Starting phenix.real_space_refine on Wed Sep 17 22:44:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ksr_23024/09_2025/7ksr_23024.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ksr_23024/09_2025/7ksr_23024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ksr_23024/09_2025/7ksr_23024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ksr_23024/09_2025/7ksr_23024.map" model { file = "/net/cci-nas-00/data/ceres_data/7ksr_23024/09_2025/7ksr_23024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ksr_23024/09_2025/7ksr_23024.cif" } resolution = 4.1 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 87 5.16 5 C 7499 2.51 5 N 2106 2.21 5 O 2164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11863 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: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2909 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 3 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: "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: "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: "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 911 SG CYS A 299 60.232 45.699 88.425 1.00 77.53 S ATOM 939 SG CYS A 302 57.071 45.555 86.837 0.99 75.84 S ATOM 985 SG CYS A 307 59.522 45.519 84.292 0.87 75.70 S ATOM 1591 SG CYS A 531 70.136 60.350 100.152 1.00112.25 S ATOM 1734 SG CYS A 550 66.043 57.750 100.459 1.00102.41 S ATOM 1534 SG CYS A 524 70.650 56.219 95.707 1.00105.16 S ATOM 1719 SG CYS A 548 66.859 55.656 97.184 1.00 97.15 S ATOM 1973 SG CYS A 581 48.139 64.118 91.620 1.00100.74 S ATOM 2031 SG CYS A 589 45.612 62.751 95.386 1.00111.99 S ATOM 1819 SG CYS A 561 48.886 66.206 95.929 1.00 97.71 S ATOM 1973 SG CYS A 581 48.139 64.118 91.620 1.00100.74 S ATOM 1973 SG CYS A 581 48.139 64.118 91.620 1.00100.74 S ATOM 2031 SG CYS A 589 45.612 62.751 95.386 1.00111.99 S ATOM 2110 SG CYS A 602 44.703 63.403 90.988 1.00106.02 S Time building chain proxies: 3.01, per 1000 atoms: 0.25 Number of scatterers: 11863 At special positions: 0 Unit cell: (90.45, 170.1, 132.3, 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 87 16.00 O 2164 8.00 N 2106 7.00 C 7499 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: 0.97 Conformation dependent library (CDL) restraints added in 551.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 307 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 302 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 299 " pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb="ZN ZN A 803 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 531 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 550 " pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb="ZN ZN A 804 " pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 524 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 548 " pdb=" ZN A 805 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 589 " pdb="ZN ZN A 805 " - pdb="ZN ZN A 807 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 581 " pdb=" ZN A 806 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 581 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 561 " pdb=" ZN A 807 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 581 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 589 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 602 " 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 22 sheets defined 20.4% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 34 through 63 removed outlier: 3.759A pdb=" N LYS A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A 63 " --> pdb=" O GLU A 59 " (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 435 through 450 Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 464 through 474 Processing helix chain 'A' and resid 535 through 541 removed outlier: 3.852A pdb=" N MET A 539 " --> pdb=" O CYS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 3.850A 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 Processing helix chain 'D' and resid 12 through 28 Processing helix chain 'D' and resid 355 through 362 removed outlier: 4.058A pdb=" N ASP D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.184A pdb=" N TYR D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 107 Proline residue: C 93 - end of helix removed outlier: 3.537A pdb=" N ILE C 96 " --> pdb=" O LYS C 92 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 115 removed outlier: 3.506A pdb=" N LEU C 115 " --> pdb=" O HIS C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 145 Processing helix chain 'C' and resid 459 through 470 removed outlier: 3.533A pdb=" N LEU C 463 " --> pdb=" O LYS C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 602 removed outlier: 3.931A pdb=" N ARG C 593 " --> pdb=" O PRO C 589 " (cutoff:3.500A) removed outlier: 3.642A 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: 4.139A pdb=" N MET C 637 " --> pdb=" O ASN C 633 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU C 641 " --> pdb=" O MET C 637 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN C 645 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LYS C 646 " --> pdb=" O ASN C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 666 removed outlier: 3.707A pdb=" N PHE C 666 " --> pdb=" O SER C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 686 Processing helix chain 'B' and resid 267 through 279 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.642A pdb=" N LYS B 342 " --> pdb=" O ASP B 339 " (cutoff:3.500A) removed outlier: 3.936A 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 'B' and resid 395 through 399 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: 5.865A 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: 6.617A 