Starting phenix.real_space_refine on Sat Dec 28 22:36:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wq3_32698/12_2024/7wq3_32698.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wq3_32698/12_2024/7wq3_32698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wq3_32698/12_2024/7wq3_32698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wq3_32698/12_2024/7wq3_32698.map" model { file = "/net/cci-nas-00/data/ceres_data/7wq3_32698/12_2024/7wq3_32698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wq3_32698/12_2024/7wq3_32698.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 5915 2.51 5 N 1548 2.21 5 O 1685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9209 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2303 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 13, 'TRANS': 275} Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1787 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "L" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "R" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.64, per 1000 atoms: 0.61 Number of scatterers: 9209 At special positions: 0 Unit cell: (110.16, 125.46, 123.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 1685 8.00 N 1548 7.00 C 5915 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 187 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 39.7% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'R' and resid 32 through 61 removed outlier: 4.618A pdb=" N VAL R 38 " --> pdb=" O PHE R 34 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER R 61 " --> pdb=" O VAL R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 98 removed outlier: 3.754A pdb=" N ILE R 89 " --> pdb=" O LEU R 85 " (cutoff:3.500A) Proline residue: R 90 - end of helix removed outlier: 4.257A pdb=" N THR R 94 " --> pdb=" O PRO R 90 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL R 95 " --> pdb=" O PHE R 91 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR R 96 " --> pdb=" O GLN R 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 139 removed outlier: 4.015A pdb=" N ILE R 107 " --> pdb=" O LEU R 103 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N HIS R 112 " --> pdb=" O CYS R 108 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR R 113 " --> pdb=" O LYS R 109 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR R 116 " --> pdb=" O HIS R 112 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE R 137 " --> pdb=" O ARG R 133 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS R 139 " --> pdb=" O VAL R 135 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 147 Processing helix chain 'R' and resid 148 through 167 Processing helix chain 'R' and resid 167 through 174 removed outlier: 3.656A pdb=" N ALA R 171 " --> pdb=" O ALA R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 209 removed outlier: 3.715A pdb=" N ALA R 199 " --> pdb=" O ARG R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 231 Processing helix chain 'R' and resid 235 through 260 removed outlier: 4.429A pdb=" N TRP R 260 " --> pdb=" O PHE R 256 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 272 Processing helix chain 'R' and resid 278 through 303 removed outlier: 3.780A pdb=" N SER R 296 " --> pdb=" O ALA R 292 " (cutoff:3.500A) Proline residue: R 300 - end of helix Processing helix chain 'R' and resid 307 through 318 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 5.078A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.166A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 232 " --> pdb=" O ASP A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 232' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.543A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 removed outlier: 4.360A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.631A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.631A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.852A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.605A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.884A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.184A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.789A pdb=" N ASP S 223 " --> pdb=" O GLU S 220 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 220 through 224' Processing helix chain 'L' and resid 3 through 12 Processing sheet with id=AA1, first strand: chain 'R' and resid 175 through 177 