Starting phenix.real_space_refine on Wed Jul 30 03:35:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ksr_23024/07_2025/7ksr_23024.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ksr_23024/07_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_23024/07_2025/7ksr_23024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ksr_23024/07_2025/7ksr_23024.map" model { file = "/net/cci-nas-00/data/ceres_data/7ksr_23024/07_2025/7ksr_23024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ksr_23024/07_2025/7ksr_23024.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 7 6.06 5 S 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "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: {'GLU:plan': 3, 'ASP: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: {'GLN:plan1': 11, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 7, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 227 Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2917 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 352} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "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: 8.09, per 1000 atoms: 0.68 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: 3.00 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.34 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: 3.68 Time building geometry restraints manager: 3.60 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 33.160 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.550 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (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 TRP 0.010 0.001 TRP D 345 HIS 0.003 0.001 HIS B 397 PHE 0.013 0.001 PHE D 243 TYR 0.014 0.001 TYR B 244 ARG 0.002 0.000 ARG D 131 Details of bonding type rmsd hydrogen bonds : bond 0.17372 ( 385) hydrogen bonds : angle 7.72961 ( 1077) metal coordination : bond 0.34321 ( 17) covalent geometry : bond 0.00439 (12131) covalent geometry : angle 0.69692 (16443) *********************** 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 : 1.467 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: A 97 MET cc_start: 0.6874 (tpt) cc_final: 0.6538 (tpp) REVERT: A 278 ASP cc_start: 0.7469 (m-30) cc_final: 0.7039 (t0) REVERT: A 615 LEU cc_start: 0.8909 (mt) cc_final: 0.8695 (mp) REVERT: A 645 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7123 (mt-10) REVERT: A 670 LEU cc_start: 0.7509 (tp) cc_final: 0.7222 (tt) REVERT: D 15 ARG cc_start: 0.7544 (mpt180) cc_final: 0.7198 (mmt180) REVERT: D 24 TRP cc_start: 0.8146 (t60) cc_final: 0.7928 (t60) REVERT: D 38 HIS cc_start: 0.6880 (t70) cc_final: 0.5720 (t-90) REVERT: D 49 TRP cc_start: 0.6467 (m100) cc_final: 0.5281 (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 313 PHE cc_start: 0.7518 (m-80) cc_final: 0.7310 (m-80) REVERT: D 354 GLN cc_start: 0.7328 (pm20) cc_final: 0.6625 (pt0) REVERT: D 380 PHE cc_start: 0.7542 (p90) cc_final: 0.7213 (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: 0.3308 (t) REVERT: C 528 ILE cc_start: 0.8350 (pt) cc_final: 0.8123 (mp) REVERT: B 144 ASP cc_start: 0.7324 (p0) cc_final: 0.6966 (p0) REVERT: B 211 LYS cc_start: 0.8457 (tttt) cc_final: 0.7968 (tmtt) REVERT: B 252 MET cc_start: 0.8541 (tpp) cc_final: 0.8334 (ttt) REVERT: B 272 ASN cc_start: 0.8524 (p0) cc_final: 0.8215 (m-40) REVERT: B 319 ILE cc_start: 0.8832 (mm) cc_final: 0.7749 (mm) REVERT: B 372 PHE cc_start: 0.8177 (t80) cc_final: 0.7631 (t80) outliers start: 0 outliers final: 0 residues processed: 497 average time/residue: 0.2725 time to fit residues: 183.9714 Evaluate side-chains 237 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 117 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 ASN D 188 ASN D 267 HIS C 104 ASN C 440 GLN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.134642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.104659 restraints weight = 29794.