Starting phenix.real_space_refine on Wed Mar 4 08:27:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ktp_23025/03_2026/7ktp_23025.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ktp_23025/03_2026/7ktp_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ktp_23025/03_2026/7ktp_23025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ktp_23025/03_2026/7ktp_23025.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ktp_23025/03_2026/7ktp_23025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ktp_23025/03_2026/7ktp_23025.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ARG:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 2, 'TRP:plan': 1, 'ASP: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: {'ASP:plan': 4, 'GLU:plan': 1} 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: {'HIS:plan': 3, 'GLN:plan1': 11, 'PHE:plan': 7, 'GLU:plan': 7, 'ASN:plan1': 5, 'TYR:plan': 4, 'ARG:plan': 5, 'ASP:plan': 7, 'TRP:plan': 1} 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: {'ASP:plan': 3, 'GLU: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: 2.55, per 1000 atoms: 0.21 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: 0.71 Conformation dependent library (CDL) restraints added in 561.4 milliseconds 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: 0.35 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: 2.01 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.550 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.890 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.003 0.000 ARG A 715 TYR 0.015 0.001 TYR B 244 PHE 0.022 0.001 PHE C 86 TRP 0.010 0.001 TRP D 345 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00453 (12282) covalent geometry : angle 0.72525 (16652) hydrogen bonds : bond 0.13405 ( 389) hydrogen bonds : angle 6.83020 ( 1104) metal coordination : bond 0.27719 ( 12) *********************** 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 : 0.469 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: 0.8468 (tp30) REVERT: A 115 SER cc_start: 0.8523 (m) cc_final: 0.8313 (t) REVERT: A 607 ILE cc_start: 0.8831 (mp) cc_final: 0.8546 (tt) REVERT: A 613 LYS cc_start: 0.7632 (mmtt) cc_final: 0.6522 (mmmm) REVERT: B 94 GLN cc_start: 0.8732 (tp-100) cc_final: 0.8519 (mp10) REVERT: B 104 HIS cc_start: 0.8659 (m-70) cc_final: 0.8395 (p-80) REVERT: B 122 THR cc_start: 0.8025 (p) cc_final: 0.6583 (p) REVERT: B 124 TYR cc_start: 0.7878 (m-80) cc_final: 0.7344 (m-10) REVERT: B 157 ASN cc_start: 0.9515 (m-40) cc_final: 0.9137 (p0) REVERT: B 182 CYS cc_start: 0.6684 (t) cc_final: 0.6336 (t) REVERT: B 196 LEU cc_start: 0.9096 (mt) cc_final: 0.8727 (mt) REVERT: B 197 LYS cc_start: 0.8114 (mmtm) cc_final: 0.7874 (mmtp) REVERT: B 217 LEU cc_start: 0.9330 (tp) cc_final: 0.9118 (tp) REVERT: B 225 LEU cc_start: 0.8970 (tt) cc_final: 0.8521 (pt) REVERT: B 228 ILE cc_start: 0.9400 (mt) cc_final: 0.9083 (mm) REVERT: B 240 LEU cc_start: 0.9182 (mt) cc_final: 0.8639 (tp) REVERT: B 252 MET cc_start: 0.9172 (mmm) cc_final: 0.8890 (mmm) REVERT: B 263 TRP cc_start: 0.7467 (m100) cc_final: 0.6916 (m100) REVERT: B 271 MET cc_start: 0.9385 (mmm) cc_final: 0.9093 (mmt) REVERT: B 291 SER cc_start: 0.9075 (t) cc_final: 0.8539 (p) REVERT: B 294 ILE cc_start: 0.8987 (mm) cc_final: 0.8350 (mm) REVERT: B 314 TRP cc_start: 0.8026 (m100) cc_final: 0.6545 (m100) REVERT: B 325 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8444 (mp0) REVERT: B 330 CYS cc_start: 0.8529 (t) cc_final: 0.7376 (p) REVERT: B 331 TRP cc_start: 0.8662 (p-90) cc_final: 0.7665 (p-90) REVERT: B 340 ILE cc_start: 0.9338 (tp) cc_final: 0.8117 (tp) REVERT: C 80 GLN cc_start: 0.5374 (pt0) cc_final: 0.4876 (tp40) REVERT: C 111 LEU cc_start: 0.9475 (mt) cc_final: 0.9038 (mp) REVERT: C 574 LEU cc_start: 0.8262 (tp) cc_final: 0.7975 (tp) REVERT: C 598 THR cc_start: 0.9570 (t) cc_final: 0.9368 (p) REVERT: C 615 LYS cc_start: 0.9203 (pttt) cc_final: 0.8976 (pttp) REVERT: C 659 HIS cc_start: 0.9007 (t70) cc_final: 0.8437 (t-90) REVERT: C 660 LEU cc_start: 0.9563 (mt) cc_final: 0.9226 (mt) REVERT: C 663 MET cc_start: 0.8496 (ptp) cc_final: 0.8160 (ptt) REVERT: D 13 GLU cc_start: 0.6601 (mt-10) cc_final: 0.6373 (mt-10) REVERT: D 28 THR cc_start: 0.9080 (t) cc_final: 0.8616 (p) REVERT: D 45 LEU cc_start: 0.7392 (mt) cc_final: 0.7166 (mm) REVERT: D 48 GLN cc_start: 0.8469 (tt0) cc_final: 0.8134 (pm20) REVERT: D 115 ILE cc_start: 0.6654 (mm) cc_final: 0.5286 (mm) REVERT: D 261 ASN cc_start: 0.8575 (t0) cc_final: 0.7652 (p0) REVERT: D 275 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8004 (mp0) REVERT: D 313 PHE cc_start: 0.8722 (m-80) cc_final: 0.7851 (m-10) REVERT: D 367 LEU cc_start: 0.9154 (tp) cc_final: 0.8742 (tt) REVERT: D 403 GLN cc_start: 0.8623 (tt0) cc_final: 0.8258 (tm-30) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.1256 time to fit residues: 69.2635 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 : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 313 HIS B 235 HIS C 88 GLN C 527 HIS ** C 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN D 267 HIS ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.092143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.070853 restraints weight = 61276.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.072888 restraints weight = 40232.