Starting phenix.real_space_refine on Fri May 16 12:17:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rl5_19331/05_2025/8rl5_19331.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rl5_19331/05_2025/8rl5_19331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rl5_19331/05_2025/8rl5_19331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rl5_19331/05_2025/8rl5_19331.map" model { file = "/net/cci-nas-00/data/ceres_data/8rl5_19331/05_2025/8rl5_19331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rl5_19331/05_2025/8rl5_19331.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 53 5.16 5 C 4792 2.51 5 N 1346 2.21 5 O 1467 1.98 5 H 6713 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14373 Number of models: 1 Model: "" Number of chains: 6 Chain: "K" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1701 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "L" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1622 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 5566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 5566 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 17, 'TRANS': 415} Chain breaks: 2 Unresolved non-hydrogen bonds: 425 Unresolved non-hydrogen angles: 525 Unresolved non-hydrogen dihedrals: 347 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 227 Chain: "B" Number of atoms: 5482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 5482 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 17, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 458 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 380 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 260 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8428 SG CYS A 411 25.416 111.963 41.952 1.00156.67 S ATOM 8646 SG CYS A 427 22.490 111.340 44.298 1.00163.91 S ATOM 8680 SG CYS A 431 23.359 114.886 43.089 1.00169.16 S ATOM 8709 SG CYS A 434 21.816 112.383 40.704 1.00181.72 S ATOM 13878 SG CYS B 411 58.454 40.518 39.928 1.00142.59 S ATOM 14069 SG CYS B 427 59.754 41.620 43.474 1.00154.62 S ATOM 14103 SG CYS B 431 59.563 37.965 42.457 1.00149.97 S ATOM 14137 SG CYS B 434 62.052 40.363 40.766 1.00164.84 S Time building chain proxies: 8.11, per 1000 atoms: 0.56 Number of scatterers: 14373 At special positions: 0 Unit cell: (84.7, 153.3, 92.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 53 16.00 O 1467 8.00 N 1346 7.00 C 4792 6.00 H 6713 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS K 11 " - pdb=" SG CYS L 11 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 95 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 272 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 272 " 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: 3.85 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 411 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 431 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 434 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 427 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 434 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 427 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 431 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 411 " Number of angles added : 12 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 10 sheets defined 45.4% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'K' and resid 60 through 66 Processing helix chain 'L' and resid 60 through 66 Processing helix chain 'A' and resid 13 through 24 Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 57 through 69 removed outlier: 4.021A pdb=" N CYS A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 105 through 118 Processing helix chain 'A' and resid 129 through 135 removed outlier: 3.546A pdb=" N ALA A 134 " --> pdb=" O PRO A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 148 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 171 through 182 removed outlier: 4.195A pdb=" N ARG A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 208 removed outlier: 3.594A pdb=" N HIS A 208 " --> pdb=" O PHE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 251 removed outlier: 3.938A pdb=" N GLY A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 283 Processing helix chain 'A' and resid 294 through 307 Processing helix chain 'A' and resid 339 through 349 removed outlier: 3.789A pdb=" N ARG A 349 " --> pdb=" O GLN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 385 Processing helix chain 'A' and resid 390 through 408 Processing helix chain 'A' and resid 411 through 421 Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 436 through 451 Processing helix chain 'B' and resid 13 through 23 Processing helix chain 'B' and resid 31 through 44 Processing helix chain 'B' and resid 57 through 69 Proline residue: B 65 - end of helix Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 105 through 118 Processing helix chain 'B' and resid 129 through 135 Processing helix chain 'B' and resid 137 through 148 removed outlier: 4.525A pdb=" N THR B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 172 through 182 removed outlier: 3.892A pdb=" N ALA B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 207 Processing helix chain 'B' and resid 237 through 251 removed outlier: 3.658A pdb=" N GLY B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 283 Processing helix chain 'B' and resid 294 through 307 Processing helix chain 'B' and resid 339 through 350 removed outlier: 3.766A pdb=" N ALA B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 385 removed outlier: 3.537A pdb=" N LYS B 385 " --> pdb=" O LYS B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 408 Processing helix chain 'B' and resid 411 through 421 Processing helix chain 'B' and resid 431 through 436 Processing helix chain 'B' and resid 436 through 451 Processing sheet with id=AA1, first strand: chain 'K' and resid 5 through 7 removed outlier: 4.061A pdb=" N VAL K 5 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA K 23 " --> pdb=" O VAL K 5 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR K 68 " --> pdb=" O GLN K 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 33 through 34 Processing sheet with id=AA3, first strand: chain 'K' and resid 46 through 47 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 28 through 31 removed outlier: 3.623A pdb=" N SER L 30 " --> pdb=" O TYR L 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 57 through 58 removed outlier: 5.183A pdb=" N GLU L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ALA L 40 " --> pdb=" O GLU L 44 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N MET L 34 " --> pdb=" O ALA L 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.253A pdb=" N SER A 98 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 74 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A 48 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N THR A 192 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL A 50 " --> pdb=" O THR A 192 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 229 through 231 removed outlier: 5.928A