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: 6.785A pdb=" N PHE A 638 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA A 713 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 377 through 382 removed outlier: 3.718A pdb=" N LEU D 34 " --> pdb=" O GLN D 403 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL D 35 " --> pdb=" O LEU C 529 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C 529 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 47 through 54 removed outlier: 5.463A pdb=" N ARG D 65 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASP D 52 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE D 63 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N THR D 54 " --> pdb=" O PHE D 61 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N PHE D 61 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ASN D 77 " --> pdb=" O ASN D 122 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASN D 122 " --> pdb=" O ASN D 77 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU D 79 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS D 120 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE D 81 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 130 through 132 Processing sheet with id=AA9, first strand: chain 'D' and resid 183 through 185 removed outlier: 3.603A pdb=" N SER D 197 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 230 through 235 removed outlier: 3.809A pdb=" N LYS D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 276 through 281 removed outlier: 3.886A pdb=" N THR D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N HIS D 311 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 320 through 322 removed outlier: 7.074A pdb=" N SER D 336 " --> pdb=" O PHE D 321 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP D 346 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU D 366 " --> pdb=" O ASP D 346 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 160 through 161 removed outlier: 4.156A pdb=" N LEU C 355 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL C 317 " --> pdb=" O LEU C 355 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE C 357 " --> pdb=" O TYR C 315 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR C 315 " --> pdb=" O PHE C 357 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 203 through 210 removed outlier: 4.303A pdb=" N ARG C 204 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS C 190 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR C 208 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL C 186 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU C 185 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 187 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU C 250 " --> pdb=" O MET C 299 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 297 " --> pdb=" O PHE C 252 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 437 through 441 removed outlier: 4.212A pdb=" N ARG C 439 " --> pdb=" O PHE C 432 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE C 432 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLN C 441 " --> pdb=" O TYR C 430 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR C 430 " --> pdb=" O GLN C 441 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 83 through 89 removed outlier: 6.358A pdb=" N CYS B 84 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP B 438 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN B 86 " --> pdb=" O ARG B 436 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 98 through 101 removed outlier: 4.064A pdb=" N GLY B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN B 136 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU B 125 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU B 134 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 147 through 154 removed outlier: 4.448A pdb=" N THR B 149 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA B 166 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 167 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 184 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASN B 176 " --> pdb=" O CYS B 182 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N CYS B 182 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 193 through 198 removed outlier: 3.670A pdb=" N GLU B 195 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU B 215 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ILE B 228 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU B 217 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 10.746A pdb=" N GLN B 292 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL B 226 " --> pdb=" O GLN B 292 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 239 through 244 Processing sheet with id=AC3, first strand: chain 'B' and resid 312 through 315 removed outlier: 7.226A pdb=" N LYS B 332 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE B 352 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 368 through 369 385 hydrogen bonds defined for protein. 