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.074286 restraints weight = 29206.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.075459 restraints weight = 22859.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.076197 restraints weight = 18663.537| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12294 Z= 0.117 Angle : 0.564 6.615 16652 Z= 0.293 Chirality : 0.044 0.254 1833 Planarity : 0.004 0.053 2152 Dihedral : 4.076 17.701 1639 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.32 % Allowed : 3.74 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.19), residues: 1508 helix: -0.49 (0.28), residues: 273 sheet: -2.06 (0.25), residues: 344 loop : -2.37 (0.18), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 579 TYR 0.020 0.001 TYR D 284 PHE 0.012 0.001 PHE A 294 TRP 0.016 0.001 TRP B 218 HIS 0.009 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00257 (12282) covalent geometry : angle 0.56366 (16652) hydrogen bonds : bond 0.03665 ( 389) hydrogen bonds : angle 5.31070 ( 1104) metal coordination : bond 0.00682 ( 12) *********************** 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 261 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 257 time to evaluate : 0.327 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: A 58 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8595 (tp30) REVERT: A 71 MET cc_start: 0.2396 (ptt) cc_final: 0.2180 (ptt) REVERT: A 540 THR cc_start: 0.9188 (p) cc_final: 0.8919 (t) REVERT: A 553 ASP cc_start: 0.8303 (t0) cc_final: 0.8017 (t0) REVERT: A 651 GLU cc_start: 0.9580 (mm-30) cc_final: 0.9290 (tp30) REVERT: A 707 HIS cc_start: 0.7929 (m-70) cc_final: 0.7416 (m-70) REVERT: A 717 ILE cc_start: 0.7237 (mt) cc_final: 0.6830 (mm) REVERT: B 122 THR cc_start: 0.7913 (p) cc_final: 0.6622 (p) REVERT: B 124 TYR cc_start: 0.8193 (m-80) cc_final: 0.7570 (m-10) REVERT: B 152 TRP cc_start: 0.8927 (m100) cc_final: 0.8107 (m100) REVERT: B 157 ASN cc_start: 0.9540 (m-40) cc_final: 0.9142 (p0) REVERT: B 218 TRP cc_start: 0.8975 (m-90) cc_final: 0.8672 (m-90) REVERT: B 225 LEU cc_start: 0.9374 (tt) cc_final: 0.8838 (pt) REVERT: B 228 ILE cc_start: 0.9199 (mt) cc_final: 0.8972 (mm) REVERT: B 263 TRP cc_start: 0.7593 (m100) cc_final: 0.7080 (m100) REVERT: B 291 SER cc_start: 0.9194 (t) cc_final: 0.8946 (p) REVERT: B 294 ILE cc_start: 0.8867 (mm) cc_final: 0.8384 (mm) REVERT: B 317 ASP cc_start: 0.8502 (t0) cc_final: 0.8299 (t0) REVERT: B 320 LEU cc_start: 0.9682 (mt) cc_final: 0.9456 (mt) REVERT: B 331 TRP cc_start: 0.8866 (p-90) cc_final: 0.7620 (p-90) REVERT: B 370 MET cc_start: 0.8131 (mtm) cc_final: 0.7859 (ptt) REVERT: C 111 LEU cc_start: 0.9292 (mt) cc_final: 0.8966 (mp) REVERT: C 574 LEU cc_start: 0.8255 (tp) cc_final: 0.7082 (tp) REVERT: C 595 LYS cc_start: 0.9172 (mmmm) cc_final: 0.8851 (mmmm) REVERT: C 615 LYS cc_start: 0.9182 (pttt) cc_final: 0.8661 (pttp) REVERT: C 618 ASN cc_start: 0.8311 (m110) cc_final: 0.8037 (m110) REVERT: C 622 MET cc_start: 0.9201 (mmp) cc_final: 0.8999 (mmm) REVERT: C 638 LEU cc_start: 0.9166 (mt) cc_final: 0.8504 (mt) REVERT: C 642 ASN cc_start: 0.8582 (t0) cc_final: 0.8099 (t0) REVERT: C 659 HIS cc_start: 0.9005 (t70) cc_final: 0.8704 (t70) REVERT: C 660 LEU cc_start: 0.9456 (mt) cc_final: 0.9142 (mt) REVERT: C 684 MET cc_start: 0.8317 (mpp) cc_final: 0.7914 (mpp) REVERT: D 28 THR cc_start: 0.9087 (t) cc_final: 0.8834 (t) REVERT: D 253 MET cc_start: 0.4390 (mpp) cc_final: 0.4135 (mpp) REVERT: D 261 ASN cc_start: 0.8453 (t0) cc_final: 0.7481 (p0) REVERT: D 275 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7915 (mp0) REVERT: D 313 PHE cc_start: 0.8470 (m-80) cc_final: 0.7985 (m-10) REVERT: D 367 LEU cc_start: 0.9180 (tp) cc_final: 0.8726 (tt) REVERT: D 373 HIS cc_start: 0.7854 (m170) cc_final: 0.7400 (m170) REVERT: D 377 ILE cc_start: 0.7702 (mt) cc_final: 0.7383 (tp) REVERT: D 403 GLN cc_start: 0.8515 (tt0) cc_final: 0.8090 (tm-30) REVERT: D 404 MET cc_start: 0.8928 (ttm) cc_final: 0.7726 (ttm) outliers start: 4 outliers final: 2 residues processed: 260 average time/residue: 0.0948 time to fit residues: 36.5591 Evaluate side-chains 191 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 189 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 90 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 37 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 276 ASN A 636 ASN ** A 690 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN C 88 GLN C 527 HIS D 78 HIS ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.084039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.062405 restraints weight = 61718.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.064357 restraints weight = 39819.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.065728 restraints weight = 28784.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.066786 restraints weight = 22457.