pdb=" N GLN A 230 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL A 331 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N TYR A 362 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N HIS A 333 " --> pdb=" O TYR A 362 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE A 263 " --> pdb=" O ALA A 332 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 97 through 99 removed outlier: 6.601A pdb=" N SER B 98 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR B 73 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ILE B 72 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B 154 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 74 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL B 156 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 76 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASP B 47 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N PHE B 216 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE B 49 " --> pdb=" O PHE B 216 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 225 through 229 removed outlier: 6.091A pdb=" N PHE B 226 " --> pdb=" O CYS B 359 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LEU B 361 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASP B 228 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG B 360 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ILE B 263 " --> pdb=" O ALA B 332 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1158 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: 5.26 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6693 1.03 - 1.23: 22 1.23 - 1.42: 3293 1.42 - 1.62: 4441 1.62 - 1.81: 68 Bond restraints: 14517 Sorted by residual: bond pdb=" N GLN K 1 " pdb=" H GLN K 1 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" CB THR B 316 " pdb=" CG2 THR B 316 " ideal model delta sigma weight residual 1.521 1.550 -0.029 3.30e-02 9.18e+02 7.60e-01 bond pdb=" C GLN B 139 " pdb=" O GLN B 139 " ideal model delta sigma weight residual 1.244 1.237 0.007 1.00e-02 1.00e+04 5.00e-01 bond pdb=" CB ARG B 180 " pdb=" CG ARG B 180 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 4.70e-01 bond pdb=" C LEU L 85 " pdb=" N LYS L 86 " ideal model delta sigma weight residual 1.326 1.333 -0.008 1.12e-02 7.97e+03 4.57e-01 ... (remaining 14512 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 25796 1.64 - 3.28: 141 3.28 - 4.93: 31 4.93 - 6.57: 1 6.57 - 8.21: 1 Bond angle restraints: 25970 Sorted by residual: angle pdb=" N ILE A 83 " pdb=" CA ILE A 83 " pdb=" C ILE A 83 " ideal model delta sigma weight residual 110.62 107.61 3.01 1.02e+00 9.61e-01 8.73e+00 angle pdb=" OG1 THR B 316 " pdb=" CB THR B 316 " pdb=" CG2 THR B 316 " ideal model delta sigma weight residual 109.30 104.79 4.51 2.00e+00 2.50e-01 5.09e+00 angle pdb=" N LYS A 94 " pdb=" CA LYS A 94 " pdb=" CB LYS A 94 " ideal model delta sigma weight residual 113.65 110.38 3.27 1.47e+00 4.63e-01 4.94e+00 angle pdb=" C PHE B 138 " pdb=" N GLN B 139 " pdb=" CA GLN B 139 " ideal model delta sigma weight residual 119.78 122.30 -2.52 1.24e+00 6.50e-01 4.12e+00 angle pdb=" CB MET L 34 " pdb=" CG MET L 34 " pdb=" SD MET L 34 " ideal model delta sigma weight residual 112.70 118.52 -5.82 3.00e+00 1.11e-01 3.77e+00 ... (remaining 25965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6570 17.94 - 35.89: 372 35.89 - 53.83: 123 53.83 - 71.77: 33 71.77 - 89.72: 7 Dihedral angle restraints: 7105 sinusoidal: 3445 harmonic: 3660 Sorted by residual: dihedral pdb=" CB CYS B 266 " pdb=" SG CYS B 266 " pdb=" SG CYS B 272 " pdb=" CB CYS B 272 " ideal model delta sinusoidal sigma weight residual -86.00 -140.33 54.33 1 1.00e+01 1.00e-02 4.00e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 95 " pdb=" CB CYS L 95 " ideal model delta sinusoidal sigma weight residual 93.00 135.52 -42.52 1 1.00e+01 1.00e-02 2.52e+01 dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 272 " pdb=" CB CYS A 272 " ideal model delta sinusoidal sigma weight residual -86.00 -123.60 37.60 1 1.00e+01 1.00e-02 1.99e+01 ... (remaining 7102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 924 0.033 - 0.066: 197 0.066 - 0.099: 76 0.099 - 0.132: 46 0.132 - 0.165: 1 Chirality restraints: 1244 Sorted by residual: chirality pdb=" CB THR B 316 " pdb=" CA THR B 316 " pdb=" OG1 THR B 316 " pdb=" CG2 THR B 316 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA VAL A 310 " pdb=" N VAL A 310 " pdb=" C VAL A 310 " pdb=" CB VAL A 310 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA ILE L 28 " pdb=" N ILE L 28 " pdb=" C ILE L 28 " pdb=" CB ILE L 28 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 ... (remaining 1241 not shown) Planarity restraints: 2464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 129 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO A 130 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 130 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 130 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 218 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO B 219 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 219 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 219 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 129 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO B 130 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 130 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 130 " 0.020 5.00e-02 4.00e+02 ... (remaining 2461 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 299 2.12 - 2.74: 24967 2.74 - 3.36: 40197 3.36 - 3.98: 48573 3.98 - 4.60: 75311 Nonbonded interactions: 189347 Sorted by model distance: nonbonded pdb=" O VAL K 63 " pdb=" H PHE K 67 " model vdw 1.501 2.450 nonbonded pdb=" HH TYR L 101 " pdb=" O GLY B 421 " model vdw 1.534 2.450 nonbonded pdb=" O ARG B 180 " pdb="HH11 ARG B 180 " model vdw 1.597 2.450 nonbonded pdb=" O PHE A 226 " pdb=" H CYS A 359 " model vdw 1.598 2.450 nonbonded pdb=" O ARG B 329 " pdb=" HG SER B 357 " model vdw 1.605 2.450 ... (remaining 189342 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 20 or (resid 21 through 22 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 23 through 26 \ or (resid 27 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 28 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 36 through 74 or (resid 7 \ 5 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 76 through 89 or (resid 90 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 91 through 92 or (resid 93 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 94 \ through 95 or (resid 96 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 97 through 100 or (resid 101 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 102 or (resid \ 103 through 104 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 105 through 106 or (resid 107 through 110 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 111 thr \ ough 116 or (resid 117 through 120 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 121 through 127 or (resid 128 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 