Starting phenix.real_space_refine on Fri Feb 6 05:58:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mge_48253/02_2026/9mge_48253_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mge_48253/02_2026/9mge_48253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mge_48253/02_2026/9mge_48253_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mge_48253/02_2026/9mge_48253_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mge_48253/02_2026/9mge_48253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mge_48253/02_2026/9mge_48253.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 S 35 5.16 5 C 7333 2.51 5 N 2043 2.21 5 O 2321 1.98 5 H 10953 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22685 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 10588 Classifications: {'peptide': 777} Link IDs: {'PTRANS': 29, 'TRANS': 747} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 582 Unresolved non-hydrogen angles: 846 Unresolved non-hydrogen dihedrals: 350 Unresolved non-hydrogen chiralities: 190 Planarities with less than four sites: {'PHE:plan': 7, 'ASP:plan': 13, 'HIS:plan': 1, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 10, 'ASN:plan1': 6, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 264 Chain: "B" Number of atoms: 5216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 5216 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 344} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 872 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 7, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3419 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1370 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "F" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1189 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 2 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 31 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 4.24, per 1000 atoms: 0.19 Number of scatterers: 22685 At special positions: 0 Unit cell: (105.41, 127.82, 128.65, 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) S 35 16.00 O 2321 8.00 N 2043 7.00 C 7333 6.00 H 10953 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 866.9 milliseconds 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2616 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 17 sheets defined 23.9% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 55 through 70 Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 126 through 145 Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.912A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 233 Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 297 through 315 Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.653A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 391 Processing helix chain 'A' and resid 449 through 452 Processing helix chain 'A' and resid 542 through 552 removed outlier: 4.283A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 729 through 731 No H-bonds generated for 'chain 'A' and resid 729 through 731' Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'C' and resid 31 through 36 removed outlier: 3.681A pdb=" N SER C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 68 through 82 removed outlier: 3.550A pdb=" N LEU D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP D 74 " --> pdb=" O GLN D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.571A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.361A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 242 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 726 through 731 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.512A pdb=" N VAL A 86 " --> pdb=" O HIS A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 99 removed outlier: 5.800A pdb=" N ILE A 94 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU A 165 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N SER A 96 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU A 167 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 5.503A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 274 removed outlier: 4.417A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL A 271 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL A 339 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL A 273 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 341 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 376 removed outlier: 3.736A pdb=" N ALA A 375 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 802 through 806 removed outlier: 3.559A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 536 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 507 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL A 483 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR A 477 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE F 802 " --> pdb=" O TYR A 432 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY F 807 " --> pdb=" O PRO F 782 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 662 through 663 removed