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.067572 restraints weight = 18523.305| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5009 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= 0.160 Angle : 0.610 6.976 16652 Z= 0.321 Chirality : 0.045 0.217 1833 Planarity : 0.004 0.052 2152 Dihedral : 4.475 19.406 1639 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.20), residues: 1508 helix: 0.42 (0.30), residues: 283 sheet: -1.61 (0.25), residues: 372 loop : -1.91 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 367 TYR 0.017 0.002 TYR A 659 PHE 0.020 0.002 PHE A 687 TRP 0.020 0.002 TRP B 218 HIS 0.007 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00342 (12282) covalent geometry : angle 0.61022 (16652) hydrogen bonds : bond 0.03885 ( 389) hydrogen bonds : angle 5.20525 ( 1104) metal coordination : bond 0.00409 ( 12) *********************** 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 212 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8798 (tp30) REVERT: A 62 LYS cc_start: 0.9350 (ptpp) cc_final: 0.9069 (pttp) REVERT: A 97 MET cc_start: 0.8347 (tpt) cc_final: 0.7925 (tpt) REVERT: A 99 MET cc_start: 0.6921 (mtp) cc_final: 0.6099 (tpp) REVERT: A 553 ASP cc_start: 0.8594 (t0) cc_final: 0.8338 (t0) REVERT: A 611 LEU cc_start: 0.9355 (mm) cc_final: 0.9093 (mm) REVERT: A 612 LYS cc_start: 0.8221 (pptt) cc_final: 0.7949 (pptt) REVERT: A 651 GLU cc_start: 0.9491 (mm-30) cc_final: 0.9205 (tp30) REVERT: A 702 MET cc_start: 0.8031 (ptt) cc_final: 0.7803 (ptt) REVERT: A 707 HIS cc_start: 0.8192 (m-70) cc_final: 0.7702 (m-70) REVERT: B 124 TYR cc_start: 0.8523 (m-80) cc_final: 0.8161 (m-80) REVERT: B 157 ASN cc_start: 0.9549 (m-40) cc_final: 0.9210 (p0) REVERT: B 218 TRP cc_start: 0.9258 (m-90) cc_final: 0.8073 (m-90) REVERT: B 228 ILE cc_start: 0.9334 (mt) cc_final: 0.9049 (mm) REVERT: B 291 SER cc_start: 0.9307 (t) cc_final: 0.8939 (p) REVERT: B 310 ASP cc_start: 0.7156 (m-30) cc_final: 0.6863 (m-30) REVERT: B 315 LEU cc_start: 0.9470 (tp) cc_final: 0.9194 (tp) REVERT: B 331 TRP cc_start: 0.9046 (p-90) cc_final: 0.7601 (p-90) REVERT: B 366 MET cc_start: 0.7006 (mmp) cc_final: 0.6643 (mmm) REVERT: B 376 MET cc_start: 0.9120 (pmm) cc_final: 0.8660 (ppp) REVERT: C 569 ASP cc_start: 0.9113 (p0) cc_final: 0.8863 (p0) REVERT: C 570 THR cc_start: 0.8720 (p) cc_final: 0.8324 (p) REVERT: C 590 GLU cc_start: 0.8376 (tp30) cc_final: 0.7533 (mm-30) REVERT: C 594 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8492 (mm-30) REVERT: C 595 LYS cc_start: 0.9175 (mmmm) cc_final: 0.8850 (mmmm) REVERT: C 612 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8316 (mm-30) REVERT: C 629 ASP cc_start: 0.9163 (m-30) cc_final: 0.8829 (m-30) REVERT: C 638 LEU cc_start: 0.9383 (mt) cc_final: 0.8692 (mt) REVERT: D 34 LEU cc_start: 0.9281 (mt) cc_final: 0.8771 (pp) REVERT: D 250 GLN cc_start: 0.8038 (mp10) cc_final: 0.7808 (mp10) REVERT: D 252 LEU cc_start: 0.9337 (mp) cc_final: 0.9132 (mp) REVERT: D 253 MET cc_start: 0.5321 (mpp) cc_final: 0.5107 (mpp) REVERT: D 275 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8158 (mp0) REVERT: D 343 ASN cc_start: 0.9273 (m110) cc_final: 0.9021 (m-40) REVERT: D 367 LEU cc_start: 0.9224 (tp) cc_final: 0.8825 (tt) REVERT: D 373 HIS cc_start: 0.7578 (m170) cc_final: 0.7259 (m170) REVERT: D 377 ILE cc_start: 0.7529 (mt) cc_final: 0.7203 (tp) REVERT: D 399 MET cc_start: 0.9427 (tmm) cc_final: 0.9032 (tmm) REVERT: D 403 GLN cc_start: 0.8693 (tt0) cc_final: 0.8398 (tm-30) REVERT: D 404 MET cc_start: 0.8916 (ttm) cc_final: 0.7889 (ttm) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.0900 time to fit residues: 29.2989 Evaluate side-chains 163 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 113 optimal weight: 0.2980 chunk 72 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 3 optimal weight: 0.0870 chunk 126 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 92 optimal weight: 30.0000 chunk 121 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 98 optimal weight: 0.0470 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS A 690 HIS ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN C 88 GLN C 618 ASN ** D 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.086001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.064628 restraints weight = 64317.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.066521 restraints weight = 41325.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.067879 restraints weight = 29612.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.068856 restraints weight = 23044.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.069587 restraints weight = 19026.968| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12294 Z= 0.093 Angle : 0.521 6.674 16652 Z= 0.270 Chirality : 0.043 0.194 1833 Planarity : 0.003 0.035 2152 Dihedral : 4.044 19.478 1639 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.08 % Allowed : 2.23 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.21), residues: 1508 helix: 0.89 (0.32), residues: 273 sheet: -1.30 (0.25), residues: 367 loop : -1.61 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 121 TYR 0.013 0.001 TYR A 659 PHE 0.012 0.001 PHE C 86 TRP 0.017 0.001 TRP B 218 HIS 0.004 0.001 HIS D 272 Details of bonding type rmsd covalent geometry : bond 0.00204 (12282) covalent geometry : angle 0.52059 (16652) hydrogen bonds : bond 0.03310 ( 389) hydrogen bonds : angle 4.83679 ( 1104) metal coordination : bond 0.00154 ( 12) *********************** 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 : 0.528 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: 0.9036 (mm-30) cc_final: 