1 \ 29 through 156 or (resid 157 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 158 through 166 or (resid 167 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 168 or \ (resid 169 through 170 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 171 or (resid 172 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 173 through 175 or (resid \ 176 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 177 through 200 or (resid 201 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 202 through 210 or (resid 211 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 212 through 226 or (resid 227 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 228 through 231 or (resid 232 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 233 through 262 or (resid 263 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 264 through 266 or (resid 267 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 268 th \ rough 300 or (resid 301 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 302 through 303 or (resid 304 through 305 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 306 through 316 or (resid 317 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 318 through 319 or resid 325 through 328 or \ (resid 329 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 330 through 332 or (resid 333 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 334 through 345 or (resi \ d 346 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 347 through 348 or (resid 349 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 350 through 360 or (resid 361 \ through 362 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 363 through 366 or (resid 367 through 368 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 369 or (resi \ d 370 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 371 through 373 or (resid 374 through 379 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 380 through 401 or \ (resid 402 through 403 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 404 through 417 or (resid 418 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 419 through \ 423 or (resid 424 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 425 through 431 or (resid 432 through 433 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 434 th \ rough 451 or resid 501)) selection = (chain 'B' and (resid 12 through 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 18 through 29 or (resid \ 30 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 31 through 42 or (resid 43 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 44 or (resid 45 through 47 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 48 \ through 59 or (resid 60 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 61 through 63 or (resid 64 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 65 through 67 \ or (resid 68 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 69 through 71 or (resid 72 through 73 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 74 through 81 o \ r (resid 82 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 83 through 84 or (resid 85 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 86 through 87 or (resid 88 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 89 through 99 or (resid 100 through 101 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 102 through 112 or (resid \ 113 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 114 through 125 or (resid 126 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 127 through 130 or (resid 131 th \ rough 132 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 133 through 137 or (resid 138 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 139 through 143 or (resid \ 144 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 145 through 151 or (resid 152 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 153 through 178 or (resid 179 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 180 through 184 or (resid 185 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 186 through 191 or (resid 192 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 1 \ 93 through 224 or (resid 225 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 226 through 242 or (resid 243 through 244 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 245 through 246 or (resid 247 through 248 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 249 through 254 or (resid \ 255 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 256 through 272 or (resid 273 through 275 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 276 or (resid 277 th \ rough 279 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 280 through 308 or (resid 309 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 310 through 395 or (resid \ 396 through 397 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 398 through 407 or (resid 408 through 409 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 410 thro \ ugh 432 or (resid 433 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 434 through 440 or (resid 441 through 442 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 44 \ 3 or (resid 444 through 445 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 446 through 451 or resid 501)) } ncs_group { reference = (chain 'K' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 3 through 12 or (resid 13 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 14 through 27 o \ r (resid 28 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 29 through 30 or (resid 31 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 32 through 38 or (resid 39 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 40 through 50 or (resid 51 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 52 through 82 or (resid 83 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 84 th \ rough 85 or (resid 86 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 87 or (resid 88 through 89 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 90 through 118 or \ (resid 119 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 120 through 124)) selection = (chain 'L' and (resid 2 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 26 through 37 or (resid 3 \ 8 through 39 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 40 through 88 or (resid 89 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 90 through 91 or (resid 92 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 93 through 124)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.840 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: 0.310 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 40.110 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 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 : 0.002 0.029 7817 Z= 0.090 Angle : 0.445 5.825 10680 Z= 0.235 Chirality : 0.038 0.165 1244 Planarity : 0.003 0.044 1400 Dihedral : 12.740 89.716 2536 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.27), residues: 1096 helix: 2.78 (0.24), residues: 465 sheet: -1.61 (0.29), residues: 279 loop : 0.44 