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.299A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.973A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.033A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.010A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.789A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.177A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.121A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.620A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.292A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.292A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.928A pdb=" N THR S 141 " --> pdb=" O ARG S 160 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG S 160 " --> pdb=" O THR S 141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 4.028A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG S 191 " --> pdb=" O ASN S 194 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1311 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2915 1.34 - 1.46: 2281 1.46 - 1.58: 4113 1.58 - 1.70: 25 1.70 - 1.81: 91 Bond restraints: 9425 Sorted by residual: bond pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " ideal model delta sigma weight residual 1.332 1.652 -0.320 2.00e-02 2.50e+03 2.56e+02 bond pdb=" C5 CLR R 402 " pdb=" C6 CLR R 402 " ideal model delta sigma weight residual 1.332 1.651 -0.319 2.00e-02 2.50e+03 2.54e+02 bond pdb=" C5 CLR R 405 " pdb=" C6 CLR R 405 " ideal model delta sigma weight residual 1.332 1.651 -0.319 2.00e-02 2.50e+03 2.54e+02 bond pdb=" C5 CLR R 403 " pdb=" C6 CLR R 403 " ideal model delta sigma weight residual 1.332 1.651 -0.319 2.00e-02 2.50e+03 2.54e+02 bond pdb=" C5 CLR R 404 " pdb=" C6 CLR R 404 " ideal model delta sigma weight residual 1.332 1.650 -0.318 2.00e-02 2.50e+03 2.53e+02 ... (remaining 9420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 12667 2.66 - 5.32: 91 5.32 - 7.98: 19 7.98 - 10.64: 10 10.64 - 13.30: 10 Bond angle restraints: 12797 Sorted by residual: angle pdb=" C5 CLR R 405 " pdb=" C6 CLR R 405 " pdb=" C7 CLR R 405 " ideal model delta sigma weight residual 125.11 111.81 13.30 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C5 CLR R 403 " pdb=" C6 CLR R 403 " pdb=" C7 CLR R 403 " ideal model delta sigma weight residual 125.11 111.81 13.30 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C5 CLR R 402 " pdb=" C6 CLR R 402 " pdb=" C7 CLR R 402 " ideal model delta sigma weight residual 125.11 111.81 13.30 3.00e+00 1.11e-01 1.96e+01 angle pdb=" C5 CLR R 404 " pdb=" C6 CLR R 404 " pdb=" C7 CLR R 404 " ideal model delta sigma weight residual 125.11 111.82 13.29 3.00e+00 1.11e-01 1.96e+01 angle pdb=" C4 CLR R 401 " pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " ideal model delta sigma weight residual 120.33 107.93 12.40 3.00e+00 1.11e-01 1.71e+01 ... (remaining 12792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.56: 5564 15.56 - 31.12: 165 31.12 - 46.68: 53 46.68 - 62.24: 23 62.24 - 77.79: 3 Dihedral angle restraints: 5808 sinusoidal: 2443 harmonic: 3365 Sorted by residual: dihedral pdb=" N ARG S 191 " pdb=" CA ARG S 191 " pdb=" CB ARG S 191 " pdb=" CG ARG S 191 " ideal model delta sinusoidal sigma weight residual -60.00 -119.85 59.85 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N PHE B 234 " pdb=" CA PHE B 234 " pdb=" CB PHE B 234 " pdb=" CG PHE B 234 " ideal model delta sinusoidal sigma weight residual -180.00 -122.95 -57.05 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" N PHE R 114 " pdb=" CA PHE R 114 " pdb=" CB PHE R 114 " pdb=" CG PHE R 114 " ideal model delta sinusoidal sigma weight residual -60.00 -113.13 53.13 3 1.50e+01 4.44e-03 9.18e+00 ... (remaining 5805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1408 0.112 - 0.223: 29 0.223 - 0.335: 11 0.335 - 0.446: 4 0.446 - 0.558: 5 Chirality restraints: 1457 Sorted by residual: chirality pdb=" C13 CLR R 405 " pdb=" C12 CLR R 405 " pdb=" C14 CLR R 405 " pdb=" C17 CLR R 405 " both_signs ideal model delta sigma weight residual False -2.93 -2.37 -0.56 2.00e-01 2.50e+01 7.78e+00 chirality pdb=" C13 CLR R 404 " pdb=" C12 CLR R 404 " pdb=" C14 CLR R 404 " pdb=" C17 CLR R 404 " both_signs ideal model delta sigma weight residual False -2.93 -2.38 -0.56 2.00e-01 2.50e+01 7.74e+00 chirality pdb=" C13 CLR R 401 " pdb=" C12 CLR R 401 " pdb=" C14 CLR R 401 " pdb=" C17 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.93 -2.38 -0.55 2.00e-01 2.50e+01 7.69e+00 ... (remaining 1454 not shown) Planarity restraints: 1586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 299 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO R 300 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 300 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 300 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA S 40 " -0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO S 41 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO S 41 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO S 41 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO B 236 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.016 5.00e-02 4.00e+02 ... (remaining 1583 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 435 2.73 - 3.27: 9049 3.27 - 3.82: 14930 3.82 - 4.36: 17758 4.36 - 4.90: 31232 Nonbonded interactions: 73404 Sorted by model distance: nonbonded pdb=" O LYS A 248 " pdb=" OD1 ASP A 251 " model vdw 2.189 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR A 230 " pdb=" OG SER A 281 " model vdw 2.248 3.040 nonbonded pdb=" O PHE S 29 " pdb=" NH2 ARG S 72 " model vdw 2.263 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.269 3.040 ... (remaining 73399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.540 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4588 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 : 0.011 0.320 9425 Z= 0.733 Angle : 0.724 13.301 12797 Z= 0.335 Chirality : 0.061 0.558 1457 Planarity : 0.003 0.032 1586 Dihedral : 9.420 77.794 3633 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.40 % Allowed : 2.43 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.34 (0.23), residues: 1144 helix: 0.07 (0.25), residues: 408 sheet: -1.00 (0.27), residues: 292 loop : -1.59 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.000 HIS B 183 PHE 0.008 0.001 PHE A 274 TYR 0.006 0.001 TYR S 102 ARG 0.002 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 227 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: R 71 ASN cc_start: 0.6883 (m110) cc_final: 0.6622 (m110) REVERT: R 244 LYS cc_start: 0.6246 (mttt) cc_final: 0.5999 (mtmm) REVERT: A 248 LYS cc_start: 0.6669 (ttmm) cc_final: 0.6377 (tmmm) REVERT: A 266 LEU cc_start: 0.5029 (tp) cc_final: 0.4807 (tm) REVERT: A 276 GLU cc_start: 0.7628 (mp0) cc_final: 0.7292 (mp0) REVERT: A 305 CYS cc_start: 0.6720 (m) cc_final: 0.6438 (m) REVERT: A 314 LYS cc_start: 0.6025 (mttt) cc_final: 0.5625 (tppt) REVERT: A 342 VAL cc_start: 0.6855 (t) cc_final: 0.6526 (m) REVERT: G 20 LYS cc_start: 0.7013 (ptpp) cc_final: 0.6256 (pttm) REVERT: G 60 PRO cc_start: 0.6335 (Cg_endo) cc_final: 0.6097 (Cg_exo) REVERT: S 53 SER cc_start: 0.6534 (t) cc_final: 0.6274 (p) outliers start: 4 outliers final: 0 residues processed: 231 average time/residue: 1.1016 time to fit residues: 274.1207 Evaluate side-chains 136 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 0.0170 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 71 ASN R 173 HIS R 190 GLN A 204 GLN B 91 HIS B 142 HIS B 176 GLN G 18 GLN G 59 ASN S 39 GLN S 194 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9425 Z= 0.229 Angle : 0.691 10.469 12797 Z= 0.349 Chirality : 0.044 0.173 1457 Planarity : 0.005 0.054 1586 Dihedral : 6.943 55.688 1574 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.04 % Allowed : 11.94 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.10 (0.24), residues: 1144 helix: 1.30 (0.27), residues: 396 sheet: -0.31 (0.28), residues: 288 loop : -1.06 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP S 36 HIS 0.014 0.002 HIS R 173 PHE 0.028 0.002 PHE R 91 TYR 0.015 0.002 TYR G 40 ARG 0.006 0.001 ARG S 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: R 78 SER cc_start: 0.7122 (m) cc_final: 0.6119 (p) REVERT: A 10 LYS cc_start: 0.6808 (mttt) cc_final: 0.6556 (mttp) REVERT: A 198 MET cc_start: 0.7799 (mtp) cc_final: 0.7300 (mtm) REVERT: A 248 LYS cc_start: 0.7136 (ttmm) cc_final: 0.6824 (tmmm) REVERT: A 276 GLU cc_start: 0.7583 (mp0) cc_final: 0.7311 (mp0) REVERT: A 305 CYS cc_start: 0.7089 (m) cc_final: 0.6625 (m) REVERT: A 314 LYS cc_start: 0.6426 (mttt) cc_final: 0.6193 (tppt) REVERT: B 61 MET cc_start: 0.7343 (tmt) cc_final: 0.7020 (tmt) REVERT: B 134 ARG cc_start: 0.7432 (mtp180) cc_final: 0.6625 (mtp-110) REVERT: B 190 LEU cc_start: 0.8538 (mt) cc_final: 0.7987 (pp) REVERT: B 219 ARG cc_start: 0.7812 (mmt180) cc_final: 0.7176 (mpt-90) REVERT: G 38 MET cc_start: 0.5317 (OUTLIER) cc_final: 0.5035 (mmm) REVERT: S 46 GLU cc_start: 0.7068 (pt0) cc_final: 0.6575 (pt0) REVERT: S 58 ILE cc_start: 0.6039 (mt) cc_final: 0.5822 (mt) REVERT: S 83 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7823 (ptp) outliers start: 30 outliers final: 10 residues processed: 200 average time/residue: 1.1023 time to fit residues: 237.4148 Evaluate side-chains 128 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 164 SER Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 190 GLN R 228 HIS R 299 ASN A 204 GLN B 88 ASN B 125 ASN B 340 