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.106519 restraints weight = 16309.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.108033 restraints weight = 11192.992| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12148 Z= 0.178 Angle : 0.617 6.854 16443 Z= 0.329 Chirality : 0.046 0.229 1815 Planarity : 0.005 0.059 2118 Dihedral : 4.561 21.157 1617 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.24 % Allowed : 3.95 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.19), residues: 1484 helix: -0.61 (0.27), residues: 287 sheet: -2.30 (0.24), residues: 336 loop : -2.62 (0.18), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 103 HIS 0.010 0.001 HIS C 659 PHE 0.021 0.002 PHE B 101 TYR 0.017 0.002 TYR C 434 ARG 0.010 0.001 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 385) hydrogen bonds : angle 5.49413 ( 1077) metal coordination : bond 0.00622 ( 17) covalent geometry : bond 0.00389 (12131) covalent geometry : angle 0.61717 (16443) *********************** 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 259 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 256 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 TYR cc_start: 0.5115 (p90) cc_final: 0.3191 (t80) REVERT: D 19 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7385 (mm-30) REVERT: D 55 ARG cc_start: 0.8048 (mtt-85) cc_final: 0.7615 (mpp80) REVERT: D 85 GLN cc_start: 0.7088 (mt0) cc_final: 0.6272 (mp10) REVERT: D 354 GLN cc_start: 0.7791 (pm20) cc_final: 0.7125 (pt0) REVERT: C 467 LEU cc_start: 0.9006 (mp) cc_final: 0.8734 (mt) REVERT: C 588 ASP cc_start: 0.5443 (p0) cc_final: 0.5049 (m-30) REVERT: C 612 GLU cc_start: 0.8695 (tp30) cc_final: 0.8481 (mm-30) REVERT: B 139 VAL cc_start: 0.8014 (t) cc_final: 0.7602 (p) REVERT: B 172 ILE cc_start: 0.9221 (mt) cc_final: 0.8913 (tt) REVERT: B 252 MET cc_start: 0.9252 (tpp) cc_final: 0.8626 (ttt) REVERT: B 271 MET cc_start: 0.9379 (mmt) cc_final: 0.9121 (mmt) REVERT: B 319 ILE cc_start: 0.8840 (mm) cc_final: 0.8194 (mm) outliers start: 3 outliers final: 0 residues processed: 258 average time/residue: 0.2235 time to fit residues: 84.8082 Evaluate side-chains 175 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 99 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 0.0570 chunk 75 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 HIS A 704 ASN D 38 HIS D 272 HIS D 277 ASN D 316 HIS C 607 ASN C 624 HIS B 415 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.133833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.104308 restraints weight = 30390.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.105427 restraints weight = 16267.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.106507 restraints weight = 11469.781| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 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 = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4741 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 : 0.544 6.967 16443 Z= 0.290 Chirality : 0.044 0.166 1815 Planarity : 0.004 0.039 2118 Dihedral : 4.349 21.169 1617 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.19), residues: 1484 helix: 0.09 (0.30), residues: 290 sheet: -1.89 (0.25), residues: 341 loop : -2.39 (0.18), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 345 HIS 0.006 0.001 HIS C 471 PHE 0.020 0.001 PHE B 101 TYR 0.022 0.001 TYR C 434 ARG 0.005 0.001 ARG A 579 Details of bonding type rmsd hydrogen bonds : bond 0.03260 ( 385) hydrogen bonds : angle 5.00667 ( 1077) metal coordination : bond 0.00401 ( 17) covalent geometry : bond 0.00250 (12131) covalent geometry : angle 0.54409 (16443) *********************** 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 236 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 690 HIS cc_start: 0.7119 (t-90) cc_final: 0.6823 (m90) REVERT: D 20 GLU cc_start: 0.8284 (tp30) cc_final: 0.7955 (tp30) REVERT: D 38 HIS cc_start: 0.7087 (t70) cc_final: 0.6553 (t-90) REVERT: D 55 ARG cc_start: 0.8113 (mtt-85) cc_final: 0.7678 (mpp80) REVERT: D 85 GLN cc_start: 0.7154 (mt0) cc_final: 0.6275 (mp10) REVERT: D 153 ASP cc_start: 0.7379 (t0) cc_final: 0.6869 (p0) REVERT: C 441 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7532 (tm-30) REVERT: C 612 GLU cc_start: 0.8605 (tp30) cc_final: 0.8331 (mm-30) REVERT: B 124 TYR cc_start: 0.9039 (m-80) cc_final: 0.8782 (m-80) REVERT: B 139 VAL cc_start: 0.8291 (t) cc_final: 0.7975 (p) REVERT: B 140 ASP cc_start: 0.6300 (p0) cc_final: 0.5833 (p0) REVERT: B 142 ASP cc_start: 0.7655 (p0) cc_final: 0.7109 (p0) REVERT: B 172 ILE cc_start: 0.9207 (mt) cc_final: 0.8863 (tt) REVERT: B 243 ASP cc_start: 0.8354 (t0) cc_final: 0.7855 (t0) REVERT: B 252 MET cc_start: 0.9369 (tpp) cc_final: 0.8822 (ttt) REVERT: B 319 ILE cc_start: 0.8848 (mm) cc_final: 0.8258 (mm) REVERT: B 372 PHE cc_start: 0.8386 (t80) cc_final: 0.7647 (t80) REVERT: B 391 LEU cc_start: 0.8747 (tp) cc_final: 0.8121 (tp) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2106 time to fit residues: 73.9480 Evaluate side-chains 159 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 140 optimal weight: 0.0570 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 61 optimal weight: 0.0970 chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 272 HIS B 397 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.133550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.101808 restraints weight = 29602.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.104467 restraints weight = 16785.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.106269 restraints weight = 11239.403| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 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 = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12148 Z= 0.105 Angle : 0.527 7.047 16443 Z= 0.279 Chirality : 0.043 0.165 1815 Planarity : 0.003 0.042 2118 Dihedral : 4.216 18.728 1617 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.20), residues: 1484 helix: 0.29 (0.30), residues: 289 sheet: -1.43 (0.26), residues: 335 loop : -2.18 (0.18), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 345 HIS 0.006 0.001 HIS B 213 PHE 0.021 0.001 PHE B 101 TYR 0.052 0.002 TYR A 42 ARG 0.006 0.000 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 385) hydrogen bonds : angle 4.88850 ( 1077) metal coordination : bond 0.00355 ( 17) covalent geometry : bond 0.00234 (12131) covalent geometry : angle 0.52657 (16443) *********************** 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 225 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.7287 (tpt) cc_final: 0.7035 (tpp) REVERT: A 99 MET cc_start: 0.7718 (tpp) cc_final: 0.7406 (tpp) REVERT: A 660 ASP cc_start: 0.7413 (m-30) cc_final: 0.7163 (m-30) REVERT: A 690 HIS cc_start: 0.7167 (t-90) cc_final: 0.6839 (m90) REVERT: D 38 HIS cc_start: 0.7060 (t70) cc_final: 0.6761 (t70) REVERT: D 55 ARG cc_start: 0.8040 (mtt-85) cc_final: 0.7638 (mpp80) REVERT: D 85 GLN cc_start: 0.7129 (mt0) cc_final: 0.6359 (mp10) REVERT: D 153 ASP cc_start: 0.7237 (t0) cc_final: 0.6791 (p0) REVERT: D 313 PHE cc_start: 0.7589 (m-80) cc_final: 0.7071 (m-80) REVERT: C 612 GLU cc_start: 0.8601 (tp30) cc_final: 0.8299 (mm-30) REVERT: B 139 VAL cc_start: 0.8253 (t) cc_final: 0.7721 (p) REVERT: B 172 ILE cc_start: 0.9274 (mt) cc_final: 0.8912 (tt) REVERT: B 243 ASP cc_start: 0.8366 (t0) cc_final: 0.8100 (t0) REVERT: B 252 MET cc_start: 0.9437 (tpp) cc_final: 0.8945 (ttt) REVERT: B 271 MET cc_start: 0.9248 (mmt) cc_final: 0.8983 (mmt) REVERT: B 319 ILE cc_start: 0.8785 (mm) cc_final: 0.8423 (mm) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2109 time to fit residues: 71.1240 Evaluate side-chains 161 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 106 optimal weight: 0.0060 chunk 127 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 HIS D 272 HIS D 277 ASN ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 HIS ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.127829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.097363 restraints weight = 30254.