outlier: 3.925A pdb=" N GLY A 662 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.577A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.821A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER B 49 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 387 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AB2, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.786A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.637A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.681A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 253 through 254 removed outlier: 6.858A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.544A pdb=" N MET B 306 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.196A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.896A pdb=" N ILE E 32 " --> pdb=" O GLN E 80 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN E 103 " --> pdb=" O THR E 94 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN E 96 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU E 101 " --> pdb=" O ASN E 96 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1563 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: 6.19 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 10952 1.03 - 1.23: 49 1.23 - 1.43: 5202 1.43 - 1.62: 6668 1.62 - 1.82: 67 Bond restraints: 22938 Sorted by residual: bond pdb=" C LEU A 165 " pdb=" O LEU A 165 " ideal model delta sigma weight residual 1.236 1.198 0.037 1.19e-02 7.06e+03 9.93e+00 bond pdb=" N GLU B 352 " pdb=" CA GLU B 352 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.79e+00 bond pdb=" C ARG D 166 " pdb=" O ARG D 166 " ideal model delta sigma weight residual 1.237 1.200 0.036 1.19e-02 7.06e+03 9.40e+00 bond pdb=" N ASN B 287 " pdb=" CA ASN B 287 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.58e+00 bond pdb=" N ILE A 290 " pdb=" CA ILE A 290 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.30e+00 ... (remaining 22933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 39594 1.91 - 3.82: 1224 3.82 - 5.73: 107 5.73 - 7.64: 18 7.64 - 9.55: 5 Bond angle restraints: 40948 Sorted by residual: angle pdb=" CA PRO A 602 " pdb=" N PRO A 602 " pdb=" CD PRO A 602 " ideal model delta sigma weight residual 112.00 105.05 6.95 1.40e+00 5.10e-01 2.46e+01 angle pdb=" N PRO F 779 " pdb=" CA PRO F 779 " pdb=" C PRO F 779 " ideal model delta sigma weight residual 113.86 107.91 5.95 1.25e+00 6.40e-01 2.27e+01 angle pdb=" CA ILE D 35 " pdb=" C ILE D 35 " pdb=" O ILE D 35 " ideal model delta sigma weight residual 121.05 116.14 4.91 1.04e+00 9.25e-01 2.23e+01 angle pdb=" CA VAL D 27 " pdb=" C VAL D 27 " pdb=" N PRO D 28 " ideal model delta sigma weight residual 116.90 123.67 -6.77 1.50e+00 4.44e-01 2.03e+01 angle pdb=" N ASN D 33 " pdb=" CA ASN D 33 " pdb=" C ASN D 33 " ideal model delta sigma weight residual 113.01 107.61 5.40 1.20e+00 6.94e-01 2.03e+01 ... (remaining 40943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 9644 17.94 - 35.88: 790 35.88 - 53.83: 256 53.83 - 71.77: 91 71.77 - 89.71: 16 Dihedral angle restraints: 10797 sinusoidal: 5746 harmonic: 5051 Sorted by residual: dihedral pdb=" CA LYS F 808 " pdb=" C LYS F 808 " pdb=" N THR F 809 " pdb=" CA THR F 809 " ideal model delta harmonic sigma weight residual 180.00 151.91 28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA PRO A 409 " pdb=" C PRO A 409 " pdb=" N ASP A 410 " pdb=" CA ASP A 410 " ideal model delta harmonic sigma weight residual -180.00 -152.07 -27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA TYR A 522 " pdb=" C TYR A 522 " pdb=" N ASN A 523 " pdb=" CA ASN A 523 " ideal model delta harmonic sigma weight residual -180.00 -152.47 -27.53 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 10794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1312 0.057 - 0.114: 290 0.114 - 0.170: 68 0.170 - 0.227: 7 0.227 - 0.284: 3 Chirality restraints: 1680 Sorted by residual: chirality pdb=" CB THR C 70 " pdb=" CA THR C 70 " pdb=" OG1 THR C 70 " pdb=" CG2 THR C 70 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA ILE B 227 " pdb=" N ILE B 227 " pdb=" C ILE B 227 " pdb=" CB ILE B 227 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ILE A 290 " pdb=" N ILE A 290 " pdb=" C ILE A 290 " pdb=" CB ILE A 290 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 1677 not shown) Planarity restraints: 3682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 34 " -0.219 2.00e-02 2.50e+03 4.03e-01 2.43e+03 pdb=" CD GLN C 34 " 0.016 2.00e-02 2.50e+03 pdb=" OE1 GLN C 34 " 0.211 2.00e-02 2.50e+03 pdb=" NE2 GLN C 34 " 0.003 2.00e-02 2.50e+03 pdb="HE21 GLN C 34 " 0.658 2.00e-02 2.50e+03 pdb="HE22 GLN C 34 " -0.668 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 302 " 0.222 2.00e-02 2.50e+03 4.02e-01 2.42e+03 pdb=" CG ASN B 302 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN B 302 " -0.212 2.00e-02 2.50e+03 pdb=" ND2 ASN B 302 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN B 302 " -0.653 2.00e-02 2.50e+03 pdb="HD22 ASN B 302 " 0.668 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 