0.8670 (tp30) REVERT: A 62 LYS cc_start: 0.9366 (ptpp) cc_final: 0.9073 (pttp) REVERT: A 99 MET cc_start: 0.6885 (mtp) cc_final: 0.5773 (tpp) REVERT: A 298 PHE cc_start: 0.9486 (t80) cc_final: 0.9193 (t80) REVERT: A 553 ASP cc_start: 0.8561 (t0) cc_final: 0.8303 (t0) REVERT: A 611 LEU cc_start: 0.9437 (mm) cc_final: 0.9207 (mm) REVERT: A 651 GLU cc_start: 0.9546 (mm-30) cc_final: 0.9049 (tp30) REVERT: A 707 HIS cc_start: 0.8139 (m-70) cc_final: 0.7621 (m-70) REVERT: B 148 TYR cc_start: 0.7983 (m-80) cc_final: 0.7766 (m-80) REVERT: B 152 TRP cc_start: 0.9158 (m100) cc_final: 0.8629 (m100) REVERT: B 157 ASN cc_start: 0.9509 (m-40) cc_final: 0.9153 (p0) REVERT: B 180 MET cc_start: 0.8489 (mpp) cc_final: 0.8152 (mpp) REVERT: B 195 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8262 (tm-30) REVERT: B 218 TRP cc_start: 0.9208 (m-90) cc_final: 0.8481 (m-90) REVERT: B 260 LEU cc_start: 0.9108 (mm) cc_final: 0.8814 (mt) REVERT: B 271 MET cc_start: 0.9328 (mmp) cc_final: 0.9120 (mmt) REVERT: B 291 SER cc_start: 0.9237 (t) cc_final: 0.9008 (p) REVERT: B 331 TRP cc_start: 0.8873 (p-90) cc_final: 0.7434 (p-90) REVERT: B 377 LEU cc_start: 0.9081 (tp) cc_final: 0.8538 (mm) REVERT: B 391 LEU cc_start: 0.8735 (mt) cc_final: 0.8369 (tt) REVERT: C 111 LEU cc_start: 0.9091 (mt) cc_final: 0.8883 (mt) REVERT: C 117 TYR cc_start: 0.7133 (p90) cc_final: 0.6388 (p90) REVERT: C 469 LEU cc_start: 0.9177 (mt) cc_final: 0.8942 (mt) REVERT: C 569 ASP cc_start: 0.9146 (p0) cc_final: 0.8776 (p0) REVERT: C 570 THR cc_start: 0.8464 (p) cc_final: 0.8084 (p) REVERT: C 595 LYS cc_start: 0.9192 (mmmm) cc_final: 0.8872 (mmmm) REVERT: C 612 GLU cc_start: 0.8544 (mm-30) cc_final: 0.7610 (mm-30) REVERT: C 615 LYS cc_start: 0.9158 (pttt) cc_final: 0.8623 (pttt) REVERT: C 618 ASN cc_start: 0.8894 (m-40) cc_final: 0.8645 (m-40) REVERT: D 34 LEU cc_start: 0.9320 (mt) cc_final: 0.8788 (pp) REVERT: D 252 LEU cc_start: 0.9422 (mp) cc_final: 0.9203 (mp) REVERT: D 275 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8102 (mp0) REVERT: D 367 LEU cc_start: 0.9162 (tp) cc_final: 0.8761 (tt) REVERT: D 373 HIS cc_start: 0.7720 (m170) cc_final: 0.7346 (m170) REVERT: D 377 ILE cc_start: 0.7508 (mt) cc_final: 0.7111 (tp) REVERT: D 399 MET cc_start: 0.9444 (tmm) cc_final: 0.9056 (tmm) REVERT: D 403 GLN cc_start: 0.8530 (tt0) cc_final: 0.8133 (tm-30) REVERT: D 404 MET cc_start: 0.8809 (ttm) cc_final: 0.7913 (ttm) outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.0855 time to fit residues: 28.9000 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 : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 108 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 86 optimal weight: 0.4980 chunk 23 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 0.0470 overall best weight: 1.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 120 ASN A 470 GLN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN B 397 HIS C 80 GLN C 88 GLN ** C 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS D 305 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.081301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.060161 restraints weight = 65231.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.061997 restraints weight = 42211.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.063318 restraints weight = 30613.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.064282 restraints weight = 23978.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.064916 restraints weight = 19889.832| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.6253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12294 Z= 0.158 Angle : 0.593 7.026 16652 Z= 0.313 Chirality : 0.044 0.159 1833 Planarity : 0.004 0.059 2152 Dihedral : 4.415 22.901 1639 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.08 % Allowed : 2.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.21), residues: 1508 helix: 0.84 (0.32), residues: 280 sheet: -0.89 (0.26), residues: 362 loop : -1.54 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 113 TYR 0.023 0.002 TYR B 124 PHE 0.015 0.002 PHE A 687 TRP 0.013 0.002 TRP B 437 HIS 0.008 0.001 HIS C 659 Details of bonding type rmsd covalent geometry : bond 0.00334 (12282) covalent geometry : angle 0.59349 (16652) hydrogen bonds : bond 0.03686 ( 389) hydrogen bonds : angle 5.07597 ( 1104) metal coordination : bond 0.00393 ( 12) *********************** 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 182 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8775 (tp30) REVERT: A 553 ASP cc_start: 0.8648 (t0) cc_final: 0.8409 (t0) REVERT: A 651 GLU cc_start: 0.9559 (mm-30) cc_final: 0.9096 (tp30) REVERT: A 707 HIS cc_start: 0.8394 (m-70) cc_final: 0.7932 (m-70) REVERT: B 100 GLN cc_start: 0.8310 (mm110) cc_final: 0.8072 (mt0) REVERT: B 115 THR cc_start: 0.9180 (p) cc_final: 0.8913 (t) REVERT: B 132 ILE cc_start: 0.9158 (mm) cc_final: 0.8956 (mp) REVERT: B 157 ASN cc_start: 0.9600 (m-40) cc_final: 0.9283 (p0) REVERT: B 180 MET cc_start: 0.8581 (mpp) cc_final: 0.8186 (mpp) REVERT: B 207 LEU cc_start: 0.9508 (tt) cc_final: 0.9281 (tt) REVERT: B 218 TRP cc_start: 0.9147 (m-90) cc_final: 0.8522 (m-90) REVERT: B 271 MET cc_start: 0.9280 (mmp) cc_final: 0.9074 (mmm) REVERT: B 291 SER cc_start: 0.9099 (t) cc_final: 