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 47 HIS 0.002 0.000 HIS B 149 PHE 0.009 0.001 PHE B 420 TYR 0.009 0.001 TYR A 265 ARG 0.003 0.000 ARG A 443 Details of bonding type rmsd hydrogen bonds : bond 0.14290 ( 397) hydrogen bonds : angle 5.36281 ( 1158) metal coordination : bond 0.00412 ( 8) metal coordination : angle 2.42660 ( 12) SS BOND : bond 0.00288 ( 5) SS BOND : angle 0.83350 ( 10) covalent geometry : bond 0.00183 ( 7804) covalent geometry : angle 0.43723 (10658) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 25 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 132 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue THR 192 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue TYR 289 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue VAL 312 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue VAL 331 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue ILE 396 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Residue LEU 444 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue TYR 227 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue TYR 289 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue VAL 312 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue VAL 331 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue LEU 374 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue LEU 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.152 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: A 143 ASN cc_start: 0.8723 (m110) cc_final: 0.8465 (m110) REVERT: A 154 LEU cc_start: 0.5138 (tp) cc_final: 0.4571 (tt) REVERT: A 161 CYS cc_start: 0.6940 (m) cc_final: 0.6486 (m) REVERT: A 224 ASN cc_start: 0.7039 (m-40) cc_final: 0.6579 (m-40) REVERT: A 302 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8585 (tm-30) REVERT: A 367 ASP cc_start: 0.8453 (m-30) cc_final: 0.8206 (m-30) REVERT: B 85 ASP cc_start: 0.7205 (m-30) cc_final: 0.6981 (m-30) REVERT: B 302 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8687 (tm-30) REVERT: B 303 ASN cc_start: 0.8890 (m110) cc_final: 0.8515 (m110) REVERT: B 344 TYR cc_start: 0.8260 (t80) cc_final: 0.7934 (t80) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.3765 time to fit residues: 108.9364 Evaluate side-chains 191 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.0970 chunk 44 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 7 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.147795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.124612 restraints weight = 49606.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.131391 restraints weight = 25845.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.135796 restraints weight = 15078.247| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7817 Z= 0.133 Angle : 0.484 5.706 10680 Z= 0.259 Chirality : 0.038 0.135 1244 Planarity : 0.004 0.049 1400 Dihedral : 3.276 16.477 1176 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.15 % Allowed : 10.04 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.27), residues: 1096 helix: 2.79 (0.24), residues: 481 sheet: -1.65 (0.30), residues: 268 loop : 0.51 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 47 HIS 0.007 0.001 HIS A 149 PHE 0.012 0.001 PHE B 138 TYR 0.009 0.001 TYR B 62 ARG 0.002 0.000 ARG A 443 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 397) hydrogen bonds : angle 4.56567 ( 1158) metal coordination : bond 0.00543 ( 8) metal coordination : angle 2.57741 ( 12) SS BOND : bond 0.00303 ( 5) SS BOND : angle 0.98719 ( 10) covalent geometry : bond 0.00272 ( 7804) covalent geometry : angle 0.47618 (10658) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 25 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 132 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue THR 192 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue TYR 289 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue VAL 312 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue VAL 331 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue ILE 396 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Residue LEU 444 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue TYR 227 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue TYR 289 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue VAL 312 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue VAL 331 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue LEU 374 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue LEU 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 1.139 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: K 29 PHE cc_start: 0.8432 (t80) cc_final: 0.8180 (t80) REVERT: L 20 LEU cc_start: 0.7563 (mm) cc_final: 0.7042 (mm) REVERT: A 161 CYS cc_start: 0.7019 (m) cc_final: 0.6539 (m) REVERT: A 224 ASN cc_start: 0.7173 (m-40) cc_final: 0.6747 (m-40) REVERT: A 302 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8530 (tm-30) REVERT: A 422 ASP cc_start: 0.6927 (p0) cc_final: 0.6683 (p0) REVERT: B 302 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8628 (tm-30) outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.4002 time to fit residues: 106.0691 Evaluate side-chains 189 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.139663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.117269 restraints weight = 49656.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.123493 restraints weight = 25901.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.127619 restraints weight = 15234.529| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7817 Z= 0.238 Angle : 0.574 8.019 10680 Z= 0.315 Chirality : 0.039 0.130 1244 Planarity : 0.004 0.039 1400 Dihedral : 3.863 15.052 1176 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.20 % Allowed : 13.64 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.27), residues: 1096 helix: 2.43 (0.24), residues: 481 sheet: -1.65 (0.30), residues: 269 loop : 0.26 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 47 HIS 0.003 0.001 HIS A 167 PHE 0.014 0.002 PHE K 29 TYR 0.012 0.002 TYR A 265 ARG 0.003 0.000 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 397) hydrogen bonds : angle 4.85507 ( 1158) metal coordination : bond 0.01273 ( 8) metal coordination : angle 4.61997 ( 12) SS BOND : bond 0.00570 ( 5) SS BOND : angle 1.31261 ( 10) covalent geometry : bond 0.00461 ( 7804) covalent geometry : angle 0.55224 (10658) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 25 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 132 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue THR 192 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue TYR 289 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue VAL 312 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue VAL 331 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue ILE 396 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Residue LEU 444 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue TYR 227 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue TYR 289 