166 " 0.241 9.50e-02 1.11e+02 3.07e-01 1.99e+03 pdb=" NE ARG D 166 " 0.108 2.00e-02 2.50e+03 pdb=" CZ ARG D 166 " 0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG D 166 " 0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG D 166 " -0.049 2.00e-02 2.50e+03 pdb="HH11 ARG D 166 " -0.579 2.00e-02 2.50e+03 pdb="HH12 ARG D 166 " 0.615 2.00e-02 2.50e+03 pdb="HH21 ARG D 166 " 0.075 2.00e-02 2.50e+03 pdb="HH22 ARG D 166 " -0.238 2.00e-02 2.50e+03 ... (remaining 3679 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 932 2.15 - 2.76: 41061 2.76 - 3.38: 61910 3.38 - 3.99: 77887 3.99 - 4.60: 120673 Nonbonded interactions: 302463 Sorted by model distance: nonbonded pdb="HD22 ASN A 422 " pdb=" O TRP F 810 " model vdw 1.539 2.450 nonbonded pdb=" HG SER A 680 " pdb=" OE1 GLU A 689 " model vdw 1.557 2.450 nonbonded pdb=" OD1 ASN A 731 " pdb=" HG SER A 732 " model vdw 1.581 2.450 nonbonded pdb=" HG SER A 360 " pdb=" OE2 GLU A 420 " model vdw 1.612 2.450 nonbonded pdb=" O ARG A 661 " pdb=" HG SER A 769 " model vdw 1.633 2.450 ... (remaining 302458 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.160 Extract box with map and model: 0.360 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 24.180 Find NCS groups from input model: 0.090 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 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 : 0.005 0.066 11986 Z= 0.263 Angle : 0.934 8.729 16234 Z= 0.564 Chirality : 0.052 0.284 1680 Planarity : 0.009 0.128 2186 Dihedral : 15.079 89.708 4227 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 1.10 % Allowed : 14.70 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.20), residues: 1553 helix: -0.65 (0.24), residues: 337 sheet: 0.12 (0.23), residues: 457 loop : -1.40 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.003 ARG A 200 TYR 0.041 0.005 TYR A 754 PHE 0.025 0.003 PHE F 804 TRP 0.022 0.004 TRP B 143 HIS 0.010 0.003 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00455 (11985) covalent geometry : angle 0.93420 (16232) SS BOND : bond 0.00152 ( 1) SS BOND : angle 1.22130 ( 2) hydrogen bonds : bond 0.18187 ( 560) hydrogen bonds : angle 8.10529 ( 1563) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue TYR 688 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Evaluate side-chains 262 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 249 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 TYR cc_start: 0.8733 (t80) cc_final: 0.8492 (t80) REVERT: A 232 ASP cc_start: 0.8716 (t0) cc_final: 0.8418 (m-30) REVERT: A 303 LYS cc_start: 0.8384 (tmtt) cc_final: 0.8174 (tptp) REVERT: B 300 ASP cc_start: 0.7357 (t0) cc_final: 0.7127 (t0) REVERT: E 54 GLN cc_start: 0.8389 (mt0) cc_final: 0.8116 (mt0) outliers start: 13 outliers final: 4 residues processed: 255 average time/residue: 0.2499 time to fit residues: 91.1450 Evaluate side-chains 220 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 216 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain F residue 720 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 GLN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN D 209 GLN E 33 ASN E 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.189125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.130998 restraints weight = 38547.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.135876 restraints weight = 20079.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138882 restraints weight = 13691.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.140902 restraints weight = 10929.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141904 restraints weight = 9559.110| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11986 Z= 0.278 Angle : 0.692 6.669 16234 Z= 0.385 Chirality : 0.047 0.179 1680 Planarity : 0.005 0.064 2186 Dihedral : 6.536 52.695 1719 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.04 % Allowed : 15.80 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.20), residues: 1553 helix: 0.90 (0.27), residues: 335 sheet: -0.16 (0.22), residues: 460 loop : -1.19 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 421 TYR 0.017 0.002 TYR A 618 PHE 0.020 0.002 PHE A 517 TRP 0.018 0.002 TRP A 745 HIS 0.005 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00605 (11985) covalent geometry : angle 0.69218 (16232) SS BOND : bond 0.00052 ( 1) SS BOND : angle 0.62368 ( 2) hydrogen bonds : bond 0.04936 ( 560) hydrogen bonds : angle 5.71840 ( 1563) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue TYR 688 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Evaluate side-chains 245 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.7864 (p90) cc_final: 0.7331 (p90) REVERT: B 42 PHE cc_start: 0.6326 (OUTLIER) cc_final: 0.4579 (m-80) outliers start: 24 outliers final: 14 residues processed: 239 average time/residue: 0.2375 time to fit residues: 81.9930 Evaluate side-chains 206 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain F residue 720 THR Chi-restraints excluded: chain F residue 726 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 14 optimal weight: 50.0000 chunk 119 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 55 optimal weight: 0.0970 chunk 142 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 GLN B 223 GLN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.192312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.147985 restraints weight = 37983.