0.8594 (p) REVERT: B 310 ASP cc_start: 0.7210 (m-30) cc_final: 0.6896 (m-30) REVERT: B 331 TRP cc_start: 0.9024 (p-90) cc_final: 0.7532 (p-90) REVERT: C 117 TYR cc_start: 0.7242 (p90) cc_final: 0.6764 (p90) REVERT: C 469 LEU cc_start: 0.9232 (mt) cc_final: 0.8994 (mt) REVERT: C 569 ASP cc_start: 0.9176 (p0) cc_final: 0.8790 (p0) REVERT: C 585 ASP cc_start: 0.6714 (t70) cc_final: 0.6425 (t0) REVERT: C 594 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8461 (mm-30) REVERT: C 595 LYS cc_start: 0.9192 (mmmm) cc_final: 0.8855 (mmmm) REVERT: C 622 MET cc_start: 0.9464 (mmp) cc_final: 0.9261 (mmm) REVERT: C 629 ASP cc_start: 0.9317 (m-30) cc_final: 0.9048 (m-30) REVERT: D 20 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8618 (mt-10) REVERT: D 34 LEU cc_start: 0.9409 (mt) cc_final: 0.8880 (pp) REVERT: D 275 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8184 (mp0) REVERT: D 367 LEU cc_start: 0.9232 (tp) cc_final: 0.8931 (tt) REVERT: D 399 MET cc_start: 0.9395 (tmm) cc_final: 0.8867 (tmm) REVERT: D 403 GLN cc_start: 0.8672 (tt0) cc_final: 0.8191 (mm-40) REVERT: D 404 MET cc_start: 0.9168 (ttm) cc_final: 0.8117 (ttm) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.0828 time to fit residues: 24.2390 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 : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 8 optimal weight: 2.9990 chunk 86 optimal weight: 0.0050 chunk 91 optimal weight: 8.9990 chunk 19 optimal weight: 0.0020 chunk 28 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 58 optimal weight: 0.2980 chunk 147 optimal weight: 1.9990 overall best weight: 1.0606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.081829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.060861 restraints weight = 64742.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.062698 restraints weight = 41715.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.064007 restraints weight = 30276.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.064972 restraints weight = 23775.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.065604 restraints weight = 19658.580| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.6573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12294 Z= 0.118 Angle : 0.541 6.958 16652 Z= 0.284 Chirality : 0.043 0.158 1833 Planarity : 0.003 0.036 2152 Dihedral : 4.313 22.069 1639 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.21), residues: 1508 helix: 0.80 (0.31), residues: 285 sheet: -0.89 (0.25), residues: 387 loop : -1.40 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 216 TYR 0.019 0.001 TYR A 659 PHE 0.013 0.001 PHE C 90 TRP 0.011 0.001 TRP D 388 HIS 0.019 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00257 (12282) covalent geometry : angle 0.54140 (16652) hydrogen bonds : bond 0.03517 ( 389) hydrogen bonds : angle 4.96019 ( 1104) metal coordination : bond 0.00253 ( 12) *********************** 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 180 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8748 (tp30) REVERT: A 117 LEU cc_start: 0.9558 (mt) cc_final: 0.9348 (mm) REVERT: A 470 GLN cc_start: 0.9372 (mm110) cc_final: 0.9140 (mm110) REVERT: A 553 ASP cc_start: 0.8591 (t0) cc_final: 0.8326 (t0) REVERT: A 651 GLU cc_start: 0.9529 (mm-30) cc_final: 0.9107 (tp30) REVERT: A 707 HIS cc_start: 0.8385 (m-70) cc_final: 0.7992 (m-70) REVERT: B 115 THR cc_start: 0.9216 (p) cc_final: 0.8822 (t) REVERT: B 132 ILE cc_start: 0.9041 (mm) cc_final: 0.8715 (mp) REVERT: B 157 ASN cc_start: 0.9660 (m-40) cc_final: 0.9293 (p0) REVERT: B 180 MET cc_start: 0.8439 (mpp) cc_final: 0.8176 (mpp) REVERT: B 218 TRP cc_start: 0.9240 (m-90) cc_final: 0.8632 (m-90) REVERT: B 225 LEU cc_start: 0.9131 (tp) cc_final: 0.8589 (pp) REVERT: B 256 MET cc_start: 0.8947 (mmm) cc_final: 0.8735 (mmt) REVERT: B 310 ASP cc_start: 0.7227 (m-30) cc_final: 0.6894 (m-30) REVERT: B 318 LEU cc_start: 0.9526 (tt) cc_final: 0.9323 (mt) REVERT: B 331 TRP cc_start: 0.9015 (p-90) cc_final: 0.7406 (p-90) REVERT: B 366 MET cc_start: 0.6591 (mmp) cc_final: 0.6273 (mmm) REVERT: C 111 LEU cc_start: 0.9325 (mm) cc_final: 0.8532 (mm) REVERT: C 569 ASP cc_start: 0.9202 (p0) cc_final: 0.8646 (p0) REVERT: C 574 LEU cc_start: 0.8133 (mt) cc_final: 0.7830 (mt) REVERT: C 585 ASP cc_start: 0.6541 (t70) cc_final: 0.6240 (t0) REVERT: C 595 LYS cc_start: 0.9180 (mmmm) cc_final: 0.8925 (mmmm) REVERT: C 618 ASN cc_start: 0.9349 (m-40) cc_final: 0.9057 (m110) REVERT: C 622 MET cc_start: 0.9478 (mmp) cc_final: 0.9159 (mmp) REVERT: C 629 ASP cc_start: 0.9288 (m-30) cc_final: 0.9071 (m-30) REVERT: D 20 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8671 (mt-10) REVERT: D 34 LEU cc_start: 0.9447 (mt) cc_final: 0.8915 (pp) REVERT: D 275 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8008 (mp0) REVERT: D 367 LEU cc_start: 0.9331 (tp) cc_final: 0.8916 (tt) REVERT: D 399 MET cc_start: 0.9422 (tmm) cc_final: 0.8799 (tmm) REVERT: D 403 GLN cc_start: 0.8656 (tt0) cc_final: 0.8256 (mm-40) REVERT: D 404 MET cc_start: 0.9121 (ttm) cc_final: 0.8047 (ttm) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.0884 time to fit residues: 24.7777 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 : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 66 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 D 272 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.081185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.060652 restraints weight = 62150.