASP cc_start: 0.9289 (m-30) cc_final: 0.9053 (m-30) REVERT: C 638 LEU cc_start: 0.9521 (mt) cc_final: 0.9061 (mt) REVERT: C 684 MET cc_start: 0.8718 (mpp) cc_final: 0.8134 (mpp) REVERT: D 20 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8605 (mt-10) REVERT: D 34 LEU cc_start: 0.9499 (mt) cc_final: 0.9017 (pp) REVERT: D 248 ASP cc_start: 0.9183 (m-30) cc_final: 0.8958 (m-30) REVERT: D 252 LEU cc_start: 0.9346 (mp) cc_final: 0.9123 (mp) REVERT: D 253 MET cc_start: 0.5944 (mpp) cc_final: 0.5534 (mpp) REVERT: D 258 ARG cc_start: 0.8408 (mtt90) cc_final: 0.8147 (mmp80) REVERT: D 322 GLN cc_start: 0.7796 (tp-100) cc_final: 0.6349 (mt0) REVERT: D 367 LEU cc_start: 0.9293 (tp) cc_final: 0.8877 (tt) REVERT: D 399 MET cc_start: 0.9417 (tmm) cc_final: 0.8846 (tmm) REVERT: D 403 GLN cc_start: 0.8742 (tt0) cc_final: 0.8499 (tm-30) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1918 time to fit residues: 55.1021 Evaluate side-chains 136 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 0.2980 chunk 134 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 89 optimal weight: 0.0980 chunk 88 optimal weight: 9.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN C 80 GLN ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.080549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.059876 restraints weight = 64555.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.061730 restraints weight = 40918.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.062964 restraints weight = 29262.933| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.7200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12294 Z= 0.106 Angle : 0.552 9.140 16652 Z= 0.289 Chirality : 0.044 0.154 1833 Planarity : 0.003 0.039 2152 Dihedral : 4.417 18.683 1639 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.21), residues: 1508 helix: 0.68 (0.31), residues: 278 sheet: -0.83 (0.25), residues: 396 loop : -1.29 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 325 HIS 0.011 0.001 HIS B 92 PHE 0.014 0.001 PHE A 725 TYR 0.023 0.001 TYR A 659 ARG 0.005 0.000 ARG B 367 Details of bonding type rmsd hydrogen bonds : bond 0.03432 ( 389) hydrogen bonds : angle 4.86462 ( 1104) metal coordination : bond 0.00141 ( 12) covalent geometry : bond 0.00232 (12282) covalent geometry : angle 0.55213 (16652) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 GLN cc_start: 0.9470 (mm110) cc_final: 0.9102 (mm110) REVERT: A 553 ASP cc_start: 0.8669 (t0) cc_final: 0.8394 (t0) REVERT: A 641 GLU cc_start: 0.8088 (pp20) cc_final: 0.7853 (pp20) REVERT: A 651 GLU cc_start: 0.9556 (mm-30) cc_final: 0.9224 (tp30) REVERT: A 655 ARG cc_start: 0.8930 (mmt90) cc_final: 0.7544 (tpt170) REVERT: A 668 PHE cc_start: 0.8081 (t80) cc_final: 0.7574 (t80) REVERT: A 707 HIS cc_start: 0.8517 (m-70) cc_final: 0.8149 (m170) REVERT: B 115 THR cc_start: 0.9388 (p) cc_final: 0.8875 (t) REVERT: B 123 LEU cc_start: 0.9739 (mt) cc_final: 0.9526 (mm) REVERT: B 152 TRP cc_start: 0.9201 (m100) cc_final: 0.8489 (m100) REVERT: B 157 ASN cc_start: 0.9665 (m-40) cc_final: 0.9187 (p0) REVERT: B 163 LEU cc_start: 0.9452 (tp) cc_final: 0.9218 (tp) REVERT: B 180 MET cc_start: 0.8485 (mmm) cc_final: 0.8283 (mmm) REVERT: B 195 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8148 (tm-30) REVERT: B 218 TRP cc_start: 0.9242 (m-90) cc_final: 0.8597 (m-90) REVERT: B 376 MET cc_start: 0.9151 (ppp) cc_final: 0.8486 (ppp) REVERT: C 104 ASN cc_start: 0.9098 (p0) cc_final: 0.8639 (t0) REVERT: C 137 MET cc_start: 0.6484 (mmp) cc_final: 0.6202 (mtp) REVERT: C 569 ASP cc_start: 0.9111 (p0) cc_final: 0.8653 (p0) REVERT: C 579 MET cc_start: 0.8937 (mmm) cc_final: 0.8727 (mmm) REVERT: C 585 ASP cc_start: 0.6613 (t70) cc_final: 0.6346 (t0) REVERT: C 595 LYS