Starting phenix.real_space_refine on Sat Jul 26 15:30:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ezh_31387/07_2025/7ezh_31387.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ezh_31387/07_2025/7ezh_31387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ezh_31387/07_2025/7ezh_31387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ezh_31387/07_2025/7ezh_31387.map" model { file = "/net/cci-nas-00/data/ceres_data/7ezh_31387/07_2025/7ezh_31387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ezh_31387/07_2025/7ezh_31387.cif" } resolution = 3.2 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= 0.003 sd= 0.037 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 72 5.16 5 C 5643 2.51 5 N 1489 2.21 5 O 1634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8838 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1753 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2306 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "G" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 404 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "P" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 5.45, per 1000 atoms: 0.62 Number of scatterers: 8838 At special positions: 0 Unit cell: (106.59, 112.86, 119.13, 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 72 16.00 O 1634 8.00 N 1489 7.00 C 5643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 114 " - pdb=" SG CYS D 196 " 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: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 13 sheets defined 41.1% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.509A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.995A pdb=" N LYS A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 205 removed outlier: 4.053A pdb=" N ARG A 205 " --> pdb=" O GLY A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.928A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.513A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 282 through 286 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 26 removed outlier: 5.355A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.657A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 69 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 74 through 105 Proline residue: D 96 - end of helix Proline residue: D 101 - end of helix Processing helix chain 'D' and resid 110 through 145 Processing helix chain 'D' and resid 145 through 153 removed outlier: 3.589A pdb=" N ARG D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP D 152 " --> pdb=" O GLN D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 173 Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 202 through 218 Processing helix chain 'D' and resid 218 through 245 removed outlier: 3.693A pdb=" N GLY D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 339 removed outlier: 3.508A pdb=" N LYS D 308 " --> pdb=" O ASN D 304 " (cutoff:3.500A) Proline residue: D 328 - end of helix Processing helix chain 'D' and resid 339 through 348 Processing helix chain 'D' and resid 349 through 370 removed outlier: 3.719A pdb=" N SER D 362 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS D 364 " --> pdb=" O TYR D 360 " (cutoff:3.500A) Proline residue: D 367 - end of helix Processing helix chain 'D' and resid 371 through 373 No H-bonds generated for 'chain 'D' and resid 371 through 373' Processing helix chain 'D' and resid 374 through 384 removed outlier: 4.364A pdb=" N MET D 382 " --> pdb=" O ARG D 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 25 removed outlier: 3.662A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.658A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.926A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.570A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.867A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.483A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.722A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.771A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.801A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 180 through 187 removed outlier: 3.609A pdb=" N ARG D 197 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN D 191 " --> pdb=" O LYS D 187 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.561A pdb=" N ALA H 92 " --> pdb=" O