1077 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: 1.91 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3911 1.35 - 1.46: 2795 1.46 - 1.58: 5305 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 12131 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 5.26e+00 bond pdb=" CB ILE A 456 " pdb=" CG2 ILE A 456 " ideal model delta sigma weight residual 1.521 1.565 -0.044 3.30e-02 9.18e+02 1.80e+00 bond pdb=" C ASN D 186 " pdb=" N PRO D 187 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.74e+00 bond pdb=" C ASN D 282 " pdb=" N PRO D 283 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.69e+00 bond pdb=" C SER D 326 " pdb=" N PRO D 327 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.62e+00 ... (remaining 12126 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 15927 1.63 - 3.25: 419 3.25 - 4.88: 58 4.88 - 6.51: 32 6.51 - 8.13: 7 Bond angle restraints: 16443 Sorted by residual: angle pdb=" N THR D 28 " pdb=" CA THR D 28 " pdb=" C THR D 28 " ideal model delta sigma weight residual 109.81 116.61 -6.80 2.21e+00 2.05e-01 9.48e+00 angle pdb=" CA THR D 28 " pdb=" C THR D 28 " pdb=" N PRO D 29 " ideal model delta sigma weight residual 118.44 122.81 -4.37 1.59e+00 3.96e-01 7.55e+00 angle pdb=" C LYS C 587 " pdb=" N ASP C 588 " pdb=" CA ASP C 588 " ideal model delta sigma weight residual 121.80 128.43 -6.63 2.44e+00 1.68e-01 7.39e+00 angle pdb=" CA LYS C 92 " pdb=" C LYS C 92 " pdb=" N PRO C 93 " ideal model delta sigma weight residual 118.44 122.75 -4.31 1.59e+00 3.96e-01 7.36e+00 angle pdb=" N SER D 184 " pdb=" CA SER D 184 " pdb=" C SER D 184 " ideal model delta sigma weight residual 108.32 112.42 -4.10 1.64e+00 3.72e-01 6.25e+00 ... (remaining 16438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 6781 17.54 - 35.08: 390 35.08 - 52.61: 51 52.61 - 70.15: 13 70.15 - 87.69: 8 Dihedral angle restraints: 7243 sinusoidal: 2773 harmonic: 4470 Sorted by residual: 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 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA LYS D 251 " pdb=" C LYS D 251 " pdb=" N LEU D 252 " pdb=" CA LEU D 252 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 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 180.00 160.26 19.74 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 7240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1146 0.035 - 0.071: 459 0.071 - 0.106: 117 0.106 - 0.142: 77 0.142 - 0.177: 16 Chirality restraints: 1815 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 7.83e-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 0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA ILE D 81 " pdb=" N ILE D 81 " pdb=" C ILE D 81 " pdb=" CB ILE D 81 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 1812 not shown) Planarity restraints: 2118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 201 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.54e+00 pdb=" N PRO C 202 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 202 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 202 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 28 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO D 29 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 29 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 29 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 86 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO D 87 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 87 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 87 " -0.024 5.00e-02 4.00e+02 ... (remaining 2115 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 756 2.74 - 3.28: 11601 3.28 - 3.82: 17769 3.82 - 4.36: 21450 4.36 - 4.90: 37885 Nonbonded interactions: 89461 Sorted by model distance: nonbonded pdb=" OG SER D 147 " pdb=" O HIS D 176 " model vdw 2.200 3.040 nonbonded pdb=" O ASP C 136 " pdb=" OG SER C 139 " model vdw 2.216 3.040 nonbonded pdb=" OG SER D 285 " pdb=" OD1 ASP C 135 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASP B 431 " pdb=" OG SER B 433 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR A 315 " pdb=" OD1 ASN A 317 " model vdw 2.308 3.040 ... (remaining 89456 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.490 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 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 : 0.014 0.638 12148 Z= 0.476 Angle : 0.697 8.135 16443 Z= 0.366 Chirality : 0.047 0.177 1815 Planarity : 0.004 0.047 2118 Dihedral : 11.737 87.689 4319 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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 aren not related in a simple way. whole: -4.46 (0.16), residues: 1484 helix: -2.26 (0.21), residues: 274 sheet: -3.18 (0.23), residues: 303 loop : -3.26 (0.16), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 131 TYR 0.014 0.001 TYR B 244 PHE 0.013 0.001 PHE D 243 TRP 0.010 0.001 TRP D 345 HIS 0.003 0.001 HIS B 397 Details of bonding type rmsd covalent geometry : bond 0.00439 (12131) covalent geometry : angle 0.69692 (16443) hydrogen bonds : bond 0.17372 ( 385) hydrogen bonds : angle 7.72961 ( 1077) metal coordination : bond 0.34321 ( 17) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 497 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 ASP cc_start: 0.7469 (m-30) cc_final: 0.7040 (t0) REVERT: A 615 LEU cc_start: 0.8909 (mt) cc_final: 0.8681 (mp) REVERT: A 645 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7124 (mt-10) REVERT: A 670 LEU cc_start: 0.7509 (tp) cc_final: 0.7206 (tt) REVERT: D 15 ARG cc_start: 0.7544 (mpt180) cc_final: 0.7197 (mmt180) REVERT: D 24 TRP cc_start: 0.8146 (t60) cc_final: 0.7929 (t60) REVERT: D 38 HIS cc_start: 0.6880 (t70) cc_final: 0.5708 (t-90) REVERT: D 49 TRP cc_start: 0.6467 (m100) cc_final: 0.5284 (m100) REVERT: D 55 ARG cc_start: 0.7900 (mtt-85) cc_final: 0.7467 (mpp80) REVERT: D 85 GLN cc_start: 0.7178 (mt0) cc_final: 0.6704 (mp10) REVERT: D 251 LYS cc_start: 0.7794 (mttm) cc_final: 0.7594 (ptpt) REVERT: D 313 PHE cc_start: 0.7518 (m-80) cc_final: 0.7309 (m-80) REVERT: D 380 PHE cc_start: 0.7542 (p90) cc_final: 0.7342 (p90) REVERT: D 403 GLN cc_start: 0.7353 (tt0) cc_final: 0.6991 (tm-30) REVERT: C 453 CYS cc_start: 0.4715 (t) cc_final: 0.3313 (t) REVERT: C 528 ILE cc_start: 0.8350 (pt) cc_final: 0.8125 (mp) REVERT: B 144 ASP cc_start: 0.7324 (p0) cc_final: 0.6971 (p0) REVERT: B 175 ILE cc_start: 0.9192 (mm) cc_final: 0.8992 (mt) REVERT: B 211 LYS cc_start: 0.8457 (tttt) cc_final: 0.7967 (tmtt) REVERT: B 252 MET cc_start: 0.8541 (tpp) cc_final: 0.8337 (ttt) REVERT: B 272 ASN cc_start: 0.8524 (p0) cc_final: 0.8219 (m-40) REVERT: B 319 ILE cc_start: 0.8832 (mm) cc_final: 0.7747 (mm) REVERT: B 372 PHE cc_start: 0.8177 (t80) cc_final: 0.7626 (t80) outliers start: 0 outliers final: 0 residues processed: 497 average time/residue: 0.1329 time to fit residues: 90.3371 Evaluate side-chains 234 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.0270 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 ASN D 354 GLN C 104 ASN C 624 HIS C 634 HIS C 664 HIS B 104 HIS B 194 ASN B 204 ASN B 235 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.138235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.106967 restraints weight = 30395.