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.138321 restraints weight = 23019.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.142255 restraints weight = 14401.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.144425 restraints weight = 10919.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.145621 restraints weight = 9347.712| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11986 Z= 0.135 Angle : 0.567 6.293 16234 Z= 0.308 Chirality : 0.043 0.165 1680 Planarity : 0.004 0.052 2186 Dihedral : 5.365 26.142 1712 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.61 % Allowed : 16.23 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.21), residues: 1553 helix: 1.75 (0.28), residues: 335 sheet: -0.03 (0.22), residues: 468 loop : -0.98 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 273 TYR 0.015 0.001 TYR B 123 PHE 0.011 0.001 PHE A 426 TRP 0.010 0.001 TRP A 449 HIS 0.004 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00288 (11985) covalent geometry : angle 0.56733 (16232) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.70094 ( 2) hydrogen bonds : bond 0.03589 ( 560) hydrogen bonds : angle 5.06687 ( 1563) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue TYR 688 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LYS cc_start: 0.8497 (tmtt) cc_final: 0.8210 (tptp) REVERT: A 754 TYR cc_start: 0.7560 (m-80) cc_final: 0.7280 (m-80) REVERT: B 42 PHE cc_start: 0.6293 (OUTLIER) cc_final: 0.4578 (m-80) REVERT: B 63 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8005 (tt) REVERT: B 123 TYR cc_start: 0.7631 (m-10) cc_final: 0.7385 (m-10) REVERT: B 146 LYS cc_start: 0.9277 (ttmt) cc_final: 0.9042 (tttm) REVERT: B 213 ASN cc_start: 0.7407 (t0) cc_final: 0.7200 (t0) REVERT: D 84 ASP cc_start: 0.8197 (t0) cc_final: 0.7873 (t70) outliers start: 19 outliers final: 14 residues processed: 217 average time/residue: 0.2419 time to fit residues: 76.2108 Evaluate side-chains 202 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain F residue 720 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 50.0000 chunk 19 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 6 optimal weight: 50.0000 chunk 100 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.185684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 125)---------------| | r_work = 0.3668 r_free = 0.3668 target = 0.129000 restraints weight = 38558.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.132178 restraints weight = 19046.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.133344 restraints weight = 15668.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.133759 restraints weight = 12754.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.134483 restraints weight = 12453.278| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 11986 Z= 0.268 Angle : 0.620 6.220 16234 Z= 0.340 Chirality : 0.045 0.165 1680 Planarity : 0.004 0.046 2186 Dihedral : 5.385 28.396 1712 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.14 % Allowed : 16.31 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.21), residues: 1553 helix: 1.84 (0.28), residues: 341 sheet: -0.32 (0.23), residues: 471 loop : -1.06 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 767 TYR 0.020 0.002 TYR D 79 PHE 0.017 0.002 PHE A 517 TRP 0.013 0.001 TRP A 745 HIS 0.005 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00585 (11985) covalent geometry : angle 0.61983 (16232) SS BOND : bond 0.00099 ( 1) SS BOND : angle 0.58952 ( 2) hydrogen bonds : bond 0.03761 ( 560) hydrogen bonds : angle 5.18817 ( 1563) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue TYR 688 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 754 TYR cc_start: 0.7769 (m-80) cc_final: 0.7514 (m-80) REVERT: B 42 PHE cc_start: 0.6460 (OUTLIER) cc_final: 0.4756 (m-80) REVERT: B 63 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8165 (tt) REVERT: B 76 ASP cc_start: 0.6374 (t0) cc_final: 0.6064 (t0) REVERT: D 67 TYR cc_start: 0.7722 (m-80) cc_final: 0.7416 (m-80) REVERT: D 84 ASP cc_start: 0.8335 (t0) cc_final: 0.7954 (t70) REVERT: E 84 GLU cc_start: 0.4974 (mm-30) cc_final: 0.4757 (mm-30) outliers start: 37 outliers final: 28 residues processed: 219 average time/residue: 0.2458 time to fit residues: 76.8633 Evaluate side-chains 215 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 720 THR Chi-restraints excluded: chain F residue 744 VAL Chi-restraints excluded: chain F residue 778 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 141 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 117 optimal weight: 0.3980 chunk 96 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 140 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.186558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.134569 restraints weight = 37968.