LEU H 117 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.730A pdb=" N CYS H 159 " --> pdb=" O PHE H 212 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE H 212 " --> pdb=" O CYS H 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.760A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1317 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: 2.71 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2822 1.35 - 1.47: 2251 1.47 - 1.59: 3841 1.59 - 1.71: 1 1.71 - 1.83: 107 Bond restraints: 9022 Sorted by residual: bond pdb=" O1 TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.462 1.635 -0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" OH TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.679 1.537 0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" N VAL H 119 " pdb=" CA VAL H 119 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.15e-02 7.56e+03 1.42e+01 bond pdb=" N SER H 120 " pdb=" CA SER H 120 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.29e-02 6.01e+03 5.13e+00 bond pdb=" N ASP A 350 " pdb=" CA ASP A 350 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.46e+00 ... (remaining 9017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 11975 1.93 - 3.85: 225 3.85 - 5.78: 26 5.78 - 7.71: 9 7.71 - 9.63: 3 Bond angle restraints: 12238 Sorted by residual: angle pdb=" N SER A 326 " pdb=" CA SER A 326 " pdb=" C SER A 326 " ideal model delta sigma weight residual 111.14 104.94 6.20 1.08e+00 8.57e-01 3.30e+01 angle pdb=" C GLN D 153 " pdb=" CA GLN D 153 " pdb=" CB GLN D 153 " ideal model delta sigma weight residual 111.88 104.45 7.43 1.41e+00 5.03e-01 2.77e+01 angle pdb=" C THR A 329 " pdb=" CA THR A 329 " pdb=" CB THR A 329 " ideal model delta sigma weight residual 110.42 118.59 -8.17 1.99e+00 2.53e-01 1.69e+01 angle pdb=" CA ALA H 136 " pdb=" C ALA H 136 " pdb=" O ALA H 136 " ideal model delta sigma weight residual 121.54 117.25 4.29 1.16e+00 7.43e-01 1.37e+01 angle pdb=" N GLY B 141 " pdb=" CA GLY B 141 " pdb=" C GLY B 141 " ideal model delta sigma weight residual 113.18 121.71 -8.53 2.37e+00 1.78e-01 1.30e+01 ... (remaining 12233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 4876 16.62 - 33.23: 384 33.23 - 49.85: 55 49.85 - 66.46: 13 66.46 - 83.08: 8 Dihedral angle restraints: 5336 sinusoidal: 2000 harmonic: 3336 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 149.62 -56.62 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CA LEU D 200 " pdb=" C LEU D 200 " pdb=" N PRO D 201 " pdb=" CA PRO D 201 " ideal model delta harmonic sigma weight residual -180.00 -152.44 -27.56 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 153.31 26.69 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 5333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1296 0.079 - 0.159: 110 0.159 - 0.238: 3 0.238 - 0.317: 0 0.317 - 0.397: 1 Chirality restraints: 1410 Sorted by residual: chirality pdb=" CA THR A 329 " pdb=" N THR A 329 " pdb=" C THR A 329 " pdb=" CB THR A 329 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA GLN D 153 " pdb=" N GLN D 153 " pdb=" C GLN D 153 " pdb=" CB GLN D 153 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA THR A 327 " pdb=" N THR A 327 " pdb=" C THR A 327 " pdb=" CB THR A 327 " both_signs ideal model delta sigma weight residual False 2.53 2.70 -0.17 2.00e-01 2.50e+01 7.47e-01 ... (remaining 1407 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 214 " -0.021 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C LEU D 214 " 0.074 2.00e-02 2.50e+03 pdb=" O LEU D 214 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU D 215 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 325 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C CYS A 325 " 0.072 2.00e-02 2.50e+03 pdb=" O CYS A 325 " -0.027 2.00e-02 2.50e+03 pdb=" N SER A 326 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.007 2.00e-02 2.50e+03 2.47e-02 1.22e+01 pdb=" CG TYR B 105 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.032 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " -0.032 2.00e-02 2.50e+03 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2178 2.80 - 3.33: 8692 3.33 - 3.85: 14958 3.85 - 4.38: 17905 4.38 - 4.90: 30344 Nonbonded interactions: 74077 Sorted by model distance: nonbonded pdb=" OH TYR B 145 " pdb=" OD2 ASP B 186 " model vdw 2.278 