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.098817 restraints weight = 17146.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.099447 restraints weight = 12569.049| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.6003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12148 Z= 0.169 Angle : 0.605 7.390 16443 Z= 0.322 Chirality : 0.046 0.228 1815 Planarity : 0.004 0.040 2118 Dihedral : 4.630 24.362 1617 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.21), residues: 1484 helix: 0.49 (0.31), residues: 284 sheet: -1.35 (0.27), residues: 355 loop : -1.85 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 345 HIS 0.006 0.001 HIS B 213 PHE 0.027 0.002 PHE B 101 TYR 0.034 0.002 TYR A 42 ARG 0.009 0.001 ARG C 473 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 385) hydrogen bonds : angle 5.01129 ( 1077) metal coordination : bond 0.00736 ( 17) covalent geometry : bond 0.00374 (12131) covalent geometry : angle 0.60497 (16443) *********************** 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 189 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.7374 (tpt) cc_final: 0.7134 (tpp) REVERT: A 553 ASP cc_start: 0.8312 (t0) cc_final: 0.8081 (t70) REVERT: A 660 ASP cc_start: 0.7844 (m-30) cc_final: 0.7507 (m-30) REVERT: A 690 HIS cc_start: 0.7079 (t70) cc_final: 0.6790 (m90) REVERT: D 19 GLU cc_start: 0.7257 (mm-30) cc_final: 0.7047 (mm-30) REVERT: D 20 GLU cc_start: 0.8300 (tp30) cc_final: 0.8000 (tp30) REVERT: C 84 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7646 (tm-30) REVERT: C 441 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7567 (tm-30) REVERT: C 612 GLU cc_start: 0.8731 (tp30) cc_final: 0.8317 (tp30) REVERT: B 172 ILE cc_start: 0.9300 (mt) cc_final: 0.8886 (tt) REVERT: B 243 ASP cc_start: 0.8284 (t0) cc_final: 0.8061 (t0) REVERT: B 252 MET cc_start: 0.9331 (tpp) cc_final: 0.8764 (ttt) REVERT: B 377 LEU cc_start: 0.8315 (tt) cc_final: 0.8105 (tt) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2096 time to fit residues: 60.4452 Evaluate side-chains 146 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 52 optimal weight: 0.0970 chunk 4 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 272 HIS ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.128137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.097965 restraints weight = 30013.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.099335 restraints weight = 17311.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.100113 restraints weight = 12812.890| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.6211 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= 0.119 Angle : 0.538 7.030 16443 Z= 0.285 Chirality : 0.044 0.198 1815 Planarity : 0.003 0.035 2118 Dihedral : 4.398 23.728 1617 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.21), residues: 1484 helix: 0.68 (0.31), residues: 286 sheet: -0.84 (0.28), residues: 340 loop : -1.82 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 345 HIS 0.007 0.001 HIS B 213 PHE 0.019 0.001 PHE A 46 TYR 0.025 0.001 TYR A 42 ARG 0.003 0.000 ARG B 120 Details of bonding type rmsd hydrogen bonds : bond 0.03274 ( 385) hydrogen bonds : angle 4.80592 ( 1077) metal coordination : bond 0.00567 ( 17) covalent geometry : bond 0.00268 (12131) covalent geometry : angle 0.53789 (16443) *********************** 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 181 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.7366 (tpt) cc_final: 0.7012 (tpp) REVERT: A 586 CYS cc_start: 0.5828 (m) cc_final: 0.5587 (m) REVERT: A 660 ASP cc_start: 0.7975 (m-30) cc_final: 0.7613 (m-30) REVERT: D 179 GLU cc_start: 0.6718 (pt0) cc_final: 0.6297 (pm20) REVERT: D 253 MET cc_start: 0.7857 (pmm) cc_final: 0.7594 (pmm) REVERT: D 373 HIS cc_start: 0.6639 (m-70) cc_final: 0.6431 (m-70) REVERT: C 84 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7496 (tm-30) REVERT: C 594 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7235 (tm-30) REVERT: C 612 GLU cc_start: 0.8612 (tp30) cc_final: 0.8108 (tp30) REVERT: B 172 ILE cc_start: 0.9305 (mt) cc_final: 0.8899 (tt) REVERT: B 243 ASP cc_start: 0.8311 (t0) cc_final: 0.8082 (t0) REVERT: B 252 MET cc_start: 0.9369 (tpp) cc_final: 0.9012 (ttm) REVERT: B 271 MET cc_start: 0.9301 (mmt) cc_final: 0.9067 (mmt) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1891 time to fit residues: 53.9944 Evaluate side-chains 153 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 1 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 HIS D 71 HIS ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 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 = 0.127393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.097286 restraints weight = 29941.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.098683 restraints weight = 17790.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.099990 restraints weight = 12390.142| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.6487 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= 0.125 Angle : 0.539 6.973 16443 Z= 0.287 Chirality : 0.045 0.186 1815 Planarity : 0.003 0.034 2118 Dihedral : 4.354 24.352 1617 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.21), residues: 1484 helix: 0.60 (0.31), residues: 288 sheet: -0.75 (0.29), residues: 336 loop : -1.69 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 345 HIS 0.009 0.001 HIS B 213 PHE 0.021 0.001 PHE A 312 TYR 0.022 0.001 TYR A 42 ARG 0.006 0.000 ARG C 473 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 385) hydrogen bonds : angle 4.72497 ( 1077) metal coordination : bond 0.00565 ( 17) covalent geometry : bond 0.00280 (12131) covalent geometry : angle 0.53916 (16443) *********************** 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 175 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.7186 (tpt) cc_final: 0.6842 (tpp) REVERT: A 660 ASP cc_start: 0.7910 (m-30) cc_final: 0.7572 (m-30) REVERT: D 179 GLU cc_start: 0.6542 (pt0) cc_final: 0.6122 (pm20) REVERT: D 253 MET cc_start: 0.7876 (pmm) cc_final: 0.7569 (pmm) REVERT: C 84 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7592 (tm-30) REVERT: C 612 GLU cc_start: 0.8609 (tp30) cc_final: 0.8178 (tp30) REVERT: B 172 ILE cc_start: 0.9309 (mt) cc_final: 0.8923 (tt) REVERT: B 243 ASP cc_start: 0.8346 (t0) cc_final: 0.8035 (t0) REVERT: B 252 MET cc_start: 0.9406 (tpp) cc_final: 0.8959 (ttt) REVERT: B 271 MET cc_start: 0.9403 (mmt) cc_final: 0.9163 (mmt) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1858 time to fit residues: 51.2106 Evaluate side-chains 141 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 65 optimal weight: 0.4980 chunk 83 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 GLN ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.126386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.096956 restraints weight = 29917.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.098071 restraints weight = 18025.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.098823 restraints weight = 13391.266| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.6795 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= 0.149 Angle : 0.576 6.898 16443 Z= 0.304 Chirality : 0.045 0.174 1815 Planarity : 0.003 0.034 2118 Dihedral : 4.493 25.961 1617 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.08 % Allowed : 1.29 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.21), residues: 1484 helix: 0.57 (0.31), residues: 288 sheet: -0.74 (0.27), residues: 369 loop : -1.70 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 345 HIS 0.007 0.001 HIS B 213 PHE 0.020 0.002 PHE A 46 TYR 0.020 0.002 TYR A 42 ARG 0.004 0.000 ARG B 269 