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue VAL 312 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue VAL 331 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue LEU 374 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue LEU 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 205 time to evaluate : 1.204 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: K 29 PHE cc_start: 0.8643 (t80) cc_final: 0.8413 (t80) REVERT: L 4 LEU cc_start: 0.7717 (mm) cc_final: 0.7501 (mm) REVERT: L 7 ASN cc_start: 0.6426 (OUTLIER) cc_final: 0.5888 (m-40) REVERT: L 20 LEU cc_start: 0.7972 (mm) cc_final: 0.7382 (mm) REVERT: A 59 SER cc_start: 0.8833 (p) cc_final: 0.8463 (t) REVERT: A 161 CYS cc_start: 0.7021 (m) cc_final: 0.6589 (m) REVERT: A 207 LEU cc_start: 0.8612 (mm) cc_final: 0.8411 (mp) REVERT: A 302 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8482 (tm-30) REVERT: B 61 CYS cc_start: 0.8708 (t) cc_final: 0.8467 (t) REVERT: B 152 SER cc_start: 0.8560 (t) cc_final: 0.8214 (p) REVERT: B 302 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8716 (tm-30) outliers start: 8 outliers final: 7 residues processed: 207 average time/residue: 0.4152 time to fit residues: 113.9825 Evaluate side-chains 205 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 197 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 261 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 98 optimal weight: 0.2980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 7 ASN K 32 ASN K 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.141277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.119049 restraints weight = 49137.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.125353 restraints weight = 25586.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.129439 restraints weight = 14933.789| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7817 Z= 0.149 Angle : 0.506 6.159 10680 Z= 0.269 Chirality : 0.038 0.132 1244 Planarity : 0.004 0.036 1400 Dihedral : 3.717 17.012 1176 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.95 % Allowed : 15.74 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.27), residues: 1096 helix: 2.65 (0.24), residues: 481 sheet: -1.54 (0.30), residues: 268 loop : 0.31 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 47 HIS 0.005 0.001 HIS B 149 PHE 0.010 0.001 PHE B 405 TYR 0.011 0.001 TYR L 101 ARG 0.002 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.03019 ( 397) hydrogen bonds : angle 4.53310 ( 1158) metal coordination : bond 0.00686 ( 8) metal coordination : angle 3.75074 ( 12) SS BOND : bond 0.00334 ( 5) SS BOND : angle 0.67401 ( 10) covalent geometry : bond 0.00294 ( 7804) covalent geometry : angle 0.49041 (10658) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 25 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 132 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue THR 192 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue TYR 289 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue VAL 312 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue VAL 331 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue ILE 396 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Residue LEU 444 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue TYR 227 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue TYR 289 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue VAL 312 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue VAL 331 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue LEU 374 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue LEU 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 205 time to evaluate : 1.165 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: K 29 PHE cc_start: 0.8530 (t80) cc_final: 0.8295 (t80) REVERT: K 88 GLU cc_start: 0.9031 (mp0) cc_final: 0.8529 (pm20) REVERT: L 7 ASN cc_start: 0.6425 (OUTLIER) cc_final: 0.5963 (m-40) REVERT: L 20 LEU cc_start: 0.7976 (mm) cc_final: 0.7402 (mm) REVERT: A 59 SER cc_start: 0.8784 (p) cc_final: 0.8416 (t) REVERT: A 117 GLU cc_start: 0.6616 (tp30) cc_final: 0.6047 (tp30) REVERT: A 143 ASN cc_start: 0.8730 (m110) cc_final: 0.8449 (m110) REVERT: A 161 CYS cc_start: 0.7051 (m) cc_final: 0.6556 (m) REVERT: A 302 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8469 (tm-30) REVERT: B 61 CYS cc_start: 0.8682 (t) cc_final: 0.8386 (t) REVERT: B 139 GLN cc_start: 0.8595 (tp40) cc_final: 0.8230 (mp10) REVERT: B 152 SER cc_start: 0.8431 (t) cc_final: 0.8112 (p) REVERT: B 224 ASN cc_start: 0.7278 (m-40) cc_final: 0.7075 (m-40) REVERT: B 302 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8662 (tm-30) outliers start: 13 outliers final: 9 residues processed: 209 average time/residue: 0.4183 time to fit residues: 116.4447 Evaluate side-chains 208 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 198 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 300 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 7 ASN K 32 ASN K 120 GLN L 7 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.139698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.116981 restraints weight = 48948.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.123255 restraints weight = 25624.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.127337 restraints weight = 15114.166| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7817 Z= 0.161 Angle : 0.518 6.571 10680 Z= 0.275 Chirality : 0.038 0.138 1244 Planarity : 0.004 0.036 1400 Dihedral : 3.793 17.048 1176 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.95 % Allowed : 17.99 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.27), residues: 1096 helix: 2.61 (0.24), residues: 481 sheet: -1.53 (0.30), residues: 267 loop : 0.34 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 47 HIS 0.003 0.001 HIS B 160 PHE 0.010 0.001 PHE A 221 TYR 0.014 0.001 TYR A 265 ARG 0.003 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.03060 ( 397) hydrogen bonds : angle 4.52838 ( 1158) metal coordination : bond 0.00810 ( 8) metal coordination : angle 3.86876 ( 12) SS BOND : bond 0.00433 ( 5) SS BOND : angle 1.00251 ( 10) covalent geometry : bond 0.00315 ( 7804) covalent geometry : angle 0.50092 (10658) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 25 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 132 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue THR 192 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue TYR 289 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue VAL 312 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue VAL 331 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue ILE 396 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Residue LEU 444 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue TYR 227 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue TYR 289 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue VAL 312 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue VAL 331 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue LEU 374 