3.040 nonbonded pdb=" OD1 ASN D 304 " pdb=" NZ LYS D 308 " model vdw 2.283 3.120 nonbonded pdb=" O ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.283 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.348 3.040 nonbonded pdb=" OG SER H 161 " pdb=" O LYS H 163 " model vdw 2.360 3.040 ... (remaining 74072 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: 0.300 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.360 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 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 : 0.004 0.173 9024 Z= 0.195 Angle : 0.680 9.633 12242 Z= 0.412 Chirality : 0.045 0.397 1410 Planarity : 0.007 0.057 1537 Dihedral : 12.747 83.080 3172 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.21 % Rotamer: Outliers : 0.74 % Allowed : 2.33 % Favored : 96.93 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.03 % 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: -1.38 (0.23), residues: 1127 helix: -1.09 (0.22), residues: 406 sheet: -0.18 (0.30), residues: 277 loop : -1.01 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.022 0.002 PHE D 354 TYR 0.037 0.005 TYR B 105 ARG 0.053 0.008 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.15273 ( 474) hydrogen bonds : angle 6.97626 ( 1317) SS BOND : bond 0.00401 ( 2) SS BOND : angle 1.58853 ( 4) covalent geometry : bond 0.00359 ( 9022) covalent geometry : angle 0.67968 (12238) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 317 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7824 (ttpt) cc_final: 0.7518 (ttpt) REVERT: A 33 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6426 (mt-10) REVERT: A 186 GLU cc_start: 0.6591 (tt0) cc_final: 0.5926 (tt0) REVERT: A 197 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7524 (mtpp) REVERT: A 210 LYS cc_start: 0.7691 (mmmt) cc_final: 0.7453 (mmtt) REVERT: A 243 MET cc_start: 0.7404 (tpp) cc_final: 0.7156 (tpp) REVERT: A 272 ASP cc_start: 0.7260 (t0) cc_final: 0.6936 (t0) REVERT: A 330 LYS cc_start: 0.6983 (mmtt) cc_final: 0.6424 (mmtt) REVERT: B 43 ILE cc_start: 0.8993 (mm) cc_final: 0.8747 (mt) REVERT: B 83 ASP cc_start: 0.6948 (t0) cc_final: 0.6418 (t0) REVERT: B 121 CYS cc_start: 0.6087 (t) cc_final: 0.5699 (t) REVERT: B 188 MET cc_start: 0.7480 (mmm) cc_final: 0.7132 (mmm) REVERT: B 204 CYS cc_start: 0.7584 (m) cc_final: 0.7309 (m) REVERT: B 205 ASP cc_start: 0.7097 (p0) cc_final: 0.6852 (p0) REVERT: B 219 ARG cc_start: 0.6994 (mmt180) cc_final: 0.6775 (mmt-90) REVERT: B 228 ASP cc_start: 0.5841 (t0) cc_final: 0.5626 (t70) REVERT: B 232 ILE cc_start: 0.8525 (tt) cc_final: 0.8196 (tt) REVERT: B 239 ASN cc_start: 0.7401 (m-40) cc_final: 0.7189 (m-40) REVERT: B 261 LEU cc_start: 0.8006 (mp) cc_final: 0.7803 (mt) REVERT: B 277 SER cc_start: 0.8371 (t) cc_final: 0.7748 (m) REVERT: B 312 ASP cc_start: 0.5952 (t0) cc_final: 0.5590 (t70) REVERT: B 322 ASP cc_start: 0.6255 (t0) cc_final: 0.6038 (t0) REVERT: B 333 ASP cc_start: 0.6065 (m-30) cc_final: 0.5609 (m-30) REVERT: D 47 LEU cc_start: 0.7675 (mt) cc_final: 0.7423 (mt) REVERT: D 178 ILE cc_start: 0.7526 (mt) cc_final: 0.7284 (mt) REVERT: D 218 PHE cc_start: 0.7195 (t80) cc_final: 0.6946 (t80) REVERT: D 314 MET cc_start: 0.7046 (tpp) cc_final: 0.6522 (mpp) REVERT: H 94 TYR cc_start: 0.7747 (m-80) cc_final: 0.7327 (m-80) REVERT: H 140 MET cc_start: 0.8153 (mmm) cc_final: 0.7888 (mmm) REVERT: H 173 TYR cc_start: 0.8330 (m-80) cc_final: 0.8067 (m-80) REVERT: H 178 LEU cc_start: 0.8174 (tp) cc_final: 0.7957 (tt) REVERT: H 226 VAL cc_start: 0.7971 (t) cc_final: 0.7670 (m) REVERT: H 243 THR cc_start: 0.8580 (m) cc_final: 0.8336 (p) outliers start: 7 outliers final: 2 residues processed: 322 average time/residue: 0.2161 time to fit residues: 94.6771 Evaluate side-chains 276 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 274 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 326 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.4980 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.0570 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 33 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN D 153 GLN H 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.144487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.127366 restraints weight = 12255.951| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.01 