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.109739 restraints weight = 17002.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.111549 restraints weight = 11300.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.112821 restraints weight = 8458.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.113677 restraints weight = 6891.089| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12148 Z= 0.131 Angle : 0.570 6.765 16443 Z= 0.301 Chirality : 0.045 0.217 1815 Planarity : 0.004 0.068 2118 Dihedral : 4.415 19.228 1617 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.24 % Allowed : 3.55 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.19 (0.18), residues: 1484 helix: -0.72 (0.27), residues: 287 sheet: -2.22 (0.25), residues: 314 loop : -2.67 (0.17), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 458 TYR 0.019 0.001 TYR C 434 PHE 0.018 0.002 PHE B 101 TRP 0.018 0.002 TRP B 103 HIS 0.008 0.001 HIS C 659 Details of bonding type rmsd covalent geometry : bond 0.00295 (12131) covalent geometry : angle 0.57002 (16443) hydrogen bonds : bond 0.03604 ( 385) hydrogen bonds : angle 5.40804 ( 1077) metal coordination : bond 0.00574 ( 17) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 276 time to evaluate : 0.520 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 673 ASP cc_start: 0.8147 (m-30) cc_final: 0.7874 (m-30) REVERT: A 727 TYR cc_start: 0.5524 (p90) cc_final: 0.3596 (t80) REVERT: D 19 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7454 (mm-30) REVERT: D 55 ARG cc_start: 0.7948 (mtt-85) cc_final: 0.7541 (mpp80) REVERT: D 85 GLN cc_start: 0.7019 (mt0) cc_final: 0.6295 (mp10) REVERT: D 366 LEU cc_start: 0.9049 (tp) cc_final: 0.8757 (tp) REVERT: C 467 LEU cc_start: 0.8985 (mp) cc_final: 0.8724 (mt) REVERT: B 125 GLU cc_start: 0.8760 (tp30) cc_final: 0.8418 (tm-30) REVERT: B 126 CYS cc_start: 0.9342 (m) cc_final: 0.8888 (m) REVERT: B 139 VAL cc_start: 0.7992 (t) cc_final: 0.7575 (p) REVERT: B 172 ILE cc_start: 0.9160 (mt) cc_final: 0.8877 (tt) REVERT: B 252 MET cc_start: 0.9115 (tpp) cc_final: 0.8549 (ttt) REVERT: B 271 MET cc_start: 0.9307 (mmt) cc_final: 0.9069 (mmt) REVERT: B 308 TYR cc_start: 0.6266 (m-80) cc_final: 0.5994 (m-80) REVERT: B 319 ILE cc_start: 0.8802 (mm) cc_final: 0.8202 (mm) REVERT: B 358 TYR cc_start: 0.7539 (p90) cc_final: 0.7276 (p90) REVERT: B 372 PHE cc_start: 0.8151 (t80) cc_final: 0.7601 (t80) outliers start: 3 outliers final: 0 residues processed: 278 average time/residue: 0.1052 time to fit residues: 42.9291 Evaluate side-chains 179 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 17 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 81 optimal weight: 0.3980 chunk 99 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 ASN D 38 HIS D 188 ASN D 200 HIS D 272 HIS D 277 ASN B 397 HIS B 415 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.130592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.098811 restraints weight = 30401.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.101463 restraints weight = 17110.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.103178 restraints weight = 11408.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.104439 restraints weight = 8634.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.105207 restraints weight = 7066.692| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12148 Z= 0.162 Angle : 0.595 7.034 16443 Z= 0.319 Chirality : 0.045 0.171 1815 Planarity : 0.004 0.047 2118 Dihedral : 4.573 21.976 1617 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.08 % Allowed : 3.87 % Favored : 96.05 % 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 aren not related in a simple way. whole: -2.56 (0.20), residues: 1484 helix: 0.10 (0.30), residues: 289 sheet: -1.94 (0.25), residues: 360 loop : -2.31 (0.18), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 287 TYR 0.051 0.002 TYR A 42 PHE 0.026 0.002 PHE A 471 TRP 0.014 0.002 TRP D 205 HIS 0.012 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00366 (12131) covalent geometry : angle 0.59486 (16443) hydrogen bonds : bond 0.03689 ( 385) hydrogen bonds : angle 5.08599 ( 1077) metal coordination : bond 0.00725 ( 17) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 660 ASP cc_start: 0.7465 (m-30) cc_final: 0.7224 (m-30) REVERT: A 723 LEU cc_start: 0.9091 (mp) cc_final: 0.8764 (mp) REVERT: A 727 TYR cc_start: 0.5528 (p90) cc_final: 0.3210 (t80) REVERT: D 19 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7225 (mm-30) REVERT: D 20 GLU cc_start: 0.8329 (tp30) cc_final: 0.8097 (tp30) REVERT: D 38 HIS cc_start: 0.7085 (t70) cc_final: 0.6430 (t-90) REVERT: D 55 ARG cc_start: 0.8033 (mtt-85) cc_final: 0.7693 (mpp80) REVERT: D 86 LEU cc_start: 0.7833 (mp) cc_final: 0.7112 (tt) REVERT: D 205 TRP cc_start: 0.5516 (m-90) cc_final: 0.4603 (m-90) REVERT: D 380 PHE cc_start: 0.7831 (p90) cc_final: 0.7608 (p90) REVERT: C 84 GLU cc_start: 