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.062371 restraints weight = 41151.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.063622 restraints weight = 30305.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.064538 restraints weight = 23948.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.065206 restraints weight = 19983.834| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.6801 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= 0.110 Angle : 0.543 7.007 16652 Z= 0.284 Chirality : 0.043 0.150 1833 Planarity : 0.003 0.038 2152 Dihedral : 4.271 27.023 1639 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.21), residues: 1508 helix: 0.87 (0.32), residues: 282 sheet: -0.65 (0.26), residues: 368 loop : -1.22 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 287 TYR 0.018 0.001 TYR A 659 PHE 0.012 0.001 PHE C 90 TRP 0.011 0.001 TRP D 325 HIS 0.018 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00238 (12282) covalent geometry : angle 0.54271 (16652) hydrogen bonds : bond 0.03405 ( 389) hydrogen bonds : angle 4.93570 ( 1104) metal coordination : bond 0.00173 ( 12) *********************** 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 182 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8767 (tp30) REVERT: A 117 LEU cc_start: 0.9577 (mt) cc_final: 0.9377 (mm) REVERT: A 470 GLN cc_start: 0.9412 (mm110) cc_final: 0.9143 (mm110) REVERT: A 553 ASP cc_start: 0.8661 (t0) cc_final: 0.8349 (t0) REVERT: A 651 GLU cc_start: 0.9555 (mm-30) cc_final: 0.9127 (tp30) REVERT: A 707 HIS cc_start: 0.8363 (m-70) cc_final: 0.7908 (m-70) REVERT: B 115 THR cc_start: 0.9230 (p) cc_final: 0.8541 (t) REVERT: B 132 ILE cc_start: 0.9060 (mm) cc_final: 0.8750 (mp) REVERT: B 157 ASN cc_start: 0.9653 (m-40) cc_final: 0.9247 (p0) REVERT: B 180 MET cc_start: 0.8497 (mpp) cc_final: 0.8260 (mpp) REVERT: B 218 TRP cc_start: 0.9218 (m-90) cc_final: 0.8534 (m-90) REVERT: B 256 MET cc_start: 0.8919 (mmm) cc_final: 0.8648 (mmt) REVERT: B 271 MET cc_start: 0.9144 (mmp) cc_final: 0.8912 (mmm) REVERT: B 292 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8129 (mm110) REVERT: B 310 ASP cc_start: 0.7183 (m-30) cc_final: 0.6896 (m-30) REVERT: C 104 ASN cc_start: 0.9033 (p0) cc_final: 0.8548 (t0) REVERT: C 117 TYR cc_start: 0.7131 (p90) cc_final: 0.6825 (p90) REVERT: C 137 MET cc_start: 0.7783 (mtp) cc_final: 0.7238 (mmm) REVERT: C 469 LEU cc_start: 0.9432 (mt) cc_final: 0.9163 (mt) REVERT: C 569 ASP cc_start: 0.9019 (p0) cc_final: 0.8571 (p0) REVERT: C 570 THR cc_start: 0.8739 (p) cc_final: 0.8493 (p) REVERT: C 574 LEU cc_start: 0.8152 (mt) cc_final: 0.7841 (mt) REVERT: C 582 ASP cc_start: 0.7858 (m-30) cc_final: 0.7616 (m-30) REVERT: C 595 LYS cc_start: 0.9251 (mmmm) cc_final: 0.8937 (mmmm) REVERT: C 612 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8276 (tp30) REVERT: C 615 LYS cc_start: 0.9058 (pttt) cc_final: 0.8809 (ptmt) REVERT: C 618 ASN cc_start: 0.9406 (m-40) cc_final: 0.9113 (m110) REVERT: C 622 MET cc_start: 0.9485 (mmp) cc_final: 0.9187 (mmp) REVERT: C 629 ASP cc_start: 0.9273 (m-30) cc_final: 0.8945 (m-30) REVERT: D 20 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8616 (mt-10) REVERT: D 34 LEU cc_start: 0.9449 (mt) cc_final: 0.8894 (pp) REVERT: D 275 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7874 (mp0) REVERT: D 367 LEU cc_start: 0.9305 (tp) cc_final: 0.8931 (tt) REVERT: D 399 MET cc_start: 0.9420 (tmm) cc_final: 0.8772 (tmm) REVERT: D 403 GLN cc_start: 0.8671 (tt0) cc_final: 0.8228 (mm-40) REVERT: D 404 MET cc_start: 0.9180 (ttm) cc_final: 0.8106 (ttm) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.0867 time to fit residues: 24.7184 Evaluate side-chains 144 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 8 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.077041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.057158 restraints weight = 61316.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.058783 restraints weight = 40829.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.059922 restraints weight = 30145.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.060793 restraints weight = 23885.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.061350 restraints weight = 19988.877| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.7751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12294 Z= 0.208 Angle : 0.664 7.408 16652 Z= 0.350 Chirality : 0.045 0.251 1833 Planarity : 0.004 0.061 2152 Dihedral : 4.950 26.204 1639 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.21), residues: 1508 helix: 0.49 (0.31), residues: 283 sheet: -0.86 (0.26), residues: 376 loop : -1.29 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 287 TYR 0.034 0.002 TYR A 659 PHE 0.019 0.002 PHE A 294 TRP 0.053 0.002 TRP D 325 HIS 0.014 0.002 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00438 (12282) covalent geometry : angle 0.66414 (16652) hydrogen bonds : bond 0.04007 ( 389) hydrogen bonds : angle 5.44503 ( 1104) metal coordination : bond 0.00501 ( 12) *********************** 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 