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue LEU 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 1.186 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: K 29 PHE cc_start: 0.8584 (t80) cc_final: 0.8353 (t80) REVERT: K 120 GLN cc_start: 0.6449 (mt0) cc_final: 0.6240 (mt0) REVERT: L 20 LEU cc_start: 0.8007 (mm) cc_final: 0.7475 (mm) REVERT: A 59 SER cc_start: 0.8832 (p) cc_final: 0.8455 (t) REVERT: A 117 GLU cc_start: 0.6626 (tp30) cc_final: 0.6086 (tp30) REVERT: A 143 ASN cc_start: 0.8745 (m110) cc_final: 0.8466 (m110) REVERT: A 161 CYS cc_start: 0.7064 (m) cc_final: 0.6579 (m) REVERT: A 207 LEU cc_start: 0.8643 (mm) cc_final: 0.8421 (mp) REVERT: A 302 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8461 (tm-30) REVERT: B 61 CYS cc_start: 0.8710 (t) cc_final: 0.8446 (t) REVERT: B 139 GLN cc_start: 0.8624 (tp40) cc_final: 0.8239 (mp10) REVERT: B 152 SER cc_start: 0.8499 (t) cc_final: 0.8178 (p) REVERT: B 224 ASN cc_start: 0.7382 (m-40) cc_final: 0.7166 (m-40) REVERT: B 302 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8619 (tm-30) outliers start: 13 outliers final: 13 residues processed: 200 average time/residue: 0.4365 time to fit residues: 114.7215 Evaluate side-chains 206 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 447 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.139915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.117105 restraints weight = 49235.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.123443 restraints weight = 25714.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.127562 restraints weight = 15137.997| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7817 Z= 0.142 Angle : 0.511 7.063 10680 Z= 0.268 Chirality : 0.038 0.132 1244 Planarity : 0.004 0.044 1400 Dihedral : 3.786 17.197 1176 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.70 % Allowed : 17.84 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.27), residues: 1096 helix: 2.74 (0.24), residues: 481 sheet: -1.47 (0.31), residues: 258 loop : 0.27 (0.36), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 47 HIS 0.004 0.001 HIS B 149 PHE 0.015 0.001 PHE L 29 TYR 0.015 0.001 TYR A 265 ARG 0.003 0.000 ARG B 175 Details of bonding type rmsd hydrogen bonds : bond 0.02870 ( 397) hydrogen bonds : angle 4.41471 ( 1158) metal coordination : bond 0.00674 ( 8) metal coordination : angle 3.73442 ( 12) SS BOND : bond 0.00344 ( 5) SS BOND : angle 0.80062 ( 10) covalent geometry : bond 0.00282 ( 7804) covalent geometry : angle 0.49508 (10658) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 25 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 132 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue THR 192 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue TYR 289 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue VAL 312 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue VAL 331 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue ILE 396 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Residue LEU 444 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue TYR 227 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue TYR 289 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue VAL 312 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue VAL 331 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue LEU 374 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue LEU 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 1.062 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: K 29 PHE cc_start: 0.8551 (t80) cc_final: 0.8315 (t80) REVERT: L 20 LEU cc_start: 0.8036 (mm) cc_final: 0.7498 (mm) REVERT: L 45 ARG cc_start: 0.7074 (mpt180) cc_final: 0.6800 (mpt180) REVERT: A 59 SER cc_start: 0.8854 (p) cc_final: 0.8462 (t) REVERT: A 117 GLU cc_start: 0.6648 (tp30) cc_final: 0.6309 (tp30) REVERT: A 143 ASN cc_start: 0.8738 (m110) cc_final: 0.8458 (m110) REVERT: A 161 CYS cc_start: 0.7034 (m) cc_final: 0.6536 (m) REVERT: A 207 LEU cc_start: 0.8669 (mm) cc_final: 0.8459 (mp) REVERT: A 224 ASN cc_start: 0.7472 (m-40) cc_final: 0.6993 (m-40) REVERT: A 302 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8412 (tm-30) REVERT: B 43 LYS cc_start: 0.8525 (tttp) cc_final: 0.8185 (tttp) REVERT: B 61 CYS cc_start: 0.8706 (t) cc_final: 0.8404 (t) REVERT: B 139 GLN cc_start: 0.8672 (tp40) cc_final: 0.8250 (mp10) REVERT: B 152 SER cc_start: 0.8411 (t) cc_final: 0.8102 (p) REVERT: B 224 ASN cc_start: 0.7412 (m-40) cc_final: 0.7210 (m-40) REVERT: B 302 GLN cc_start: 0.8995 (tm-30) cc_final: 0.8612 (tm-30) outliers start: 18 outliers final: 17 residues processed: 204 average time/residue: 0.4329 time to fit residues: 117.5151 Evaluate side-chains 211 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 300 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 32 ASN A 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.137416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.114826 restraints weight = 49740.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.121072 restraints weight = 25605.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.125177 restraints weight = 14999.767| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7817 Z= 0.198 Angle : 0.560 7.464 10680 Z= 0.300 Chirality : 0.039 0.136 1244 Planarity : 0.004 0.038 1400 Dihedral : 4.057 17.247 1176 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.70 % Allowed : 19.19 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.27), residues: 1096 helix: 2.43 (0.23), residues: 481 sheet: -1.49 (0.31), residues: 267 loop : 0.14 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 334 HIS 0.002 0.001 HIS B 433 PHE 0.011 0.002 PHE K 29 TYR 0.014 0.002 TYR L 101 ARG 0.004 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 397) hydrogen bonds : angle 4.67527 ( 1158) metal coordination : bond 0.00923 ( 8) metal coordination : angle 4.39015 ( 12) SS BOND : bond 0.00462 ( 5) SS BOND : angle 0.87282 ( 10) covalent geometry : bond 0.00384 ( 7804) covalent geometry : angle 0.53974 (10658) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 25 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 132 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue THR 192 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue TYR 289 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue VAL 312 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue VAL 331 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue ILE 396 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Residue LEU 444 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue TYR 227 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue TYR 289 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue VAL 312 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue VAL 331 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue LEU 374 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue LEU 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 1.037 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: K 29 PHE cc_start: 0.8634 (t80) cc_final: 0.8419 (t80) REVERT: L 20 LEU cc_start: 0.8084 (mm) cc_final: 0.7550 (mm) REVERT: L 45 ARG cc_start: 0.7158 (mpt180) cc_final: 0.6892 (mpt180) REVERT: A 59 SER cc_start: 0.8894 (p) cc_final: 0.8500 (t) REVERT: A 117 GLU cc_start: 0.6700 (tp30) cc_final: 0.6351 (tp30) REVERT: A 143 ASN cc_start: 0.8789 (m110) cc_final: 0.8508 (m110) REVERT: A 161 CYS cc_start: 0.7122 (m) cc_final: 0.6626 (m) REVERT: A 164 GLN cc_start: 0.7962 (tp40) cc_final: 0.7471 (tp40) REVERT: A 207 LEU cc_start: 0.8738 (mm) cc_final: 0.8532 (mp) REVERT: A 302 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8414 (tm-30) REVERT: B 43 LYS cc_start: 0.8599 (tttp) cc_final: 0.8262 (tttp) REVERT: B 61 CYS cc_start: 0.8733 (t) cc_final: 0.8460 (t) REVERT: B 139 GLN cc_start: 0.8748 (tp40) cc_final: 0.8310 (mp10) REVERT: B 152 SER cc_start: 0.8542 (t) cc_final: 0.8182 (p) REVERT: B 224 ASN cc_start: 0.7524 (m-40) cc_final: 0.7312 (m-40) REVERT: B 302 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8620 (tm-30) outliers start: 18 outliers final: 18 residues processed: 202 average time/residue: 0.4317 time to fit residues: 114.2391 Evaluate side-chains 211 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain L residue 47 TRP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 447 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 41 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.0370 chunk 56 optimal weight: 0.8980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.139101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.116431 restraints weight = 49353.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.122706 restraints weight = 25443.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.126865 restraints weight = 14907.995| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7817 Z= 0.138 Angle : 0.523 7.527 10680 Z= 0.273 Chirality : 0.038 0.138 1244 Planarity : 0.004 0.034 1400 Dihedral : 3.925 17.297 1176 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.70 % Allowed : 19.34 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.27), residues: 1096 helix: 2.67 (0.24), residues: 482 sheet: -1.46 (0.31), residues: 259 loop : 0.17 (0.36), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 47 HIS 0.004 0.001 HIS B 149 PHE 0.008 0.001 PHE B 330 TYR 0.013 0.001 TYR A 419 ARG 0.005 0.000 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.02877 ( 397) hydrogen bonds : angle 4.42146 ( 1158) metal coordination : bond 0.00671 ( 8) metal coordination : angle 3.98828 ( 12) SS BOND : bond 0.00371 ( 5) SS BOND : angle 0.70451 ( 10) covalent geometry : bond 0.00279 ( 7804) covalent geometry : angle 0.50584 (10658) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 25 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 132 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue THR 192 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue TYR 289 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue VAL 312 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue VAL 331 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue ILE 396 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Residue LEU 444 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue TYR 227 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue TYR 289 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue VAL 312 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue VAL 331 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue LEU 374 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue LEU 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 1.141 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: K 29 PHE cc_start: 0.8577 (t80) cc_final: 0.8370 (t80) REVERT: L 20 LEU cc_start: 0.8068 (mm) cc_final: 0.7571 (mm) REVERT: L 45 ARG cc_start: 0.7084 (mpt180) cc_final: 0.6825 (mpt180) REVERT: A 59 SER cc_start: 0.8878 (p) cc_final: 0.8510 (t) REVERT: A 117 GLU cc_start: 0.6681 (tp30) cc_final: 0.6351 (tp30) REVERT: A 161 CYS cc_start: 0.7072 (m) cc_final: 0.6556 (m) REVERT: A 164 GLN cc_start: 0.7888 (tp40) cc_final: 0.7407 (tp40) REVERT: A 207 LEU cc_start: 0.8724 (mm) cc_final: 0.8517 (mp) REVERT: A 302 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8379 (tm-30) REVERT: B 43 LYS cc_start: 0.8572 (tttp) cc_final: 0.8238 (tttp) REVERT: B 61 CYS cc_start: 0.8694 (t) cc_final: 0.8414 (t) REVERT: B 139 GLN cc_start: 0.8741 (tp40) cc_final: 0.8324 (mp10) REVERT: B 152 SER cc_start: 0.8426 (t) cc_final: 0.8105 (p) REVERT: B 224 ASN cc_start: 0.7499 (m-40) cc_final: 0.7286 (m-40) outliers start: 18 outliers final: 16 residues processed: 205 average time/residue: 0.4234 time to fit residues: 114.6182 Evaluate side-chains 211 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 447 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 74 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 50 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 7 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.138941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.116261 restraints weight = 48879.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.122598 restraints weight = 25324.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.126760 restraints weight = 14800.483| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7817 Z= 0.145 Angle : 0.526 7.943 10680 Z= 0.276 Chirality : 0.038 0.133 1244 Planarity : 0.004 0.035 1400 Dihedral : 3.908 17.526 1176 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.70 % Allowed : 20.09 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.27), residues: 1096 helix: 2.67 (0.24), residues: 481 sheet: -1.28 (0.31), residues: 268 loop : 0.13 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 47 HIS 0.003 0.001 HIS B 160 PHE 0.018 0.001 PHE B 405 TYR 0.013 0.001 TYR A 419 ARG 0.005 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.02852 ( 397) hydrogen bonds : angle 4.35414 ( 1158) metal coordination : bond 0.00768 ( 8) metal coordination : angle 3.93683 ( 12) SS BOND : bond 0.00401 ( 5) SS BOND : angle 0.74713 ( 10) covalent geometry : bond 0.00293 ( 7804) covalent geometry : angle 0.50895 (10658) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 25 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 132 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue THR 192 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue TYR 289 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue VAL 312 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue VAL 331 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue ILE 396 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Residue LEU 444 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue TYR 227 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue TYR 289 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue VAL 312 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue VAL 331 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue LEU 374 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue LEU 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 