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.137171 restraints weight = 33909.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.142094 restraints weight = 19205.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.141237 restraints weight = 14736.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141531 restraints weight = 12508.325| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11986 Z= 0.124 Angle : 0.535 6.361 16234 Z= 0.287 Chirality : 0.043 0.160 1680 Planarity : 0.004 0.075 2186 Dihedral : 4.980 23.752 1712 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.29 % Allowed : 16.82 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.22), residues: 1553 helix: 2.18 (0.29), residues: 338 sheet: -0.30 (0.23), residues: 469 loop : -0.88 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 152 TYR 0.019 0.001 TYR B 123 PHE 0.015 0.001 PHE A 804 TRP 0.008 0.001 TRP A 449 HIS 0.003 0.001 HIS B 121 Details of bonding type rmsd covalent geometry : bond 0.00267 (11985) covalent geometry : angle 0.53527 (16232) SS BOND : bond 0.00078 ( 1) SS BOND : angle 0.54867 ( 2) hydrogen bonds : bond 0.03097 ( 560) hydrogen bonds : angle 4.76078 ( 1563) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue TYR 688 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 754 TYR cc_start: 0.7814 (m-80) cc_final: 0.7558 (m-80) REVERT: B 42 PHE cc_start: 0.6350 (OUTLIER) cc_final: 0.4708 (m-80) REVERT: B 63 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8181 (tt) REVERT: B 76 ASP cc_start: 0.6425 (t0) cc_final: 0.6131 (t0) REVERT: B 146 LYS cc_start: 0.9314 (ttmt) cc_final: 0.9090 (tttm) REVERT: B 213 ASN cc_start: 0.7032 (t0) cc_final: 0.6751 (t0) REVERT: D 84 ASP cc_start: 0.8300 (t0) cc_final: 0.7910 (t0) outliers start: 27 outliers final: 20 residues processed: 214 average time/residue: 0.2480 time to fit residues: 74.3979 Evaluate side-chains 207 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 720 THR Chi-restraints excluded: chain F residue 778 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 129 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.189312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 122)---------------| | r_work = 0.3732 r_free = 0.3732 target = 0.131510 restraints weight = 38181.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.135930 restraints weight = 19853.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.138545 restraints weight = 13826.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.140437 restraints weight = 11240.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.141117 restraints weight = 9873.899| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11986 Z= 0.246 Angle : 0.591 6.136 16234 Z= 0.322 Chirality : 0.044 0.160 1680 Planarity : 0.004 0.064 2186 Dihedral : 5.100 27.981 1712 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.14 % Allowed : 17.93 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.22), residues: 1553 helix: 2.06 (0.28), residues: 344 sheet: -0.50 (0.23), residues: 482 loop : -0.94 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 152 TYR 0.019 0.002 TYR A 649 PHE 0.017 0.002 PHE A 517 TRP 0.011 0.001 TRP A 745 HIS 0.004 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00536 (11985) covalent geometry : angle 0.59080 (16232) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.43263 ( 2) hydrogen bonds : bond 0.03521 ( 560) hydrogen bonds : angle 5.00615 ( 1563) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue TYR 688 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LYS cc_start: 0.8456 (tmtt) cc_final: 0.8121 (tptp) REVERT: A 488 ARG cc_start: 0.8078 (ttt-90) cc_final: 0.7716 (ttt90) REVERT: B 42 PHE cc_start: 0.6492 (OUTLIER) cc_final: 0.4865 (m-80) REVERT: D 84 ASP cc_start: 0.8255 (t0) cc_final: 0.7870 (t70) REVERT: D 205 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.8763 (m-10) outliers start: 37 outliers final: 31 residues processed: 211 average time/residue: 0.2462 time to fit residues: 74.1555 Evaluate side-chains 213 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 720 THR Chi-restraints excluded: chain F residue 744 VAL Chi-restraints excluded: chain F residue 778 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 47 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 9 optimal weight: 30.0000 chunk 4 optimal weight: 0.0470 chunk 134 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.193238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.140591 restraints weight = 37788.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.143332 restraints weight = 32606.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.147282 restraints weight = 18385.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.147086 restraints weight = 14592.