171 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8735 (tmm) cc_final: 0.8106 (tmm) REVERT: A 117 LEU cc_start: 0.9642 (mt) cc_final: 0.9370 (mm) REVERT: A 470 GLN cc_start: 0.9408 (mm110) cc_final: 0.8999 (mm110) REVERT: A 553 ASP cc_start: 0.8547 (t0) cc_final: 0.8279 (t0) REVERT: A 645 GLU cc_start: 0.7928 (tp30) cc_final: 0.7498 (tp30) REVERT: A 651 GLU cc_start: 0.9488 (mm-30) cc_final: 0.9243 (tp30) REVERT: A 707 HIS cc_start: 0.8512 (m-70) cc_final: 0.7959 (m170) REVERT: B 148 TYR cc_start: 0.8905 (m-80) cc_final: 0.8279 (m-80) REVERT: B 157 ASN cc_start: 0.9659 (m-40) cc_final: 0.9196 (p0) REVERT: C 84 GLU cc_start: 0.8687 (tp30) cc_final: 0.8388 (mm-30) REVERT: C 104 ASN cc_start: 0.9129 (p0) cc_final: 0.8635 (t0) REVERT: C 117 TYR cc_start: 0.7150 (p90) cc_final: 0.6770 (p90) REVERT: C 469 LEU cc_start: 0.9453 (mt) cc_final: 0.9221 (mt) REVERT: C 569 ASP cc_start: 0.8968 (p0) cc_final: 0.8565 (p0) REVERT: C 622 MET cc_start: 0.9503 (mmp) cc_final: 0.9199 (mmp) REVERT: C 629 ASP cc_start: 0.9340 (m-30) cc_final: 0.9039 (p0) REVERT: C 632 MET cc_start: 0.9331 (ptt) cc_final: 0.9095 (ppp) REVERT: C 638 LEU cc_start: 0.9576 (mt) cc_final: 0.9219 (mt) REVERT: D 20 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8525 (mt-10) REVERT: D 34 LEU cc_start: 0.9460 (mt) cc_final: 0.8951 (pp) REVERT: D 258 ARG cc_start: 0.8421 (mtt90) cc_final: 0.8165 (mmp80) REVERT: D 367 LEU cc_start: 0.9379 (tp) cc_final: 0.9047 (tt) REVERT: D 399 MET cc_start: 0.9378 (tmm) cc_final: 0.8775 (tmm) REVERT: D 403 GLN cc_start: 0.8676 (tt0) cc_final: 0.8233 (mm-40) REVERT: D 404 MET cc_start: 0.9341 (ttm) cc_final: 0.8644 (tmm) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.0852 time to fit residues: 22.8978 Evaluate side-chains 128 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 45 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 132 optimal weight: 50.0000 chunk 119 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 292 GLN ** D 400 GLN ** 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 = 0.3603 r_free = 0.3603 target = 0.078660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.058234 restraints weight = 64091.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.059934 restraints weight = 41768.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.061165 restraints weight = 30495.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.062080 restraints weight = 24058.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.062664 restraints weight = 20008.357| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.7958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12294 Z= 0.146 Angle : 0.604 8.138 16652 Z= 0.318 Chirality : 0.044 0.182 1833 Planarity : 0.004 0.043 2152 Dihedral : 4.771 24.352 1639 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.21), residues: 1508 helix: 0.42 (0.31), residues: 285 sheet: -0.80 (0.26), residues: 371 loop : -1.22 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 216 TYR 0.026 0.002 TYR A 659 PHE 0.016 0.001 PHE B 296 TRP 0.039 0.002 TRP D 325 HIS 0.010 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00316 (12282) covalent geometry : angle 0.60417 (16652) hydrogen bonds : bond 0.03765 ( 389) hydrogen bonds : angle 5.26950 ( 1104) metal coordination : bond 0.00236 ( 12) *********************** 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 185 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.469 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 71 MET cc_start: 0.6627 (pmm) cc_final: 0.5765 (pmm) REVERT: A 117 LEU cc_start: 0.9637 (mt) cc_final: 0.9392 (mm) REVERT: A 459 LEU cc_start: 0.9103 (mt) cc_final: 0.8855 (mt) REVERT: A 553 ASP cc_start: 0.8526 (t0) cc_final: 0.8299 (t0) REVERT: A 645 GLU cc_start: 0.7973 (tp30) cc_final: 0.7585 (tp30) REVERT: A 707 HIS cc_start: 0.8617 (m-70) cc_final: 0.8157 (m-70) REVERT: A 717 ILE cc_start: 0.7074 (mm) cc_final: 0.6649 (mt) REVERT: B 148 TYR cc_start: 0.8893 (m-80) cc_final: 0.8189 (m-80) REVERT: B 157 ASN cc_start: 0.9601 (m-40) cc_final: 0.9151 (p0) REVERT: B 193 ILE cc_start: 0.9264 (mp) cc_final: 0.8936 (mp) REVERT: C 104 ASN cc_start: 0.9144 (p0) cc_final: 0.8476 (t0) REVERT: C 117 TYR cc_start: 0.7295 (p90) cc_final: 0.6685 (p90) REVERT: C 574 LEU cc_start: 0.7874 (mt) cc_final: 0.7494 (mt) REVERT: C 612 GLU cc_start: 0.8726 (mm-30) cc_final: 0.7984 (tp30) REVERT: C 615 LYS cc_start: 0.9046 (pttt) cc_final: 0.8745 (ptpp) REVERT: C 622 MET cc_start: 0.9454 (mmp) cc_final: 0.9145 (mmp) REVERT: C 629 ASP cc_start: 0.9153 (m-30) cc_final: 0.8845 (p0) REVERT: C 638 LEU cc_start: 0.9569 (mt) cc_final: 0.8971 (mt) REVERT: C 684 MET cc_start: 0.8555 (mpp) cc_final: 0.8023 (mpp) REVERT: D 20 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8610 (mt-10) REVERT: D 34 LEU cc_start: 0.9430 (mt) cc_final: 0.8895 (pp) REVERT: D 367 LEU cc_start: 0.9346 (tp) cc_final: 0.9033 (tt) REVERT: D 395 GLU cc_start: 0.9239 (pm20) cc_final: 0.9013 (pm20) REVERT: D 399 MET cc_start: 0.9236 (tmm) cc_final: 0.8822 (tmm) REVERT: D 403 GLN cc_start: 0.8590 (tt0) cc_final: 0.8156 (mm-40) REVERT: D 404 MET cc_start: 0.9266 (ttm) cc_final: 0.8586 (tmm) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.0878 time to fit residues: 24.9678 Evaluate side-chains 135 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 16 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 18 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 292 GLN B 307 ASN B 374 GLN D 239 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 = 0.3621 r_free = 0.3621 target = 0.079608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.059207 restraints weight = 63281.