cc_start: 0.9120 (mmmm) cc_final: 0.8772 (mmmm) REVERT: C 612 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8186 (tp30) REVERT: C 615 LYS cc_start: 0.9390 (ptpp) cc_final: 0.9093 (ptpp) REVERT: C 622 MET cc_start: 0.9304 (mmp) cc_final: 0.8993 (mmp) REVERT: C 629 ASP cc_start: 0.9044 (m-30) cc_final: 0.8806 (m-30) REVERT: C 684 MET cc_start: 0.8752 (mpp) cc_final: 0.8174 (mpp) REVERT: D 20 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8585 (mt-10) REVERT: D 34 LEU cc_start: 0.9455 (mt) cc_final: 0.8965 (pp) REVERT: D 253 MET cc_start: 0.5859 (mpp) cc_final: 0.5497 (mpp) REVERT: D 258 ARG cc_start: 0.8399 (mtt90) cc_final: 0.8142 (mmp80) REVERT: D 322 GLN cc_start: 0.7821 (tp-100) cc_final: 0.6446 (mt0) REVERT: D 367 LEU cc_start: 0.9194 (tp) cc_final: 0.8736 (tt) REVERT: D 399 MET cc_start: 0.9300 (tmm) cc_final: 0.8871 (tmm) REVERT: D 403 GLN cc_start: 0.8742 (tt0) cc_final: 0.8310 (mm-40) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2047 time to fit residues: 58.7427 Evaluate side-chains 143 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 110 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 29 optimal weight: 0.0970 chunk 40 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN B 292 GLN B 307 ASN D 272 HIS ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.080308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.059947 restraints weight = 64743.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.061759 restraints weight = 41357.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.063023 restraints weight = 29651.924| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.7434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12294 Z= 0.105 Angle : 0.542 7.067 16652 Z= 0.283 Chirality : 0.043 0.157 1833 Planarity : 0.003 0.038 2152 Dihedral : 4.302 19.044 1639 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.08 % Allowed : 0.64 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.21), residues: 1508 helix: 0.80 (0.32), residues: 278 sheet: -0.89 (0.25), residues: 403 loop : -1.16 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 325 HIS 0.009 0.001 HIS B 92 PHE 0.013 0.001 PHE B 198 TYR 0.022 0.001 TYR A 659 ARG 0.005 0.000 ARG B 367 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 389) hydrogen bonds : angle 4.76841 ( 1104) metal coordination : bond 0.00138 ( 12) covalent geometry : bond 0.00232 (12282) covalent geometry : angle 0.54166 (16652) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 470 GLN cc_start: 0.9434 (mm110) cc_final: 0.9081 (mm110) REVERT: A 553 ASP cc_start: 0.8651 (t0) cc_final: 0.8401 (t0) REVERT: A 645 GLU cc_start: 0.7625 (tp30) cc_final: 0.7377 (tp30) REVERT: A 651 GLU cc_start: 0.9512 (mm-30) cc_final: 0.9270 (tp30) REVERT: A 655 ARG cc_start: 0.8957 (mmt90) cc_final: 0.7591 (tpt170) REVERT: A 668 PHE cc_start: 0.8103 (t80) cc_final: 0.7634 (t80) REVERT: A 707 HIS cc_start: 0.8554 (m-70) cc_final: 0.8191 (m-70) REVERT: B 115 THR cc_start: 0.9394 (p) cc_final: 0.8567 (t) REVERT: B 152 TRP cc_start: 0.9203 (m100) cc_final: 0.8718 (m100) REVERT: B 157 ASN cc_start: 0.9630 (m-40) cc_final: 0.9197 (p0) REVERT: B 180 MET cc_start: 0.8826 (mmm) cc_final: 0.8357 (mmm) REVERT: B 194 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7536 (t0) REVERT: B 195 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8395 (tm-30) REVERT: B 218 TRP cc_start: 0.9189 (m-90) cc_final: 0.8529 (m-90) REVERT: B 291 SER cc_start: 0.8887 (t) cc_final: 0.8619 (t) REVERT: B 292 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8327 (mm-40) REVERT: B 315 LEU cc_start: 0.9548 (tp) cc_final: 0.9151 (tp) REVERT: B 331 TRP cc_start: 0.9100 (p-90) cc_final: 0.7435 (p-90) REVERT: B 376 MET cc_start: 0.9170 (ppp) cc_final: 0.8562 (ppp) REVERT: C 80 GLN cc_start: 0.6039 (mp10) cc_final: 0.5489 (tp-100) REVERT: C 104 ASN cc_start: 0.9081 (p0) cc_final: 0.8527 (t0) REVERT: C 569 ASP cc_start: 0.9065 (p0) cc_final: 0.8554 (p0) REVERT: C 579 MET cc_start: 0.8742 (mmm) cc_final: 0.8508 (mmm) REVERT: C 595 LYS cc_start: 0.9086 (mmmm) cc_final: 0.8763 (mmmm) REVERT: C 612 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8081 (tp30) REVERT: C 615 LYS cc_start: 0.9292 (ptpp) cc_final: 0.9000 (ptpp) REVERT: C 618 ASN cc_start: 0.9236 (m-40) cc_final: 0.8953 (m-40) REVERT: C 621 VAL cc_start: 0.9368 (p) cc_final: 0.9034 (p) REVERT: C 622 MET cc_start: 0.9236 (mmp) cc_final: 0.8945 (mmp) REVERT: C 684 MET cc_start: 0.8726 (mpp) cc_final: 0.8178 (mpp) REVERT: D 20 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8566 (mt-10) REVERT: D 34 LEU cc_start: 0.9407 (mt) cc_final: 0.8935 (pp) REVERT: D 253 MET cc_start: 0.6057 (mpp) cc_final: 0.5648 (mpp) REVERT: D 258 ARG cc_start: 0.8404 (mtt90) cc_final: 0.8137 (mmp80) REVERT: D 322 GLN cc_start: 0.7858 (tp-100) cc_final: 0.6572 (mt0) REVERT: D 367 LEU cc_start: 0.9139 (tp) cc_final: 0.8715 (tt) REVERT: D 373 HIS cc_start: 0.7900 (m170) cc_final: 0.7608 (m170) REVERT: D 399 MET cc_start: 0.9277 (tmm) cc_final: 0.8827 (tmm) REVERT: D 403 GLN cc_start: 0.8618 (tt0) cc_final: 0.8162 (mm-40) REVERT: D 404 MET cc_start: 0.8178 (tmm) cc_final: 0.7960 (tmm) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.2088 time to fit residues: 61.0531 Evaluate side-chains 144 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 103 optimal weight: 0.6980 chunk 135 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 13 optimal weight: 0.0670 chunk 35 optimal weight: 0.0470 chunk 14 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 272 HIS ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.081475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.060924 restraints weight = 63942.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.062778 restraints weight = 40346.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.064101 restraints weight = 28863.579| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.7492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12294 Z= 0.095 Angle : 0.544 7.787 16652 Z= 0.282 Chirality : 0.043 0.189 1833 Planarity : 0.003 0.037 2152 Dihedral : 4.174 19.239 1639 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.96 (0.21), residues: 1508 helix: 0.70 (0.31), residues: 278 sheet: -0.56 (0.26), residues: 386 loop : -1.12 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 325 HIS 0.011 0.001 HIS C 659 PHE 0.017 0.001 PHE B 198 TYR 0.018 0.001 TYR A 659 ARG 0.003 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03248 ( 389) hydrogen bonds : angle 4.71094 ( 1104) metal coordination : bond 0.00078 ( 12) covalent geometry : bond 0.00212 (12282) covalent geometry : angle 0.54376 (16652) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 ASP cc_start: 0.8621 (t0) cc_final: 0.8349 (t0) REVERT: A 645 GLU cc_start: 0.7728 (tp30) cc_final: 0.7424 (tp30) REVERT: A 651 GLU cc_start: 0.9547 (mm-30) cc_final: 0.9191 (tp30) REVERT: A 668 PHE cc_start: 0.8065 (t80) cc_final: 0.7602 (t80) REVERT: A 707 HIS cc_start: 0.8646 (m-70) cc_final: 0.8213 (m-70) REVERT: B 115 THR cc_start: 0.9390 (p) cc_final: 0.8173 (p) REVERT: B 148 TYR cc_start: 0.8447 (m-80) cc_final: 0.7635 (m-80) REVERT: B 152 TRP cc_start: 0.9288 (m100) cc_final: 0.8588 (m100) REVERT: B 157 ASN cc_start: 0.9600 (m-40) cc_final: 0.9157 (p0) REVERT: B 193 ILE cc_start: 0.9173 (mp) cc_final: 0.8777 (mp) REVERT: B 195 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8190 (tm-30) REVERT: B 218 TRP cc_start: 0.9199 (m-90) cc_final: 0.8609 (m-90) REVERT: B 290 ILE cc_start: 0.9362 (mm) cc_final: 0.9161 (pt) REVERT: B 291 SER cc_start: 0.8892 (t) cc_final: 0.8502 (p) REVERT: B 292 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7931 (mm110) REVERT: B 315 LEU cc_start: 0.9525 (tp) cc_final: 0.9171 (tp) REVERT: B 365 TYR cc_start: 0.8141 (t80) cc_final: 0.7907 (t80) REVERT: B 376 MET cc_start: 0.9141 (ppp) cc_final: 0.8609 (ppp) REVERT: C 80 GLN cc_start: 0.5930 (mp10) cc_final: 0.5449 (tp-100) REVERT: C 104 ASN cc_start: 0.9100 (p0) cc_final: 0.8535 (t0) REVERT: C 579 MET cc_start: 0.8691 (mmm) cc_final: 0.8441 (mmm) REVERT: C 595 LYS cc_start: 0.9194 (mmmm) cc_final: 0.8864 (mmmm) REVERT: C 612 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7992 (tp30) REVERT: C 618 ASN cc_start: 0.9240 (m-40) cc_final: 0.8912 (m-40) REVERT: C 621 VAL cc_start: 0.9360 (p) cc_final: 0.9017 (p) REVERT: C 622 MET cc_start: 0.9283 (mmp) cc_final: 0.9012 (mmp) REVERT: C 629 ASP cc_start: 0.9159 (m-30) cc_final: 0.8905 (m-30) REVERT: C 632 MET cc_start: 0.9376 (ppp) cc_final: 0.9159 (ppp) REVERT: C 684 MET cc_start: 0.8681 (mpp) cc_final: 0.8076 (mpp) REVERT: D 20 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8633 (mt-10) REVERT: D 34 LEU cc_start: 0.9359 (mt) cc_final: 0.8891 (pp) REVERT: D 253 MET cc_start: 0.5953 (mpp) cc_final: 0.5575 (mpp) REVERT: D 258 ARG cc_start: 0.8356 (mtt90) cc_final: 0.8066 (mmp80) REVERT: D 322 GLN cc_start: 0.7845 (tp-100) cc_final: 0.6644 (mt0) REVERT: D 367 LEU cc_start: 0.9144 (tp) cc_final: 0.8714 (tt) REVERT: D 399 MET cc_start: 0.9306 (tmm) cc_final: 0.8841 (tmm) REVERT: D 403 GLN cc_start: 0.8706 (tt0) cc_final: 0.8174 (tp40) REVERT: D 404 MET cc_start: 0.8145 (tmm) cc_final: 0.7856 (tmm) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2109 time to fit residues: 60.7325 Evaluate side-chains 140 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 73 optimal weight: 4.9990 chunk 66 optimal weight: 0.0470 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN B 258 HIS ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.081059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.060674 restraints weight = 63613.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.062509 restraints weight = 40587.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.063783 restraints weight = 29179.614| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.7738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12294 Z= 0.104 Angle : 0.549 7.663 16652 Z= 0.286 Chirality : 0.043 0.182 1833 Planarity : 0.003 0.037 2152 Dihedral : 4.214 19.261 1639 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.97 (0.21), residues: 1508 helix: 0.69 (0.31), residues: 276 sheet: -0.55 (0.26), residues: 380 loop : -1.13 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.001 TRP D 325 HIS 0.013 0.001 HIS C 659 PHE 0.012 0.001 PHE A 725 TYR 0.018 0.001 TYR A 659 ARG 0.002 0.000 ARG C 439 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 389) hydrogen bonds : angle 4.82382 ( 1104) metal coordination : bond 0.00117 ( 12) covalent geometry : bond 0.00232 (12282) covalent geometry : angle 0.54937 (16652) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.5864 (pmm) cc_final: 0.5212 (pmm) REVERT: A 553 ASP cc_start: 0.8639 (t0) cc_final: 0.8366 (t0) REVERT: A 558 PHE cc_start: 0.8589 (t80) cc_final: 0.8270 (t80) REVERT: A 641 GLU cc_start: 0.7944 (pp20) cc_final: 0.7690 (pp20) REVERT: A 645 GLU cc_start: 0.7671 (tp30) cc_final: 0.7412 (tp30) REVERT: A 651 GLU cc_start: 0.9474 (mm-30) cc_final: 0.9208 (tp30) REVERT: A 668 PHE cc_start: 0.7968 (t80) cc_final: 0.7568 (t80) REVERT: A 707 HIS cc_start: 0.8666 (m-70) cc_final: 0.8243 (m-70) REVERT: A 725 PHE cc_start: 0.7750 (p90) cc_final: 0.7483 (p90) REVERT: B 115 THR cc_start: 0.9359 (p) cc_final: 0.8291 (t) REVERT: B 152 TRP cc_start: 0.9214 (m100) cc_final: 0.8872 (m100) REVERT: B 157 ASN cc_start: 0.9605 (m-40) cc_final: 0.9165 (p0) REVERT: B 195 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8153 (tm-30) REVERT: B 207 LEU cc_start: 0.9314 (tp) cc_final: 0.9102 (tp) REVERT: B 218 TRP cc_start: 0.9134 (m-90) cc_final: 0.8467 (m-90) REVERT: B 291 SER cc_start: 0.8945 (t) cc_final: 0.8672 (t) REVERT: B 292 GLN cc_start: 0.8307 (mm-40) cc_final: 0.8105 (mm110) REVERT: B 307 ASN cc_start: 0.8832 (m110) cc_final: 0.8196 (p0) REVERT: B 315 LEU cc_start: 0.9542 (tp) cc_final: 0.9191 (tp) REVERT: B 365 TYR cc_start: 0.8086 (t80) cc_final: 0.7811 (t80) REVERT: B 376 MET cc_start: 0.9131 (ppp) cc_final: 0.8604 (ppp) REVERT: C 80 GLN cc_start: 0.6080 (mp10) cc_final: 0.5563 (tp-100) REVERT: C 104 ASN cc_start: 0.9091 (p0) cc_final: 0.8522 (t0) REVERT: C 569 ASP cc_start: 0.9057 (p0) cc_final: 0.8620 (p0) REVERT: C 570 THR cc_start: 0.8609 (p) cc_final: 0.8374 (p) REVERT: C 579 MET cc_start: 0.8672 (mmm) cc_final: 0.8471 (mmm) REVERT: C 595 LYS cc_start: 0.9158 (mmmm) cc_final: 0.8946 (mmmm) REVERT: C 612 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7945 (tp30) REVERT: C 618 ASN cc_start: 0.9211 (m-40) cc_final: 0.8869 (m-40) REVERT: C 621 VAL cc_start: 0.9344 (p) cc_final: 0.9024 (p) REVERT: C 622 MET cc_start: 0.9358 (mmp) cc_final: 0.9093 (mmp) REVERT: C 663 MET cc_start: 0.8451 (pmm) cc_final: 0.8216 (pmm) REVERT: D 20 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8635 (mt-10) REVERT: D 34 LEU cc_start: 0.9350 (mt) cc_final: 0.8870 (pp) REVERT: D 253 MET cc_start: 0.6001 (mpp) cc_final: 0.5608 (mpp) REVERT: D 258 ARG cc_start: 0.8299 (mtt90) cc_final: 0.8070 (mmp80) REVERT: D 322 GLN cc_start: 0.7678 (tp-100) cc_final: 0.6378 (mt0) REVERT: D 367 LEU cc_start: 0.9136 (tp) cc_final: 0.8697 (tt) REVERT: D 391 CYS cc_start: 0.8729 (t) cc_final: 0.8244 (p) REVERT: D 399 MET cc_start: 0.9231 (tmm) cc_final: 0.8736 (tmm) REVERT: D 404 MET cc_start: 0.8064 (tmm) cc_final: 0.7692 (tmm) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.3529 time to fit residues: 103.4295 Evaluate side-chains 140 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 113 optimal weight: 0.0670 chunk 89 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 78 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 chunk 91 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN D 373 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.081702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.061158 restraints weight = 63594.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.063016 restraints weight = 40769.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.064330 restraints weight = 29313.385| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.7842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12294 Z= 0.096 Angle : 0.552 7.677 16652 Z= 0.285 Chirality : 0.043 0.179 1833 Planarity : 0.003 0.037 2152 Dihedral : 4.139 17.591 1639 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.89 (0.21), residues: 1508 helix: 0.65 (0.31), residues: 277 sheet: -0.52 (0.26), residues: 392 loop : -1.03 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP D 325 HIS 0.013 0.001 HIS C 659 PHE 0.013 0.001 PHE A 725 TYR 0.021 0.001 TYR B 154 ARG 0.004 0.000 ARG D 131 Details of bonding type rmsd hydrogen bonds : bond 0.03267 ( 389) hydrogen bonds : angle 4.81014 ( 1104) metal coordination : bond 0.00077 ( 12) covalent geometry : bond 0.00218 (12282) covalent geometry : angle 0.55175 (16652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5432.47 seconds wall clock time: 97 minutes 13.21 seconds (5833.21 seconds total)