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.147322 restraints weight = 12599.497| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11986 Z= 0.110 Angle : 0.524 6.040 16234 Z= 0.281 Chirality : 0.043 0.156 1680 Planarity : 0.004 0.058 2186 Dihedral : 4.773 32.455 1712 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.87 % Allowed : 19.29 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.22), residues: 1553 helix: 2.40 (0.29), residues: 343 sheet: -0.37 (0.23), residues: 480 loop : -0.80 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 152 TYR 0.017 0.001 TYR B 60 PHE 0.013 0.001 PHE A 804 TRP 0.007 0.001 TRP A 449 HIS 0.002 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00238 (11985) covalent geometry : angle 0.52409 (16232) SS BOND : bond 0.00100 ( 1) SS BOND : angle 0.49137 ( 2) hydrogen bonds : bond 0.02941 ( 560) hydrogen bonds : angle 4.59784 ( 1563) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue TYR 688 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 PHE cc_start: 0.6419 (OUTLIER) cc_final: 0.4854 (m-80) REVERT: B 76 ASP cc_start: 0.6504 (t0) cc_final: 0.6239 (t0) REVERT: B 146 LYS cc_start: 0.9345 (ttmt) cc_final: 0.9107 (tttm) REVERT: D 84 ASP cc_start: 0.8187 (t0) cc_final: 0.7982 (t70) outliers start: 22 outliers final: 18 residues processed: 212 average time/residue: 0.2463 time to fit residues: 74.7251 Evaluate side-chains 205 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain F residue 720 THR Chi-restraints excluded: chain F residue 778 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 13 optimal weight: 0.0970 chunk 98 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 0 optimal weight: 70.0000 chunk 106 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 4 optimal weight: 50.0000 chunk 136 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.191488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3737 r_free = 0.3737 target = 0.132224 restraints weight = 37970.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.137021 restraints weight = 19739.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.140167 restraints weight = 13186.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.142304 restraints weight = 10474.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.143219 restraints weight = 9080.690| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11986 Z= 0.140 Angle : 0.529 6.028 16234 Z= 0.284 Chirality : 0.043 0.155 1680 Planarity : 0.004 0.072 2186 Dihedral : 4.694 32.166 1712 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.21 % Allowed : 19.12 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.22), residues: 1553 helix: 2.51 (0.29), residues: 340 sheet: -0.36 (0.23), residues: 477 loop : -0.73 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 152 TYR 0.020 0.001 TYR A 649 PHE 0.020 0.001 PHE F 724 TRP 0.007 0.001 TRP A 449 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00304 (11985) covalent geometry : angle 0.52866 (16232) SS BOND : bond 0.00091 ( 1) SS BOND : angle 0.42422 ( 2) hydrogen bonds : bond 0.02981 ( 560) hydrogen bonds : angle 4.58002 ( 1563) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue TYR 688 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 PHE cc_start: 0.6393 (OUTLIER) cc_final: 0.4836 (m-80) REVERT: B 76 ASP cc_start: 0.6604 (t0) cc_final: 0.6345 (t0) REVERT: B 146 LYS cc_start: 0.9365 (ttmt) cc_final: 0.9118 (tttm) outliers start: 26 outliers final: 24 residues processed: 204 average time/residue: 0.2513 time to fit residues: 73.4525 Evaluate side-chains 207 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain F residue 720 THR Chi-restraints excluded: chain F residue 778 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 76 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 113 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN E 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.193914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3776 r_free = 0.3776 target = 0.135309 restraints weight = 37894.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.139890 restraints weight = 19666.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.143134 restraints weight = 13016.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.145183 restraints weight = 10292.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.146467 restraints weight = 8970.622| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11986 Z= 0.111 Angle : 0.517 5.997 16234 Z= 0.276 Chirality : 0.043 0.180 1680 Planarity : 0.004 0.069 2186 Dihedral : 4.532 33.308 1712 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.70 % Allowed : 19.80 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.22), residues: 1553 helix: 2.61 (0.29), residues: 340 sheet: -0.32 (0.23), residues: 481 loop : -0.67 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 152 TYR 0.031 0.001 TYR B 123 PHE 0.015 0.001 PHE A 804 TRP 0.008 0.001 TRP A 776 HIS 0.002 0.000 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00247 (11985) covalent geometry : angle 0.51716 (16232) SS BOND : bond 0.00066 ( 1) SS BOND : angle 0.41868 ( 