0.8313 (tt0) cc_final: 0.7928 (tm-30) REVERT: C 572 LEU cc_start: 0.9167 (mm) cc_final: 0.8945 (mm) REVERT: C 612 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8273 (mm-30) REVERT: C 614 MET cc_start: 0.9007 (mmm) cc_final: 0.8734 (mmm) REVERT: B 124 TYR cc_start: 0.8947 (m-80) cc_final: 0.8710 (m-80) REVERT: B 172 ILE cc_start: 0.9254 (mt) cc_final: 0.8873 (tt) REVERT: B 252 MET cc_start: 0.9403 (tpp) cc_final: 0.8825 (ttt) REVERT: B 256 MET cc_start: 0.9119 (ttm) cc_final: 0.8748 (ttp) REVERT: B 372 PHE cc_start: 0.8663 (t80) cc_final: 0.8048 (t80) outliers start: 1 outliers final: 1 residues processed: 225 average time/residue: 0.1026 time to fit residues: 34.6173 Evaluate side-chains 159 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 138 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 65 optimal weight: 0.3980 chunk 146 optimal weight: 0.0270 chunk 145 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 HIS D 272 HIS D 316 HIS B 194 ASN B 415 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.131769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.100107 restraints weight = 30195.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.102729 restraints weight = 17017.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104458 restraints weight = 11408.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.105643 restraints weight = 8625.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.106370 restraints weight = 7071.510| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12148 Z= 0.106 Angle : 0.528 7.086 16443 Z= 0.279 Chirality : 0.044 0.166 1815 Planarity : 0.003 0.042 2118 Dihedral : 4.357 19.472 1617 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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 aren not related in a simple way. whole: -2.09 (0.20), residues: 1484 helix: 0.44 (0.31), residues: 289 sheet: -1.26 (0.27), residues: 350 loop : -2.17 (0.19), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 458 TYR 0.033 0.001 TYR A 42 PHE 0.016 0.001 PHE B 101 TRP 0.027 0.001 TRP D 345 HIS 0.006 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00237 (12131) covalent geometry : angle 0.52804 (16443) hydrogen bonds : bond 0.03182 ( 385) hydrogen bonds : angle 4.77695 ( 1077) metal coordination : bond 0.00352 ( 17) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1387 (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: A 638 PHE cc_start: 0.8889 (t80) cc_final: 0.8408 (t80) REVERT: A 660 ASP cc_start: 0.7529 (m-30) cc_final: 0.7298 (m-30) REVERT: A 690 HIS cc_start: 0.7099 (t-90) cc_final: 0.6699 (m90) REVERT: D 20 GLU cc_start: 0.8348 (tp30) cc_final: 0.8102 (tp30) REVERT: D 38 HIS cc_start: 0.7082 (t70) cc_final: 0.6786 (t70) REVERT: D 55 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7690 (mpp80) REVERT: D 85 GLN cc_start: 0.7184 (mt0) cc_final: 0.6348 (mp10) REVERT: D 313 PHE cc_start: 0.7620 (m-80) cc_final: 0.7048 (m-80) REVERT: D 366 LEU cc_start: 0.8071 (mm) cc_final: 0.7759 (mm) REVERT: D 373 HIS cc_start: 0.7131 (m-70) cc_final: 0.6923 (m-70) REVERT: C 84 GLU cc_start: 0.8482 (tt0) cc_final: 0.7953 (tm-30) REVERT: C 612 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8140 (mm-30) REVERT: C 614 MET cc_start: 0.9175 (mmm) cc_final: 0.8668 (mmm) REVERT: B 172 ILE cc_start: 0.9283 (mt) cc_final: 0.8904 (tt) REVERT: B 252 MET cc_start: 0.9410 (tpp) cc_final: 0.8994 (ttm) REVERT: B 271 MET cc_start: 0.9250 (mmt) cc_final: 0.8986 (mmt) REVERT: B 308 TYR cc_start: 0.6427 (m-80) cc_final: 0.6146 (m-80) REVERT: B 319 ILE cc_start: 0.8805 (mm) cc_final: 0.8355 (mm) REVERT: B 372 PHE cc_start: 0.8649 (t80) cc_final: 0.8341 (t80) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.0968 time to fit residues: 31.0770 Evaluate side-chains 158 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 30.0000 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 HIS ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS C 466 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.129487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.099616 restraints weight = 29867.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.101296 restraints weight = 16097.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.102111 restraints weight = 11317.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.102849 restraints weight = 9314.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.102810 restraints weight = 8250.126| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12148 Z= 0.124 Angle : 0.541 7.107 16443 Z= 0.286 Chirality : 0.044 0.239 1815 Planarity : 0.003 0.037 2118 Dihedral : 4.310 22.031 1617 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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 aren not related in a simple way. whole: -1.77 (0.20), residues: 1484 helix: 0.63 (0.31), residues: 291 sheet: -0.97 (0.28), residues: 333 loop : -1.98 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 306 TYR 0.025 0.001 TYR A 42 PHE 0.018 0.001 PHE A 46 TRP 0.019 0.001 TRP D 345 HIS 0.009 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00278 (12131) covalent geometry : angle 0.54072 (16443) hydrogen bonds : bond 0.03334 ( 385) hydrogen bonds : angle 4.71405 ( 1077) metal coordination : bond 0.00702 ( 17) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.7445 (tpp) cc_final: 0.6837 (ttm) REVERT: A 553 ASP cc_start: 0.8302 (t0) cc_final: 0.8093 (t70) REVERT: A 608 GLN cc_start: 0.8204 (mt0) cc_final: 0.7827 (mt0) REVERT: A 638 PHE cc_start: 0.9041 (t80) cc_final: 0.8462 (t80) REVERT: A 645 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7790 (mt-10) REVERT: A 660 ASP cc_start: 0.7801 (m-30) cc_final: 0.7536 (m-30) REVERT: A 680 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7611 (mtm180) REVERT: D 19 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7107 (mm-30) REVERT: D 38 HIS cc_start: 0.6925 (t70) cc_final: 0.6596 (t70) REVERT: D 304 ARG cc_start: 0.8376 (ptt180) cc_final: 0.7799 (ptt90) REVERT: D 313 PHE cc_start: 0.7774 (m-80) cc_final: 0.7267 (m-80) REVERT: C 84 GLU cc_start: 0.8617 (tt0) cc_final: 0.8068 (tm-30) REVERT: C 441 GLN cc_start: 0.8371 (tm-30) cc_final: 0.7926 (tm-30) REVERT: C 572 LEU cc_start: 0.9146 (mm) cc_final: 0.8931 (mm) REVERT: C 612 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7954 (tp30) REVERT: C 614 MET cc_start: 0.9157 (mmm) cc_final: 0.8598 (mmm) REVERT: B 172 ILE cc_start: 0.9301 (mt) cc_final: 0.8893 (tt) REVERT: B 252 MET cc_start: 0.9378 (tpp) cc_final: 0.9025 (ttt) REVERT: B 296 PHE cc_start: 0.8391 (m-80) cc_final: 0.8174 (m-80) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1030 time to fit residues: 32.1207 Evaluate side-chains 149 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 78 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 136 optimal weight: 0.0370 chunk 120 optimal weight: 0.5980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.128766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.098855 restraints weight = 30307.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.100162 restraints weight = 17563.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.101073 restraints weight = 12860.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.101706 restraints weight = 10329.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.101954 restraints weight = 9406.632| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3461 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.6126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12148 Z= 0.109 Angle : 0.520 7.090 16443 Z= 0.274 Chirality : 0.044 0.199 1815 Planarity : 0.003 0.036 2118 Dihedral : 4.222 22.094 1617 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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 aren not related in a simple way. whole: -1.54 (0.21), residues: 1484 helix: 0.64 (0.31), residues: 295 sheet: -0.76 (0.28), residues: 346 loop : -1.82 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 458 TYR 0.019 0.001 TYR A 42 PHE 0.018 0.001 PHE A 46 TRP 0.018 0.001 TRP D 345 HIS 0.005 0.001 HIS D 272 Details of bonding type rmsd covalent geometry : bond 0.00246 (12131) covalent geometry : angle 0.52010 (16443) hydrogen bonds : bond 0.03011 ( 385) hydrogen bonds : angle 4.60506 ( 1077) metal coordination : bond 0.00474 ( 17) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.7082 (tpt) cc_final: 0.6860 (tpp) REVERT: A 638 PHE cc_start: 0.9004 (t80) cc_final: 0.8524 (t80) REVERT: A 660 ASP cc_start: 0.7730 (m-30) cc_final: 0.7382 (m-30) REVERT: D 179 GLU cc_start: 0.6763 (pt0) cc_final: 0.6267 (pm20) REVERT: C 84 GLU cc_start: 0.8629 (tt0) cc_final: 0.8129 (tm-30) REVERT: C 440 GLN cc_start: 0.7275 (tp40) cc_final: 0.7072 (mp10) REVERT: C 441 GLN cc_start: 0.8416 (tm-30) cc_final: 0.7685 (tm-30) REVERT: C 612 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7970 (tp30) REVERT: C 614 MET cc_start: 0.9154 (mmm) cc_final: 0.8650 (mmm) REVERT: B 252 MET cc_start: 0.9245 (tpp) cc_final: 0.8967 (ttt) REVERT: B 256 MET cc_start: 0.9372 (ttt) cc_final: 0.9096 (ttp) REVERT: B 271 MET cc_start: 0.9210 (mmt) cc_final: 0.8992 (mmt) REVERT: B 310 ASP cc_start: 0.8157 (m-30) cc_final: 0.7917 (m-30) REVERT: B 322 LYS cc_start: 0.8977 (tmtt) cc_final: 0.8566 (tmtt) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.0849 time to fit residues: 25.9991 Evaluate side-chains 143 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 146 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 136 optimal weight: 0.3980 chunk 78 optimal weight: 0.4980 chunk 123 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 HIS ** A 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 HIS ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.127033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.097441 restraints weight = 29544.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.099170 restraints weight = 17612.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.100396 restraints weight = 11823.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.100646 restraints weight = 9836.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.100896 restraints weight = 8911.690| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.6447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12148 Z= 0.128 Angle : 0.539 7.055 16443 Z= 0.284 Chirality : 0.044 0.178 1815 Planarity : 0.003 0.036 2118 Dihedral : 4.272 23.423 1617 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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 aren not related in a simple way. whole: -1.46 (0.21), residues: 1484 helix: 0.69 (0.31), residues: 294 sheet: -0.77 (0.28), residues: 342 loop : -1.72 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 120 TYR 0.017 0.001 TYR A 42 PHE 0.022 0.001 PHE A 312 TRP 0.031 0.001 TRP D 345 HIS 0.006 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00290 (12131) covalent geometry : angle 0.53917 (16443) hydrogen bonds : bond 0.03246 ( 385) hydrogen bonds : angle 4.64755 ( 1077) metal coordination : bond 0.00521 ( 17) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.7304 (tpt) cc_final: 0.7056 (tpp) REVERT: A 638 PHE cc_start: 0.9047 (t80) cc_final: 0.8520 (t80) REVERT: A 660 ASP cc_start: 0.7935 (m-30) cc_final: 0.7607 (m-30) REVERT: D 179 GLU cc_start: 0.6507 (pt0) cc_final: 0.6163 (pm20) REVERT: D 313 PHE cc_start: 0.7585 (m-80) cc_final: 0.7279 (m-80) REVERT: D 373 HIS cc_start: 0.6785 (m-70) cc_final: 0.6469 (m-70) REVERT: C 84 GLU cc_start: 0.8706 (tt0) cc_final: 0.8178 (tm-30) REVERT: C 612 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8206 (tp30) REVERT: C 614 MET cc_start: 0.9134 (mmm) cc_final: 0.8629 (mmm) REVERT: B 237 ASP cc_start: 0.8582 (t70) cc_final: 0.8359 (t70) REVERT: B 252 MET cc_start: 0.9346 (tpp) cc_final: 0.8996 (ttt) REVERT: B 270 MET cc_start: 0.9078 (mtp) cc_final: 0.8857 (mtm) REVERT: B 272 ASN cc_start: 0.8503 (p0) cc_final: 0.8257 (m110) REVERT: B 322 LYS cc_start: 0.8939 (tmtt) cc_final: 0.8604 (tmtt) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.0829 time to fit residues: 24.5633 Evaluate side-chains 137 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 41 optimal weight: 8.9990 chunk 120 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 ASN D 177 GLN ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.127327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.097995 restraints weight = 29876.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.099313 restraints weight = 17470.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.099902 restraints weight = 12968.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.101238 restraints weight = 10507.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.101028 restraints weight = 8843.593| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.6635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12148 Z= 0.114 Angle : 0.539 9.757 16443 Z= 0.283 Chirality : 0.044 0.170 1815 Planarity : 0.003 0.036 2118 Dihedral : 4.209 23.257 1617 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.08 % Allowed : 1.05 % Favored : 98.87 % 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 aren not related in a simple way. whole: -1.34 (0.21), residues: 1484 helix: 0.66 (0.31), residues: 289 sheet: -0.56 (0.28), residues: 350 loop : -1.64 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 120 TYR 0.026 0.001 TYR A 42 PHE 0.011 0.001 PHE A 46 TRP 0.019 0.001 TRP D 345 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00256 (12131) covalent geometry : angle 0.53897 (16443) hydrogen bonds : bond 0.03063 ( 385) hydrogen bonds : angle 4.59300 ( 1077) metal coordination : bond 0.00452 ( 17) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.7295 (tpt) cc_final: 0.7054 (tpp) REVERT: A 638 PHE cc_start: 0.9017 (t80) cc_final: 0.8472 (t80) REVERT: A 653 ASP cc_start: 0.8425 (t70) cc_final: 0.8164 (t0) REVERT: A 660 ASP cc_start: 0.8050 (m-30) cc_final: 0.7705 (m-30) REVERT: D 85 GLN cc_start: 0.7282 (mt0) cc_final: 0.6110 (mp10) REVERT: D 179 GLU cc_start: 0.6323 (pt0) cc_final: 0.6015 (pm20) REVERT: D 256 ASP cc_start: 0.6918 (t0) cc_final: 0.6633 (t0) REVERT: D 373 HIS cc_start: 0.6732 (m-70) cc_final: 0.6420 (m-70) REVERT: C 84 GLU cc_start: 0.8706 (tt0) cc_final: 0.8064 (tm-30) REVERT: C 570 THR cc_start: 0.9482 (p) cc_final: 0.9244 (p) REVERT: C 594 GLU cc_start: 0.7625 (tm-30) cc_final: 0.6928 (tm-30) REVERT: C 612 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8146 (tp30) REVERT: C 614 MET cc_start: 0.9129 (mmm) cc_final: 0.8637 (mmm) REVERT: B 206 LEU cc_start: 0.8985 (tp) cc_final: 0.8648 (mt) REVERT: B 252 MET cc_start: 0.9269 (tpp) cc_final: 0.8976 (ttt) REVERT: B 271 MET cc_start: 0.9263 (mmt) cc_final: 0.9048 (mmt) REVERT: B 272 ASN cc_start: 0.8414 (p0) cc_final: 0.8159 (m110) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.0898 time to fit residues: 26.2800 Evaluate side-chains 137 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 66 optimal weight: 0.7980 chunk 100 optimal weight: 0.0370 chunk 95 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 58 optimal weight: 0.1980 chunk 96 optimal weight: 0.0670 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.129039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.099356 restraints weight = 30014.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.101320 restraints weight = 16970.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.102238 restraints weight = 11701.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.102627 restraints weight = 9473.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.102900 restraints weight = 8510.864| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.6700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12148 Z= 0.095 Angle : 0.529 7.099 16443 Z= 0.276 Chirality : 0.044 0.190 1815 Planarity : 0.003 0.035 2118 Dihedral : 4.074 21.909 1617 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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 aren not related in a simple way. whole: -1.17 (0.21), residues: 1484 helix: 0.81 (0.31), residues: 289 sheet: -0.38 (0.28), residues: 351 loop : -1.57 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 120 TYR 0.023 0.001 TYR A 42 PHE 0.021 0.001 PHE A 46 TRP 0.027 0.001 TRP D 345 HIS 0.013 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00212 (12131) covalent geometry : angle 0.52883 (16443) hydrogen bonds : bond 0.02908 ( 385) hydrogen bonds : angle 4.45988 ( 1077) metal coordination : bond 0.00396 ( 17) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.7277 (tpt) cc_final: 0.7049 (tpp) REVERT: A 638 PHE cc_start: 0.8942 (t80) cc_final: 0.8450 (t80) REVERT: A 653 ASP cc_start: 0.8351 (t70) cc_final: 0.8147 (t0) REVERT: A 660 ASP cc_start: 0.7918 (m-30) cc_final: 0.7570 (m-30) REVERT: D 179 GLU cc_start: 0.6593 (pt0) cc_final: 0.6245 (pm20) REVERT: D 284 TYR cc_start: 0.8630 (m-80) cc_final: 0.8430 (m-10) REVERT: D 373 HIS cc_start: 0.6592 (m-70) cc_final: 0.6335 (m-70) REVERT: D 403 GLN cc_start: 0.7997 (tt0) cc_final: 0.7562 (tm-30) REVERT: C 84 GLU cc_start: 0.8654 (tt0) cc_final: 