1.243 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: K 7 ASN cc_start: 0.7194 (OUTLIER) cc_final: 0.6895 (m-40) REVERT: K 20 LEU cc_start: 0.7958 (mt) cc_final: 0.7527 (mt) REVERT: L 45 ARG cc_start: 0.7121 (mpt180) cc_final: 0.6919 (mpt180) REVERT: A 59 SER cc_start: 0.8896 (p) cc_final: 0.8535 (t) REVERT: A 117 GLU cc_start: 0.6693 (tp30) cc_final: 0.6346 (tp30) REVERT: A 161 CYS cc_start: 0.7054 (m) cc_final: 0.6552 (m) REVERT: A 164 GLN cc_start: 0.7921 (tp40) cc_final: 0.7480 (tp40) REVERT: A 207 LEU cc_start: 0.8788 (mm) cc_final: 0.8580 (mp) REVERT: A 302 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8295 (tm-30) REVERT: B 43 LYS cc_start: 0.8524 (tttp) cc_final: 0.8159 (tttp) REVERT: B 61 CYS cc_start: 0.8664 (t) cc_final: 0.8395 (t) REVERT: B 139 GLN cc_start: 0.8731 (tp40) cc_final: 0.8333 (mp10) REVERT: B 152 SER cc_start: 0.8440 (t) cc_final: 0.8116 (p) REVERT: B 224 ASN cc_start: 0.7511 (m-40) cc_final: 0.7311 (m-40) outliers start: 18 outliers final: 17 residues processed: 204 average time/residue: 0.4507 time to fit residues: 122.5753 Evaluate side-chains 213 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 447 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 7 ASN A 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.138857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.116022 restraints weight = 49554.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.122340 restraints weight = 25645.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.126551 restraints weight = 15075.887| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7817 Z= 0.155 Angle : 0.534 7.138 10680 Z= 0.284 Chirality : 0.038 0.142 1244 Planarity : 0.004 0.049 1400 Dihedral : 3.945 17.817 1176 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.40 % Allowed : 20.54 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.27), residues: 1096 helix: 2.67 (0.24), residues: 481 sheet: -1.30 (0.31), residues: 268 loop : 0.08 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 47 HIS 0.005 0.001 HIS B 149 PHE 0.014 0.001 PHE K 29 TYR 0.014 0.001 TYR A 419 ARG 0.008 0.000 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.02899 ( 397) hydrogen bonds : angle 4.37235 ( 1158) metal coordination : bond 0.00807 ( 8) metal coordination : angle 3.92635 ( 12) SS BOND : bond 0.00370 ( 5) SS BOND : angle 0.70587 ( 10) covalent geometry : bond 0.00314 ( 7804) covalent geometry : angle 0.51790 (10658) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 25 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 92 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue LEU 64 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LEU 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 132 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue THR 192 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LEU 225 is missing expected H atoms. Skipping. Residue LYS 243 is missing expected H atoms. Skipping. Residue LEU 247 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue TYR 289 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue VAL 312 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue VAL 331 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue ILE 396 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Residue LEU 444 is missing expected H atoms. Skipping. Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue LEU 104 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue ILE 128 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LEU 151 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LEU 183 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue TYR 227 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue TYR 289 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue VAL 312 is missing expected H atoms. Skipping. Residue ILE 313 is missing expected H atoms. Skipping. Residue ILE 317 is missing expected H atoms. Skipping. Residue VAL 331 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue LEU 374 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue LEU 402 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue LEU 409 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Residue LEU 424 is missing expected H atoms. Skipping. Residue LYS 429 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 1.084 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: K 7 ASN cc_start: 0.6952 (OUTLIER) cc_final: 0.6577 (m-40) REVERT: K 20 LEU cc_start: 0.7922 (mt) cc_final: 0.7516 (mt) REVERT: K 82 MET cc_start: 0.6227 (ttm) cc_final: 0.5737 (mmm) REVERT: L 45 ARG cc_start: 0.7147 (mpt180) cc_final: 0.6920 (mpt180) REVERT: A 59 SER cc_start: 0.8900 (p) cc_final: 0.8549 (t) REVERT: A 117 GLU cc_start: 0.6782 (tp30) cc_final: 0.6435 (tp30) REVERT: A 161 CYS cc_start: 0.7118 (m) cc_final: 0.6603 (m) REVERT: A 164 GLN cc_start: 0.7932 (tp40) cc_final: 0.7478 (tp40) REVERT: A 207 LEU cc_start: 0.8754 (mm) cc_final: 0.8535 (mp) REVERT: A 302 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8325 (tm-30) REVERT: B 43 LYS cc_start: 0.8552 (tttp) cc_final: 0.8173 (tttp) REVERT: B 61 CYS cc_start: 0.8696 (t) cc_final: 0.8407 (t) REVERT: B 139 GLN cc_start: 0.8778 (tp40) cc_final: 0.8367 (mp10) REVERT: B 152 SER cc_start: 0.8464 (t) cc_final: 0.8091 (p) REVERT: B 224 ASN cc_start: 0.7548 (m-40) cc_final: 0.7336 (m-40) outliers start: 16 outliers final: 14 residues processed: 204 average time/residue: 0.4373 time to fit residues: 116.7598 Evaluate side-chains 214 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 447 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 99 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 7 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.139431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.116538 restraints weight = 49191.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.122892 restraints weight = 25443.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.127117 restraints weight = 14931.754| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7817 Z= 0.133 Angle : 0.520 7.704 10680 Z= 0.275 Chirality : 0.038 0.141 1244 Planarity : 0.004 0.054 1400 Dihedral : 3.936 18.020 1176 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.55 % Allowed : 20.54 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.27), residues: 1096 helix: 2.72 (0.24), residues: 481 sheet: -1.31 (0.33), residues: 251 loop : 0.09 (0.36), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 47 HIS 0.005 0.001 HIS B 149 PHE 0.013 0.001 PHE K 29 TYR 0.014 0.001 TYR A 419 ARG 0.008 0.001 ARG A 282 Details of bonding type rmsd hydrogen bonds : bond 0.02760 ( 397) hydrogen bonds : angle 4.29105 ( 1158) metal coordination : bond 0.00662 ( 8) metal coordination : angle 3.78431 ( 12) SS BOND : bond 0.00347 ( 5) SS BOND : angle 0.67213 ( 10) covalent geometry : bond 0.00277 ( 7804) covalent geometry : angle 0.50438 (10658) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4976.85 seconds wall clock time: 86 minutes 43.05 seconds (5203.05 seconds total)