2) hydrogen bonds : bond 0.02829 ( 560) hydrogen bonds : angle 4.43953 ( 1563) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue TYR 688 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LYS cc_start: 0.8420 (tmtt) cc_final: 0.8219 (tptp) REVERT: B 42 PHE cc_start: 0.6513 (OUTLIER) cc_final: 0.5003 (m-80) REVERT: B 76 ASP cc_start: 0.6606 (t0) cc_final: 0.6345 (t0) REVERT: B 146 LYS cc_start: 0.9384 (ttmt) cc_final: 0.9182 (tttm) REVERT: B 278 MET cc_start: 0.8264 (mtp) cc_final: 0.8020 (mtm) REVERT: D 67 TYR cc_start: 0.7506 (m-80) cc_final: 0.6942 (m-80) REVERT: D 85 LEU cc_start: 0.8577 (mt) cc_final: 0.8225 (mt) outliers start: 20 outliers final: 18 residues processed: 207 average time/residue: 0.2428 time to fit residues: 72.8243 Evaluate side-chains 208 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain F residue 720 THR Chi-restraints excluded: chain F residue 778 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 126 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 131 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 HIS F 801 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.190199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 142)---------------| | r_work = 0.3741 r_free = 0.3741 target = 0.132468 restraints weight = 38100.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.136059 restraints weight = 20679.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.138943 restraints weight = 14036.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.140996 restraints weight = 11189.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141999 restraints weight = 9762.045| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11986 Z= 0.206 Angle : 0.565 6.031 16234 Z= 0.306 Chirality : 0.044 0.154 1680 Planarity : 0.004 0.074 2186 Dihedral : 4.732 35.394 1712 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.95 % Allowed : 19.80 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.22), residues: 1553 helix: 2.42 (0.28), residues: 341 sheet: -0.41 (0.23), residues: 485 loop : -0.75 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 152 TYR 0.032 0.002 TYR B 123 PHE 0.021 0.002 PHE F 724 TRP 0.010 0.001 TRP A 745 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00449 (11985) covalent geometry : angle 0.56524 (16232) SS BOND : bond 0.00139 ( 1) SS BOND : angle 0.41204 ( 2) hydrogen bonds : bond 0.03228 ( 560) hydrogen bonds : angle 4.73250 ( 1563) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3106 Ramachandran restraints generated. 1553 Oldfield, 0 Emsley, 1553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue TYR 688 is missing expected H atoms. Skipping. Residue SER 25 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LYS cc_start: 0.8364 (tmtt) cc_final: 0.8121 (tptp) REVERT: A 488 ARG cc_start: 0.8095 (ttt-90) cc_final: 0.7757 (ttt90) REVERT: B 42 PHE cc_start: 0.6541 (OUTLIER) cc_final: 0.5015 (m-80) REVERT: B 76 ASP cc_start: 0.6642 (t0) cc_final: 0.6371 (t0) REVERT: B 146 LYS cc_start: 0.9390 (ttmt) cc_final: 0.9182 (tttm) REVERT: D 85 LEU cc_start: 0.8711 (mt) cc_final: 0.8402 (mt) outliers start: 23 outliers final: 21 residues processed: 208 average time/residue: 0.2445 time to fit residues: 72.7532 Evaluate side-chains 210 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain F residue 720 THR Chi-restraints excluded: chain F residue 778 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 118 optimal weight: 0.4980 chunk 14 optimal weight: 50.0000 chunk 22 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.192196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.3764 r_free = 0.3764 target = 0.134194 restraints weight = 37854.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.138681 restraints weight = 19867.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 77)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141493 restraints weight = 13583.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.143098 restraints weight = 10868.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.144489 restraints weight = 9538.513| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11986 Z= 0.148 Angle : 0.541 7.471 16234 Z= 0.289 Chirality : 0.043 0.154 1680 Planarity : 0.004 0.076 2186 Dihedral : 4.632 36.881 1712 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.87 % Allowed : 20.22 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.22), residues: 1553 helix: 2.50 (0.29), residues: 344 sheet: -0.40 (0.23), residues: 482 loop : -0.71 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 152 TYR 0.032 0.001 TYR B 123 PHE 0.014 0.001 PHE A 804 TRP 0.009 0.001 TRP A 449 HIS 0.004 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00320 (11985) covalent geometry : angle 0.54146 (16232) SS BOND : bond 0.00116 ( 1) SS BOND : angle 0.37123 ( 2) hydrogen bonds : bond 0.03022 ( 560) hydrogen bonds : angle 4.60123 ( 1563) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4875.55 seconds wall clock time: 83 minutes 40.18 seconds (5020.18 seconds total)