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 385) hydrogen bonds : angle 4.76977 ( 1077) metal coordination : bond 0.00698 ( 17) covalent geometry : bond 0.00334 (12131) covalent geometry : angle 0.57576 (16443) *********************** 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 186 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 1.338 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 97 MET cc_start: 0.7270 (tpt) cc_final: 0.6955 (tpp) REVERT: A 653 ASP cc_start: 0.8426 (t70) cc_final: 0.8200 (t0) REVERT: A 660 ASP cc_start: 0.7980 (m-30) cc_final: 0.7670 (m-30) REVERT: D 150 LEU cc_start: 0.7040 (pt) cc_final: 0.6813 (pt) REVERT: D 179 GLU cc_start: 0.6361 (pt0) cc_final: 0.6028 (pm20) REVERT: D 253 MET cc_start: 0.7884 (pmm) cc_final: 0.7623 (pmm) REVERT: D 256 ASP cc_start: 0.7134 (t0) cc_final: 0.6886 (t0) REVERT: C 84 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7638 (tm-30) REVERT: C 118 MET cc_start: 0.7924 (tpp) cc_final: 0.7275 (tpt) REVERT: C 612 GLU cc_start: 0.8909 (tp30) cc_final: 0.8505 (tp30) REVERT: B 172 ILE cc_start: 0.9328 (mt) cc_final: 0.8924 (tt) REVERT: B 243 ASP cc_start: 0.8301 (t0) cc_final: 0.8060 (t0) REVERT: B 252 MET cc_start: 0.9313 (tpp) cc_final: 0.9014 (ttt) REVERT: B 389 TRP cc_start: 0.8485 (m-90) cc_final: 0.8091 (m-10) outliers start: 1 outliers final: 1 residues processed: 185 average time/residue: 0.2005 time to fit residues: 56.6655 Evaluate side-chains 141 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 0.2980 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 0.0370 chunk 82 optimal weight: 40.0000 chunk 90 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 272 HIS ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 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 = 0.3900 r_free = 0.3900 target = 0.127860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.096920 restraints weight = 29542.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.099299 restraints weight = 17141.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.100897 restraints weight = 11750.625| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.6868 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= 0.108 Angle : 0.552 8.782 16443 Z= 0.289 Chirality : 0.044 0.193 1815 Planarity : 0.003 0.033 2118 Dihedral : 4.327 23.147 1617 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.21), residues: 1484 helix: 0.64 (0.31), residues: 289 sheet: -0.43 (0.28), residues: 342 loop : -1.64 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 345 HIS 0.007 0.001 HIS B 213 PHE 0.034 0.001 PHE B 296 TYR 0.020 0.001 TYR A 42 ARG 0.004 0.000 ARG B 120 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 385) hydrogen bonds : angle 4.63810 ( 1077) metal coordination : bond 0.00475 ( 17) covalent geometry : bond 0.00243 (12131) covalent geometry : angle 0.55185 (16443) *********************** 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 185 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.352 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 97 MET cc_start: 0.7163 (tpt) cc_final: 0.6850 (tpp) REVERT: A 660 ASP cc_start: 0.7905 (m-30) cc_final: 0.7600 (m-30) REVERT: D 38 HIS cc_start: 0.6750 (t70) cc_final: 0.6486 (t70) REVERT: D 179 GLU cc_start: 0.6538 (pt0) cc_final: 0.6209 (pm20) REVERT: D 253 MET cc_start: 0.7933 (pmm) cc_final: 0.7627 (pmm) REVERT: D 319 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8213 (mp0) REVERT: C 84 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7595 (tm-30) REVERT: C 612 GLU cc_start: 0.8693 (tp30) cc_final: 0.8272 (tp30) REVERT: C 614 MET cc_start: 0.9186 (tpp) cc_final: 0.8882 (mmm) REVERT: B 172 ILE cc_start: 0.9316 (mt) cc_final: 0.8922 (tt) REVERT: B 243 ASP cc_start: 0.8244 (t0) cc_final: 0.7879 (t0) REVERT: B 252 MET cc_start: 0.9205 (tpp) cc_final: 0.8935 (ttt) REVERT: B 319 ILE cc_start: 0.8930 (mm) cc_final: 0.8629 (mm) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1891 time to fit residues: 54.9602 Evaluate side-chains 146 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 49 optimal weight: 0.0980 chunk 83 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 92 optimal weight: 20.0000 chunk 2 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 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 = 0.3847 r_free = 0.3847 target = 0.124102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.093670 restraints weight = 29740.