ASN L 5 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.7690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9425 Z= 0.214 Angle : 0.595 8.393 12797 Z= 0.305 Chirality : 0.042 0.149 1457 Planarity : 0.004 0.035 1586 Dihedral : 5.836 42.002 1574 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.85 % Allowed : 14.07 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.46 (0.25), residues: 1144 helix: 1.94 (0.28), residues: 392 sheet: -0.05 (0.29), residues: 283 loop : -0.86 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 63 HIS 0.011 0.001 HIS S 35 PHE 0.017 0.002 PHE B 151 TYR 0.010 0.001 TYR S 173 ARG 0.005 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: R 115 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6510 (p90) REVERT: R 252 VAL cc_start: 0.6445 (OUTLIER) cc_final: 0.6091 (m) REVERT: A 17 LYS cc_start: 0.6227 (mttt) cc_final: 0.5882 (mtmt) REVERT: A 22 ASN cc_start: 0.6928 (m-40) cc_final: 0.6677 (m110) REVERT: A 28 GLU cc_start: 0.6982 (tt0) cc_final: 0.6492 (mt-10) REVERT: A 209 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.7114 (tttm) REVERT: A 276 GLU cc_start: 0.7758 (mp0) cc_final: 0.7403 (mp0) REVERT: B 16 ASN cc_start: 0.6258 (m-40) cc_final: 0.5978 (m110) REVERT: B 19 ARG cc_start: 0.5732 (ttp80) cc_final: 0.5491 (ttp80) REVERT: B 61 MET cc_start: 0.7974 (tmt) cc_final: 0.7625 (tmt) REVERT: B 98 SER cc_start: 0.8378 (m) cc_final: 0.7725 (t) REVERT: B 134 ARG cc_start: 0.7425 (mtp180) cc_final: 0.6713 (mtp-110) REVERT: B 137 ARG cc_start: 0.7081 (mmp80) cc_final: 0.6877 (tpp-160) REVERT: B 138 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7872 (mt-10) REVERT: B 215 GLU cc_start: 0.7213 (mp0) cc_final: 0.7005 (mt-10) REVERT: B 219 ARG cc_start: 0.7651 (mmt180) cc_final: 0.7330 (mmt90) REVERT: B 226 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7475 (pm20) REVERT: B 268 ASN cc_start: 0.6779 (t0) cc_final: 0.6375 (m-40) REVERT: B 277 SER cc_start: 0.8780 (t) cc_final: 0.8080 (p) REVERT: B 312 ASP cc_start: 0.7374 (m-30) cc_final: 0.7174 (m-30) REVERT: S 46 GLU cc_start: 0.7817 (pt0) cc_final: 0.7308 (pt0) REVERT: S 76 LYS cc_start: 0.7156 (mtpt) cc_final: 0.6894 (mtpp) REVERT: S 183 GLN cc_start: 0.5536 (mm110) cc_final: 0.5321 (mp-120) REVERT: S 189 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7542 (mt) REVERT: S 191 ARG cc_start: 0.2067 (OUTLIER) cc_final: 0.1525 (tpp80) outliers start: 38 outliers final: 13 residues processed: 194 average time/residue: 1.2253 time to fit residues: 253.7346 Evaluate side-chains 154 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 190 GLN A 204 GLN B 156 GLN S 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.9872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9425 Z= 0.238 Angle : 0.603 6.604 12797 Z= 0.314 Chirality : 0.044 0.152 1457 Planarity : 0.004 0.050 1586 Dihedral : 6.181 59.839 1574 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.76 % Allowed : 17.00 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.58 (0.25), residues: 1144 helix: 1.93 (0.27), residues: 398 sheet: 0.07 (0.30), residues: 283 loop : -0.75 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.010 0.001 HIS B 54 PHE 0.030 0.002 PHE R 115 TYR 0.025 0.002 TYR B 105 ARG 0.004 0.001 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 1.100 Fit side-chains REVERT: R 78 SER cc_start: 0.7786 (OUTLIER) cc_final: 0.7366 (m) REVERT: R 82 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7268 (tp) REVERT: R 234 MET cc_start: 0.7146 (mmm) cc_final: 0.6846 (mmp) REVERT: R 252 VAL cc_start: 0.6986 (OUTLIER) cc_final: 0.6769 (m) REVERT: A 22 ASN cc_start: 0.7197 (m-40) cc_final: 0.6950 (m110) REVERT: A 24 ARG cc_start: 0.6714 (mtm-85) cc_final: 0.6500 (mtm110) REVERT: A 25 GLU cc_start: 0.6323 (tt0) cc_final: 0.5507 (tm-30) REVERT: A 28 GLU cc_start: 0.7011 (tt0) cc_final: 0.6492 (mt-10) REVERT: A 209 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7102 (mptt) REVERT: A 273 LEU cc_start: 0.7428 (tp) cc_final: 0.6977 (tp) REVERT: B 46 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.6200 (mmt90) REVERT: B 130 GLU cc_start: 0.7020 (mt-10) cc_final: 0.5923 (mp0) REVERT: B 134 ARG cc_start: 0.7326 (mtp180) cc_final: 0.6904 (ptp90) REVERT: B 137 ARG cc_start: 0.7006 (mmp80) cc_final: 0.6545 (tpt170) REVERT: B 138 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8057 (mt-10) REVERT: B 215 GLU cc_start: 0.7367 (mp0) cc_final: 0.6948 (mt-10) REVERT: B 226 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7680 (pm20) REVERT: B 312 ASP cc_start: 0.7602 (m-30) cc_final: 0.7217 (m-30) REVERT: G 26 ASP cc_start: 0.7662 (t0) cc_final: 0.7370 (p0) REVERT: G 46 LYS cc_start: 0.7850 (tppt) cc_final: 0.7585 (mmtm) REVERT: G 58 GLU cc_start: 0.6542 (mp0) cc_final: 0.5789 (tm-30) REVERT: S 18 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6843 (mmt180) REVERT: S 46 GLU cc_start: 0.7884 (pt0) cc_final: 0.7305 (pt0) REVERT: S 65 LYS cc_start: 0.7088 (ttmt) cc_final: 0.6832 (ttpt) REVERT: S 71 SER cc_start: 0.7532 (OUTLIER) cc_final: 0.7236 (p) REVERT: S 83 MET cc_start: 0.7942 (ptp) cc_final: 0.7301 (ptm) REVERT: S 160 ARG cc_start: 0.7323 (ptt90) cc_final: 0.6260 (mtm-85) REVERT: S 183 GLN cc_start: 0.6613 (mm110) cc_final: 0.6228 (mp-120) REVERT: S 186 GLN cc_start: 0.7455 (tt0) cc_final: 0.7146 (tt0) outliers start: 47 outliers final: 16 residues processed: 180 average time/residue: 1.2614 time to fit residues: 242.1437 Evaluate side-chains 158 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 120 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 346 ASN B 32 GLN S 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 1.0664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9425 Z= 0.280 Angle : 0.618 7.093 12797 Z= 0.323 Chirality : 0.044 0.175 1457 Planarity : 0.004 0.053 1586 Dihedral : 6.233 58.872 1574 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.86 % Allowed : 18.22 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.66 (0.25), residues: 1144 helix: 2.09 (0.27), residues: 392 sheet: 0.09 (0.30), residues: 279 loop : -0.73 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.007 0.001 HIS B 54 PHE 0.030 0.002 PHE R 115 TYR 0.012 0.002 TYR B 105 ARG 0.004 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 0.984 Fit side-chains REVERT: R 252 VAL cc_start: 0.7227 (OUTLIER) cc_final: 0.6895 (m) REVERT: A 22 ASN cc_start: 0.6924 (m-40) cc_final: 0.6688 (m110) REVERT: A 24 ARG cc_start: 0.6743 (mtm-85) cc_final: 0.6543 (mtm110) REVERT: A 28 GLU cc_start: 0.6969 (tt0) cc_final: 0.6445 (mt-10) REVERT: A 209 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7036 (mppt) REVERT: A 272 ASP cc_start: 0.6763 (m-30) cc_final: 0.6548 (m-30) REVERT: A 345 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.5801 (mptt) REVERT: B 46 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6304 (mmt90) REVERT: B 130 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6089 (mp0) REVERT: B 134 ARG cc_start: 0.7279 (mtp180) cc_final: 0.6889 (ptp90) REVERT: B 137 ARG cc_start: 0.6931 (mmp80) cc_final: 0.6516 (tpt170) REVERT: B 215 GLU cc_start: 0.7238 (mp0) cc_final: 0.7025 (mt-10) REVERT: B 226 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7599 (pm20) REVERT: B 312 ASP cc_start: 0.7674 (m-30) cc_final: 0.7354 (m-30) REVERT: G 58 GLU cc_start: 0.6608 (mp0) cc_final: 0.5648 (tm-30) REVERT: S 46 GLU cc_start: 0.7897 (pt0) cc_final: 0.7478 (pt0) REVERT: S 65 LYS cc_start: 0.7209 (ttmt) cc_final: 0.6865 (ttpt) REVERT: S 71 SER cc_start: 0.7225 (OUTLIER) cc_final: 0.6776 (p) REVERT: S 186 GLN cc_start: 0.7616 (tt0) cc_final: 0.7280 (tt0) REVERT: S 245 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7247 (mp) outliers start: 48 outliers final: 23 residues processed: 171 average time/residue: 1.2697 time to fit residues: 231.6331 Evaluate side-chains 161 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 166 MET Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain L residue 6 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 0.1980 chunk 89 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 104 optimal weight: 0.4980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 32 GLN B 266 HIS B 268 ASN G 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 1.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9425 Z= 0.188 Angle : 0.539 8.037 12797 Z= 0.277 Chirality : 0.042 0.136 1457 Planarity : 0.004 0.053 1586 Dihedral : 5.714 59.778 1574 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.66 % Allowed : 19.13 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.86 (0.25), residues: 1144 helix: 2.29 (0.27), residues: 394 sheet: 0.21 (0.30), residues: 281 loop : -0.68 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 211 HIS 0.004 0.001 HIS B 54 PHE 0.024 0.001 PHE R 115 TYR 0.008 0.001 TYR S 103 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 1.050 Fit side-chains REVERT: R 252 VAL cc_start: 0.7059 (OUTLIER) cc_final: 0.6805 (m) REVERT: R 308 GLU cc_start: 0.7463 (mp0) cc_final: 0.6277 (tp30) REVERT: A 22 ASN cc_start: 0.6827 (m-40) cc_final: 0.6595 (m110) REVERT: A 25 GLU cc_start: 0.6370 (tt0) cc_final: 0.5989 (tt0) REVERT: A 28 GLU cc_start: 0.6902 (tt0) cc_final: 0.6408 (mt-10) REVERT: A 192 