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.061019 restraints weight = 40195.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.062312 restraints weight = 28825.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.063160 restraints weight = 22431.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.063926 restraints weight = 18599.482| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.8091 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= 0.110 Angle : 0.584 7.869 16652 Z= 0.303 Chirality : 0.044 0.219 1833 Planarity : 0.003 0.041 2152 Dihedral : 4.568 23.258 1639 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.21), residues: 1508 helix: 0.41 (0.31), residues: 287 sheet: -0.63 (0.26), residues: 364 loop : -1.12 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 258 TYR 0.031 0.002 TYR B 154 PHE 0.021 0.001 PHE B 296 TRP 0.038 0.002 TRP D 325 HIS 0.009 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00245 (12282) covalent geometry : angle 0.58387 (16652) hydrogen bonds : bond 0.03580 ( 389) hydrogen bonds : angle 5.03016 ( 1104) metal coordination : bond 0.00125 ( 12) ********************** 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 179 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.529 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 71 MET cc_start: 0.6863 (pmm) cc_final: 0.5842 (pmm) REVERT: A 117 LEU cc_start: 0.9594 (mt) cc_final: 0.9346 (mm) REVERT: A 553 ASP cc_start: 0.8546 (t0) cc_final: 0.8306 (t0) REVERT: A 645 GLU cc_start: 0.8058 (tp30) cc_final: 0.7767 (tp30) REVERT: A 707 HIS cc_start: 0.8574 (m-70) cc_final: 0.8165 (m-70) REVERT: A 717 ILE cc_start: 0.6817 (mm) cc_final: 0.6445 (mt) REVERT: B 148 TYR cc_start: 0.8743 (m-80) cc_final: 0.8032 (m-80) REVERT: B 157 ASN cc_start: 0.9630 (m-40) cc_final: 0.9151 (p0) REVERT: B 193 ILE cc_start: 0.9177 (mp) cc_final: 0.8776 (mp) REVERT: B 256 MET cc_start: 0.8686 (mmm) cc_final: 0.8220 (mmt) REVERT: B 292 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8049 (mm110) REVERT: C 104 ASN cc_start: 0.9094 (p0) cc_final: 0.8502 (t0) REVERT: C 574 LEU cc_start: 0.7865 (mt) cc_final: 0.7484 (mt) REVERT: C 612 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8375 (tp30) REVERT: C 622 MET cc_start: 0.9503 (mmp) cc_final: 0.9223 (mmp) REVERT: C 629 ASP cc_start: 0.9134 (m-30) cc_final: 0.8929 (m-30) REVERT: C 632 MET cc_start: 0.9463 (ppp) cc_final: 0.9103 (ppp) REVERT: C 638 LEU cc_start: 0.9491 (mt) cc_final: 0.9023 (mt) REVERT: C 684 MET cc_start: 0.8596 (mpp) cc_final: 0.8036 (mpp) REVERT: D 20 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8627 (mt-10) REVERT: D 34 LEU cc_start: 0.9444 (mt) cc_final: 0.8909 (pp) REVERT: D 367 LEU cc_start: 0.9360 (tp) cc_final: 0.9028 (tt) REVERT: D 395 GLU cc_start: 0.9175 (pm20) cc_final: 0.8938 (pm20) REVERT: D 399 MET cc_start: 0.9258 (tmm) cc_final: 0.8879 (tmm) REVERT: D 403 GLN cc_start: 0.8672 (tt0) cc_final: 0.8108 (tp40) REVERT: D 404 MET cc_start: 0.9247 (ttm) cc_final: 0.8891 (ttm) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0937 time to fit residues: 25.5275 Evaluate side-chains 134 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 46 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 139 optimal weight: 0.7980 chunk 99 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 16 optimal weight: 0.3980 chunk 103 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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** ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.080010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.060029 restraints weight = 59696.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.061686 restraints weight = 39173.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.062852 restraints weight = 28698.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.063746 restraints weight = 22706.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.064323 restraints weight = 18936.330| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.8163 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= 0.101 Angle : 0.577 7.635 16652 Z= 0.295 Chirality : 0.044 0.174 1833 Planarity : 0.003 0.039 2152 Dihedral : 4.368 22.005 1639 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.21), residues: 1508 helix: 0.50 (0.31), residues: 284 sheet: -0.48 (0.26), residues: 378 loop : -1.11 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 216 TYR 0.028 0.001 TYR B 154 PHE 0.020 0.001 PHE B 296 TRP 0.035 0.002 TRP D 325 HIS 0.008 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00225 (12282) covalent geometry : angle 0.57657 (16652) hydrogen bonds : bond 0.03361 ( 389) hydrogen bonds : angle 4.92671 ( 1104) metal coordination : bond 0.00091 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2207.30 seconds wall clock time: 38 minutes 59.63 seconds (2339.63 seconds total)