r_work: 0.3475 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9024 Z= 0.130 Angle : 0.575 7.275 12242 Z= 0.306 Chirality : 0.042 0.140 1410 Planarity : 0.004 0.043 1537 Dihedral : 5.531 28.817 1236 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.22 % Allowed : 11.23 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.17 (0.25), residues: 1127 helix: 1.02 (0.26), residues: 412 sheet: -0.14 (0.29), residues: 280 loop : -0.46 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 339 HIS 0.004 0.001 HIS G 44 PHE 0.020 0.002 PHE D 218 TYR 0.012 0.001 TYR D 370 ARG 0.005 0.001 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 474) hydrogen bonds : angle 5.16279 ( 1317) SS BOND : bond 0.00670 ( 2) SS BOND : angle 1.84622 ( 4) covalent geometry : bond 0.00281 ( 9022) covalent geometry : angle 0.57416 (12238) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 281 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8000 (ttpt) cc_final: 0.7562 (ttpt) REVERT: A 186 GLU cc_start: 0.7385 (tt0) cc_final: 0.7154 (tt0) REVERT: A 210 LYS cc_start: 0.7953 (mmmt) cc_final: 0.7513 (mmtt) REVERT: A 243 MET cc_start: 0.7861 (tpp) cc_final: 0.7661 (tpp) REVERT: A 261 ASP cc_start: 0.7898 (t0) cc_final: 0.7689 (t0) REVERT: A 272 ASP cc_start: 0.7733 (t0) cc_final: 0.7426 (t0) REVERT: A 318 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7175 (mm-30) REVERT: A 330 LYS cc_start: 0.7503 (mmtt) cc_final: 0.6881 (mmtt) REVERT: B 22 ARG cc_start: 0.7142 (mtt90) cc_final: 0.6924 (mtt90) REVERT: B 74 SER cc_start: 0.8378 (m) cc_final: 0.8109 (t) REVERT: B 135 VAL cc_start: 0.8258 (OUTLIER) cc_final: 0.7963 (m) REVERT: B 137 ARG cc_start: 0.8016 (mmt-90) cc_final: 0.7700 (mmt180) REVERT: B 188 MET cc_start: 0.8239 (mmm) cc_final: 0.7856 (mmm) REVERT: B 205 ASP cc_start: 0.7559 (p0) cc_final: 0.7211 (p0) REVERT: B 219 ARG cc_start: 0.7821 (mmt180) cc_final: 0.7448 (mmt90) REVERT: B 232 ILE cc_start: 0.8642 (tt) cc_final: 0.8351 (tt) REVERT: B 256 ARG cc_start: 0.8245 (mpp80) cc_final: 0.7571 (mtt90) REVERT: B 261 LEU cc_start: 0.8354 (mp) cc_final: 0.8129 (mp) REVERT: B 275 SER cc_start: 0.8328 (t) cc_final: 0.8057 (m) REVERT: B 277 SER cc_start: 0.8566 (t) cc_final: 0.7978 (m) REVERT: B 312 ASP cc_start: 0.6635 (t0) cc_final: 0.6231 (t70) REVERT: B 331 SER cc_start: 0.8521 (OUTLIER) cc_final: 0.8210 (p) REVERT: B 333 ASP cc_start: 0.7126 (m-30) cc_final: 0.6561 (m-30) REVERT: D 218 PHE cc_start: 0.7582 (t80) cc_final: 0.7340 (t80) REVERT: D 323 PHE cc_start: 0.8224 (m-10) cc_final: 0.8021 (m-80) REVERT: H 93 MET cc_start: 0.7720 (ttm) cc_final: 0.7519 (ttm) REVERT: H 173 TYR cc_start: 0.8597 (m-80) cc_final: 0.8386 (m-80) REVERT: H 178 LEU cc_start: 0.8449 (tp) cc_final: 0.8215 (tt) REVERT: H 243 THR cc_start: 0.8631 (m) cc_final: 0.8371 (p) outliers start: 21 outliers final: 11 residues processed: 287 average time/residue: 0.2082 time to fit residues: 81.7039 Evaluate side-chains 285 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 272 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 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 = 0.3788 r_free = 0.3788 target = 0.140664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.123067 restraints weight = 12392.467| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.04 r_work: 0.3403 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9024 Z= 0.197 Angle : 0.596 6.919 12242 Z= 0.316 Chirality : 0.044 0.142 1410 Planarity : 0.004 0.050 1537 Dihedral : 5.290 27.511 1235 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.18 % Allowed : 14.51 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.47 (0.25), residues: 1127 helix: 1.40 (0.26), residues: 406 sheet: -0.20 (0.30), residues: 289 loop : -0.23 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.009 0.001 HIS B 142 PHE 0.016 0.002 PHE A 189 TYR 0.023 0.002 TYR D 179 ARG 0.004 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 474) hydrogen bonds : angle 4.92468 ( 1317) SS BOND : bond 0.01588 ( 2) SS BOND : angle 2.63882 ( 4) covalent geometry : bond 0.00440 ( 9022) covalent geometry : angle 0.59464 (12238) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 286 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.7627 (mt) cc_final: 0.7341 (mp) REVERT: A 29 LYS cc_start: 0.7800 (ttpt) cc_final: 