LYS cc_start: 0.6834 (OUTLIER) cc_final: 0.6606 (mttm) REVERT: A 209 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7143 (mptt) REVERT: A 306 GLN cc_start: 0.7204 (mm-40) cc_final: 0.6976 (mm110) REVERT: B 46 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6126 (mtp-110) REVERT: B 130 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6040 (mp0) REVERT: B 134 ARG cc_start: 0.7316 (mtp180) cc_final: 0.6911 (ptp90) REVERT: B 137 ARG cc_start: 0.6813 (mmp80) cc_final: 0.6508 (tpt170) REVERT: B 226 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7575 (pm20) REVERT: B 312 ASP cc_start: 0.7734 (m-30) cc_final: 0.7398 (m-30) REVERT: G 58 GLU cc_start: 0.6604 (mp0) cc_final: 0.5661 (tm-30) REVERT: S 46 GLU cc_start: 0.7884 (pt0) cc_final: 0.7491 (pt0) REVERT: S 65 LYS cc_start: 0.7211 (ttmt) cc_final: 0.6823 (ttpt) REVERT: S 71 SER cc_start: 0.7277 (OUTLIER) cc_final: 0.6919 (p) REVERT: S 118 THR cc_start: 0.7563 (OUTLIER) cc_final: 0.7251 (p) REVERT: S 160 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6108 (mtm-85) REVERT: S 186 GLN cc_start: 0.7634 (tt0) cc_final: 0.7291 (tt0) outliers start: 46 outliers final: 23 residues processed: 164 average time/residue: 1.2938 time to fit residues: 225.9961 Evaluate side-chains 168 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 254 VAL Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 160 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN G 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 1.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9425 Z= 0.162 Angle : 0.513 7.753 12797 Z= 0.264 Chirality : 0.041 0.135 1457 Planarity : 0.004 0.051 1586 Dihedral : 5.424 58.175 1574 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.96 % Allowed : 18.93 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.04 (0.26), residues: 1144 helix: 2.46 (0.27), residues: 394 sheet: 0.28 (0.30), residues: 281 loop : -0.57 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.003 0.001 HIS B 54 PHE 0.020 0.001 PHE R 115 TYR 0.009 0.001 TYR S 59 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 140 time to evaluate : 1.065 Fit side-chains REVERT: R 252 VAL cc_start: 0.7040 (OUTLIER) cc_final: 0.6815 (m) REVERT: R 271 GLU cc_start: 0.7281 (tp30) cc_final: 0.6928 (mm-30) REVERT: R 308 GLU cc_start: 0.7473 (mp0) cc_final: 0.7042 (mt-10) REVERT: A 22 ASN cc_start: 0.6817 (m-40) cc_final: 0.6587 (m110) REVERT: A 25 GLU cc_start: 0.6362 (tt0) cc_final: 0.6004 (tt0) REVERT: A 28 GLU cc_start: 0.6834 (tt0) cc_final: 0.6441 (mt-10) REVERT: A 192 LYS cc_start: 0.6826 (OUTLIER) cc_final: 0.6601 (mttm) REVERT: A 209 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7232 (mptt) REVERT: A 345 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.5740 (mptt) REVERT: B 46 ARG cc_start: 0.6847 (OUTLIER) cc_final: 0.6108 (mtp-110) REVERT: B 76 ASP cc_start: 0.7110 (m-30) cc_final: 0.6879 (m-30) REVERT: B 130 GLU cc_start: 0.6938 (mt-10) cc_final: 0.5966 (mp0) REVERT: B 134 ARG cc_start: 0.7294 (mtp180) cc_final: 0.6927 (ptp90) REVERT: B 137 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6262 (tpt170) REVERT: B 226 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7522 (pm20) REVERT: B 296 VAL cc_start: 0.8030 (OUTLIER) cc_final: 0.7667 (p) REVERT: B 312 ASP cc_start: 0.7690 (m-30) cc_final: 0.7336 (m-30) REVERT: G 42 GLU cc_start: 0.7079 (tm-30) cc_final: 0.5524 (mm-30) REVERT: G 58 GLU cc_start: 0.6630 (mp0) cc_final: 0.5647 (tm-30) REVERT: S 46 GLU cc_start: 0.7907 (pt0) cc_final: 0.7497 (pt0) REVERT: S 65 LYS cc_start: 0.7248 (ttmt) cc_final: 0.6840 (ttpt) REVERT: S 71 SER cc_start: 0.7205 (OUTLIER) cc_final: 0.6896 (p) REVERT: S 98 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7853 (ttp-170) REVERT: S 118 THR cc_start: 0.7418 (OUTLIER) cc_final: 0.7126 (p) REVERT: S 160 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6093 (mtm-85) REVERT: S 186 GLN cc_start: 0.7659 (tt0) cc_final: 0.7362 (tt0) outliers start: 49 outliers final: 20 residues processed: 165 average time/residue: 1.2360 time to fit residues: 217.7879 Evaluate side-chains 166 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 254 VAL Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain L residue 6 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 84 optimal weight: 0.1980 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN G 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 1.