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.095182 restraints weight = 17291.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.095835 restraints weight = 12019.712| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.7316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12148 Z= 0.195 Angle : 0.642 8.909 16443 Z= 0.338 Chirality : 0.046 0.186 1815 Planarity : 0.004 0.039 2118 Dihedral : 4.834 29.176 1617 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.21), residues: 1484 helix: 0.51 (0.31), residues: 287 sheet: -0.61 (0.27), residues: 383 loop : -1.72 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 345 HIS 0.007 0.001 HIS B 213 PHE 0.031 0.002 PHE B 296 TYR 0.019 0.002 TYR A 42 ARG 0.007 0.001 ARG B 120 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 385) hydrogen bonds : angle 5.02043 ( 1077) metal coordination : bond 0.00873 ( 17) covalent geometry : bond 0.00441 (12131) covalent geometry : angle 0.64208 (16443) ********************** 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 168 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 38 HIS cc_start: 0.6846 (t70) cc_final: 0.6627 (t70) REVERT: D 179 GLU cc_start: 0.6577 (pt0) cc_final: 0.6249 (pm20) REVERT: D 253 MET cc_start: 0.7947 (pmm) cc_final: 0.7581 (pmm) REVERT: D 319 GLU cc_start: 0.8532 (mt-10) cc_final: 0.7959 (tt0) REVERT: C 84 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7752 (tm-30) REVERT: C 612 GLU cc_start: 0.8850 (tp30) cc_final: 0.8629 (tp30) REVERT: B 172 ILE cc_start: 0.9336 (mt) cc_final: 0.8927 (tt) REVERT: B 243 ASP cc_start: 0.8374 (t0) cc_final: 0.8137 (t0) REVERT: B 252 MET cc_start: 0.9304 (tpp) cc_final: 0.8908 (ttt) REVERT: B 265 ILE cc_start: 0.9096 (pt) cc_final: 0.8847 (pt) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1940 time to fit residues: 51.1952 Evaluate side-chains 135 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 17 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 87 optimal weight: 0.0970 chunk 28 optimal weight: 0.3980 chunk 90 optimal weight: 0.0470 chunk 15 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 HIS D 370 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.127401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.095711 restraints weight = 29450.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.098168 restraints weight = 16729.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.099805 restraints weight = 11353.637| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.7273 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= 0.105 Angle : 0.567 10.369 16443 Z= 0.295 Chirality : 0.044 0.181 1815 Planarity : 0.003 0.037 2118 Dihedral : 4.424 24.871 1617 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.21), residues: 1484 helix: 0.68 (0.31), residues: 289 sheet: -0.29 (0.29), residues: 349 loop : -1.57 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 345 HIS 0.006 0.001 HIS B 213 PHE 0.016 0.001 PHE A 46 TYR 0.021 0.001 TYR C 495 ARG 0.003 0.000 ARG C 121 Details of bonding type rmsd hydrogen bonds : bond 0.03161 ( 385) hydrogen bonds : angle 4.66118 ( 1077) metal coordination : bond 0.00365 ( 17) covalent geometry : bond 0.00233 (12131) covalent geometry : angle 0.56687 (16443) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4125.10 seconds wall clock time: 72 minutes 10.12 seconds (4330.12 seconds total)