0.8141 (tm-30) REVERT: C 440 GLN cc_start: 0.7597 (tp-100) cc_final: 0.7374 (tp-100) REVERT: C 570 THR cc_start: 0.9512 (p) cc_final: 0.9278 (p) REVERT: C 594 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7365 (tm-30) REVERT: C 612 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8075 (tp30) REVERT: C 614 MET cc_start: 0.9089 (mmm) cc_final: 0.8574 (mmm) REVERT: C 632 MET cc_start: 0.9212 (mmm) cc_final: 0.8944 (mpp) REVERT: B 243 ASP cc_start: 0.8093 (t0) cc_final: 0.7418 (t0) REVERT: B 249 GLU cc_start: 0.7207 (mp0) cc_final: 0.6976 (mp0) REVERT: B 252 MET cc_start: 0.9333 (tpp) cc_final: 0.9042 (ttt) REVERT: B 271 MET cc_start: 0.9230 (mmt) cc_final: 0.8936 (mmt) REVERT: B 272 ASN cc_start: 0.8446 (p0) cc_final: 0.8197 (m110) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.0805 time to fit residues: 24.1115 Evaluate side-chains 144 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 122 optimal weight: 0.4980 chunk 120 optimal weight: 0.9990 chunk 149 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 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 = 0.3911 r_free = 0.3911 target = 0.127890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.098451 restraints weight = 29670.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.100048 restraints weight = 16719.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.100907 restraints weight = 11889.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.101670 restraints weight = 9438.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.101729 restraints weight = 8285.203| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.6865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12148 Z= 0.110 Angle : 0.543 8.604 16443 Z= 0.285 Chirality : 0.044 0.185 1815 Planarity : 0.003 0.035 2118 Dihedral : 4.106 22.679 1617 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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 aren not related in a simple way. whole: -1.13 (0.21), residues: 1484 helix: 0.85 (0.31), residues: 289 sheet: -0.40 (0.27), residues: 365 loop : -1.53 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 120 TYR 0.024 0.001 TYR A 42 PHE 0.020 0.001 PHE A 46 TRP 0.024 0.001 TRP D 345 HIS 0.007 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00251 (12131) covalent geometry : angle 0.54338 (16443) hydrogen bonds : bond 0.03001 ( 385) hydrogen bonds : angle 4.48810 ( 1077) metal coordination : bond 0.00460 ( 17) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.7279 (tpt) cc_final: 0.7023 (tpp) REVERT: A 638 PHE cc_start: 0.9019 (t80) cc_final: 0.8463 (t80) REVERT: A 653 ASP cc_start: 0.8414 (t70) cc_final: 0.8127 (t0) REVERT: A 660 ASP cc_start: 0.7933 (m-30) cc_final: 0.7600 (m-30) REVERT: D 179 GLU cc_start: 0.6594 (pt0) cc_final: 0.6234 (pm20) REVERT: D 284 TYR cc_start: 0.8729 (m-80) cc_final: 0.8481 (m-10) REVERT: D 319 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7692 (tt0) REVERT: D 373 HIS cc_start: 0.6654 (m-70) cc_final: 0.6393 (m-70) REVERT: C 84 GLU cc_start: 0.8692 (tt0) cc_final: 0.8019 (tm-30) REVERT: C 440 GLN cc_start: 0.7653 (tp-100) cc_final: 0.7415 (tp-100) REVERT: C 594 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7470 (tm-30) REVERT: C 612 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8136 (tp30) REVERT: C 614 MET cc_start: 0.9117 (mmm) cc_final: 0.8604 (mmm) REVERT: B 206 LEU cc_start: 0.9002 (tp) cc_final: 0.8776 (mt) REVERT: B 220 ILE cc_start: 0.9112 (mp) cc_final: 0.8823 (mm) REVERT: B 243 ASP cc_start: 0.8117 (t0) cc_final: 0.7490 (t0) REVERT: B 252 MET cc_start: 0.9338 (tpp) cc_final: 0.9015 (ttt) REVERT: B 271 MET cc_start: 0.9347 (mmt) cc_final: 0.9073 (mmt) REVERT: B 272 ASN cc_start: 0.8451 (p0) cc_final: 0.8183 (m110) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.0804 time to fit residues: 24.0840 Evaluate side-chains 140 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 135 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 0.0050 chunk 114 optimal weight: 0.0000 chunk 36 optimal weight: 0.0770 chunk 43 optimal weight: 7.9990 chunk 139 optimal weight: 0.5980 chunk 84 optimal weight: 0.3980 chunk 97 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.2156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.129840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.100223 restraints weight = 29862.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.102999 restraints weight = 17912.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.103453 restraints weight = 11014.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.104185 restraints weight = 9589.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.104348 restraints weight = 8392.371| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.6898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12148 Z= 0.091 Angle : 0.527 8.651 16443 Z= 0.274 Chirality : 0.043 0.179 1815 Planarity : 0.003 0.035 2118 Dihedral : 3.966 20.909 1617 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % 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 aren not related in a simple way. whole: -1.07 (0.21), residues: 1484 helix: 0.89 (0.31), residues: 289 sheet: -0.40 (0.28), residues: 361 loop : -1.47 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 120 TYR 0.023 0.001 TYR A 42 PHE 0.018 0.001 PHE A 46 TRP 0.024 0.001 TRP D 345 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00198 (12131) covalent geometry : angle 0.52690 (16443) hydrogen bonds : bond 0.02859 ( 385) hydrogen bonds : angle 4.40425 ( 1077) metal coordination : bond 0.00326 ( 17) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2178.02 seconds wall clock time: 38 minutes 27.15 seconds (2307.15 seconds total)