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9425 Z= 0.137 Angle : 0.498 9.087 12797 Z= 0.253 Chirality : 0.040 0.133 1457 Planarity : 0.003 0.051 1586 Dihedral : 5.270 55.141 1574 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.24 % Allowed : 20.95 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.16 (0.26), residues: 1144 helix: 2.61 (0.28), residues: 390 sheet: 0.25 (0.30), residues: 286 loop : -0.45 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.004 0.001 HIS R 228 PHE 0.015 0.001 PHE R 115 TYR 0.009 0.001 TYR A 302 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 1.078 Fit side-chains REVERT: R 51 ASN cc_start: 0.6602 (m-40) cc_final: 0.6219 (m110) REVERT: R 271 GLU cc_start: 0.7201 (tp30) cc_final: 0.6813 (mm-30) REVERT: R 308 GLU cc_start: 0.7516 (mp0) cc_final: 0.7069 (mt-10) REVERT: A 22 ASN cc_start: 0.6806 (m-40) cc_final: 0.6578 (m110) REVERT: A 25 GLU cc_start: 0.6351 (tt0) cc_final: 0.6006 (tt0) REVERT: A 28 GLU cc_start: 0.6820 (tt0) cc_final: 0.6433 (mt-10) REVERT: A 192 LYS cc_start: 0.6805 (OUTLIER) cc_final: 0.6583 (mttm) REVERT: A 345 LYS cc_start: 0.7110 (OUTLIER) cc_final: 0.5637 (mptt) REVERT: B 46 ARG cc_start: 0.6823 (mmp80) cc_final: 0.6105 (mtp180) REVERT: B 130 GLU cc_start: 0.6869 (mt-10) cc_final: 0.5927 (mp0) REVERT: B 134 ARG cc_start: 0.7228 (mtp180) cc_final: 0.6904 (ptp90) REVERT: B 137 ARG cc_start: 0.6673 (OUTLIER) cc_final: 0.6300 (tpt170) REVERT: B 172 GLU cc_start: 0.7008 (tp30) cc_final: 0.6620 (pt0) REVERT: B 226 GLU cc_start: 0.7975 (pt0) cc_final: 0.7461 (pm20) REVERT: B 296 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7714 (p) REVERT: B 312 ASP cc_start: 0.7746 (m-30) cc_final: 0.7386 (m-30) REVERT: G 42 GLU cc_start: 0.7055 (tm-30) cc_final: 0.5527 (mm-30) REVERT: G 58 GLU cc_start: 0.6560 (mp0) cc_final: 0.5592 (tm-30) REVERT: S 46 GLU cc_start: 0.7927 (pt0) cc_final: 0.7531 (pt0) REVERT: S 65 LYS cc_start: 0.7238 (ttmt) cc_final: 0.6851 (ttpt) REVERT: S 71 SER cc_start: 0.7239 (OUTLIER) cc_final: 0.6964 (p) REVERT: S 98 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7717 (ttp-170) REVERT: S 118 THR cc_start: 0.7402 (OUTLIER) cc_final: 0.7130 (p) REVERT: S 160 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6182 (mtm-85) REVERT: S 186 GLN cc_start: 0.7649 (tt0) cc_final: 0.7376 (tt0) REVERT: S 192 MET cc_start: 0.4485 (mpp) cc_final: 0.3111 (mpp) outliers start: 32 outliers final: 17 residues processed: 158 average time/residue: 1.3493 time to fit residues: 226.9108 Evaluate side-chains 159 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 254 VAL Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain L residue 6 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.0060 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.0980 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 268 ASN G 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 1.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9425 Z= 0.151 Angle : 0.508 8.379 12797 Z= 0.257 Chirality : 0.040 0.133 1457 Planarity : 0.004 0.051 1586 Dihedral : 5.267 55.905 1574 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.14 % Allowed : 21.66 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 1144 helix: 2.63 (0.27), residues: 389 sheet: 0.24 (0.30), residues: 288 loop : -0.43 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.004 0.001 HIS R 228 PHE 0.018 0.001 PHE R 115 TYR 0.011 0.001 TYR S 59 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: R 51 ASN cc_start: 0.6620 (m-40) cc_final: 0.6168 (m110) REVERT: R 308 GLU cc_start: 0.7548 (mp0) cc_final: 0.7076 (mt-10) REVERT: A 22 ASN cc_start: 0.6847 (m-40) cc_final: 0.6613 (m110) REVERT: A 25 GLU cc_start: 0.6359 (tt0) cc_final: 0.6010 (tt0) REVERT: A 28 GLU cc_start: 0.6836 (tt0) cc_final: 0.6458 (mt-10) REVERT: A 192 LYS cc_start: 0.6804 (OUTLIER) cc_final: 0.6576 (mttm) REVERT: B 46 ARG cc_start: 0.6873 (mmp80) cc_final: 0.6120 (mtp180) REVERT: B 130 GLU cc_start: 0.6899 (mt-10) cc_final: 0.5943 (mp0) REVERT: B 134 ARG cc_start: 0.7230 (mtp180) cc_final: 0.6912 (ptp90) REVERT: B 137 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6307 (tpt170) REVERT: B 172 GLU cc_start: 0.7084 (tp30) cc_final: 0.6717 (pt0) REVERT: B 226 GLU cc_start: 0.7991 (pt0) cc_final: 0.7460 (pm20) REVERT: B 296 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7707 (p) REVERT: B 312 ASP cc_start: 0.7731 (m-30) cc_final: 0.7373 (m-30) REVERT: G 42 GLU cc_start: 0.7139 (tm-30) cc_final: 0.5569 (mm-30) REVERT: G 58 GLU cc_start: 0.6599 (mp0) cc_final: 0.5670 (tm-30) REVERT: S 39 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7059 (tp40) REVERT: S 46 GLU cc_start: 0.7860 (pt0) cc_final: 0.7475 (pt0) REVERT: S 65 LYS cc_start: 0.7241 (ttmt) cc_final: 0.6863 (ttpt) REVERT: S 71 SER cc_start: 0.7180 (OUTLIER) cc_final: 0.6925 (p) REVERT: S 98 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7747 (ttp-170) REVERT: S 118 THR cc_start: 0.7400 (OUTLIER) cc_final: 0.7129 (p) REVERT: S 160 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6180 (mtm-85) REVERT: S 186 GLN cc_start: 0.7656 (tt0) cc_final: 0.7400 (tt0) REVERT: S 192 MET cc_start: 0.4391 (mpp) cc_final: 0.3021 (mpp) outliers start: 31 outliers final: 19 residues processed: 158 average time/residue: 1.2750 time to fit residues: 214.8758 Evaluate side-chains 158 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 254 VAL Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain L residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.0770 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN G 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 1.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9425 Z= 0.137 Angle : 0.497 8.513 12797 Z= 0.252 Chirality : 0.040 0.197 1457 Planarity : 0.003 0.051 1586 Dihedral : 5.189 56.985 1574 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.24 % Allowed : 21.56 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.26), residues: 1144 helix: 2.72 (0.28), residues: 389 sheet: 0.32 (0.30), residues: 286 loop : -0.43 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.004 0.001 HIS R 228 PHE 0.015 0.001 PHE R 115 TYR 0.008 0.001 TYR A 302 ARG 0.003 0.000 ARG B 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.977 Fit side-chains REVERT: R 51 ASN cc_start: 0.6537 (m-40) cc_final: 0.6082 (m110) REVERT: R 308 GLU cc_start: 0.7644 (mp0) cc_final: 0.7147 (mt-10) REVERT: A 22 ASN cc_start: 0.6842 (m-40) cc_final: 0.6606 (m110) REVERT: A 25 GLU cc_start: 0.6346 (tt0) cc_final: 0.6014 (tt0) REVERT: A 28 GLU cc_start: 0.6825 (tt0) cc_final: 0.6454 (mt-10) REVERT: A 192 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.6570 (mttm) REVERT: B 46 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.6128 (mtp180) REVERT: B 130 GLU cc_start: 0.6845 (mt-10) cc_final: 0.5983 (mp0) REVERT: B 134 ARG cc_start: 0.7223 (mtp180) cc_final: 0.6919 (ptp90) REVERT: B 137 ARG cc_start: 0.6656 (OUTLIER) cc_final: 0.6312 (tpt170) REVERT: B 172 GLU cc_start: 0.7085 (tp30) cc_final: 0.6720 (pt0) REVERT: B 215 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7308 (mt-10) REVERT: B 226 GLU cc_start: 0.8076 (pt0) cc_final: 0.7569 (pm20) REVERT: B 296 VAL cc_start: 0.8016 (OUTLIER) cc_final: 0.7701 (p) REVERT: B 312 ASP cc_start: 0.7732 (m-30) cc_final: 0.7390 (m-30) REVERT: G 42 GLU cc_start: 0.7139 (tm-30) cc_final: 0.5576 (mm-30) REVERT: G 46 LYS cc_start: 0.7799 (mmtm) cc_final: 0.7493 (pmtt) REVERT: G 58 GLU cc_start: 0.6563 (mp0) cc_final: 0.5633 (tm-30) REVERT: S 46 GLU cc_start: 0.7929 (pt0) cc_final: 0.7485 (pt0) REVERT: S 65 LYS cc_start: 0.7229 (ttmt) cc_final: 0.6555 (tttm) REVERT: S 71 SER cc_start: 0.7202 (OUTLIER) cc_final: 0.6955 (p) REVERT: S 98 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7789 (ttp-170) REVERT: S 160 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6173 (mtm-85) REVERT: S 186 GLN cc_start: 0.7637 (tt0) cc_final: 0.7247 (tt0) REVERT: S 192 MET cc_start: 0.4664 (mpp) cc_final: 0.3434 (mpp) outliers start: 32 outliers final: 19 residues processed: 156 average time/residue: 1.3365 time to fit residues: 222.3652 Evaluate side-chains 154 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 254 VAL Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain L residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 0.0670 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 0.0980 chunk 37 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 32 GLN G 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.168420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137749 restraints weight = 11238.710| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.90 r_work: 0.3471 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 1.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9425 Z= 0.197 Angle : 0.546 9.067 12797 Z= 0.279 Chirality : 0.042 0.200 1457 Planarity : 0.004 0.052 1586 Dihedral : 5.443 57.665 1574 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.04 % Allowed : 21.86 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 1144 helix: 2.61 (0.27), residues: 391 sheet: 0.30 (0.30), residues: 283 loop : -0.46 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.005 0.001 HIS R 228 PHE 0.024 0.001 PHE R 115 TYR 0.011 0.001 TYR S 59 ARG 0.003 0.000 ARG R 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4021.51 seconds wall clock time: 72 minutes 40.28 seconds (4360.28 seconds total)