0.7379 (ttpt) REVERT: A 33 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7228 (mt-10) REVERT: A 186 GLU cc_start: 0.7500 (tt0) cc_final: 0.7123 (tt0) REVERT: A 197 LYS cc_start: 0.8353 (mtmt) cc_final: 0.8119 (mtpp) REVERT: A 210 LYS cc_start: 0.7830 (mmmt) cc_final: 0.7499 (mmtt) REVERT: A 261 ASP cc_start: 0.7864 (t0) cc_final: 0.7647 (t0) REVERT: A 272 ASP cc_start: 0.7656 (t0) cc_final: 0.7367 (t0) REVERT: A 330 LYS cc_start: 0.7631 (mmtt) cc_final: 0.7043 (mmtt) REVERT: B 22 ARG cc_start: 0.7301 (mtt90) cc_final: 0.7037 (mtt90) REVERT: B 68 ARG cc_start: 0.8109 (ttt-90) cc_final: 0.7703 (tpp80) REVERT: B 74 SER cc_start: 0.8388 (m) cc_final: 0.8179 (t) REVERT: B 129 ARG cc_start: 0.7202 (mmp80) cc_final: 0.6885 (mmp80) REVERT: B 135 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8262 (m) REVERT: B 137 ARG cc_start: 0.8046 (mmt-90) cc_final: 0.7745 (mmt180) REVERT: B 188 MET cc_start: 0.8235 (mmm) cc_final: 0.7935 (mmm) REVERT: B 205 ASP cc_start: 0.7478 (p0) cc_final: 0.7024 (p0) REVERT: B 219 ARG cc_start: 0.7978 (mmt180) cc_final: 0.7554 (mmt90) REVERT: B 230 ASN cc_start: 0.8135 (m-40) cc_final: 0.7748 (m110) REVERT: B 239 ASN cc_start: 0.7908 (m-40) cc_final: 0.7475 (m-40) REVERT: B 256 ARG cc_start: 0.8268 (mpp80) cc_final: 0.7691 (mtt90) REVERT: B 258 ASP cc_start: 0.7785 (t70) cc_final: 0.7408 (t0) REVERT: B 263 THR cc_start: 0.8436 (m) cc_final: 0.8226 (p) REVERT: B 275 SER cc_start: 0.8329 (t) cc_final: 0.8046 (m) REVERT: B 277 SER cc_start: 0.8466 (t) cc_final: 0.7867 (m) REVERT: B 301 LYS cc_start: 0.8553 (mmmt) cc_final: 0.8348 (mtpp) REVERT: B 312 ASP cc_start: 0.6871 (t0) cc_final: 0.6561 (t70) REVERT: B 331 SER cc_start: 0.8341 (OUTLIER) cc_final: 0.8060 (p) REVERT: B 333 ASP cc_start: 0.7009 (m-30) cc_final: 0.6571 (m-30) REVERT: D 98 ASN cc_start: 0.8533 (m110) cc_final: 0.8302 (m-40) REVERT: D 102 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.7820 (t0) REVERT: D 154 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8173 (p) REVERT: H 60 TYR cc_start: 0.8274 (m-80) cc_final: 0.7926 (m-80) REVERT: H 87 ARG cc_start: 0.7424 (ptm160) cc_final: 0.7128 (ptm160) REVERT: H 93 MET cc_start: 0.7744 (ttm) cc_final: 0.7533 (ttm) REVERT: H 173 TYR cc_start: 0.8628 (m-80) cc_final: 0.8315 (m-80) REVERT: H 178 LEU cc_start: 0.8547 (tp) cc_final: 0.8315 (tt) REVERT: H 243 THR cc_start: 0.8720 (m) cc_final: 0.8327 (p) outliers start: 30 outliers final: 19 residues processed: 294 average time/residue: 0.2147 time to fit residues: 85.9173 Evaluate side-chains 291 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 268 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 368 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 15 optimal weight: 0.0470 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 93 optimal weight: 0.4980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.142162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.124862 restraints weight = 12207.143| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.04 r_work: 0.3463 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9024 Z= 0.125 Angle : 0.546 7.294 12242 Z= 0.286 Chirality : 0.042 0.139 1410 Planarity : 0.004 0.051 1537 Dihedral : 4.881 25.802 1235 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.07 % Allowed : 17.16 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.65 (0.25), residues: 1127 helix: 1.69 (0.26), residues: 406 sheet: -0.23 (0.29), residues: 292 loop : -0.19 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 339 HIS 0.003 0.001 HIS A 213 PHE 0.018 0.002 PHE A 196 TYR 0.024 0.001 TYR D 179 ARG 0.004 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 474) hydrogen bonds : angle 4.72855 ( 1317) SS BOND : bond 0.00581 ( 2) SS BOND : angle 1.83914 ( 4) covalent geometry : bond 0.00276 ( 9022) covalent geometry : angle 0.54497 (12238) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 259 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7409 (tm-30) REVERT: A 29 LYS cc_start: 0.7658 (ttpt) cc_final: 0.7299 (ttpt) REVERT: A 33 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7099 (mt-10) REVERT: A 210 LYS cc_start: 0.7859 (mmmt) cc_final: 0.7522 (mmtt) REVERT: A 272 ASP cc_start: 0.7625 (t0) cc_final: 0.7328 (t0) REVERT: A 330 LYS cc_start: 0.7665 (mmtt) cc_final: 0.7048 (mmtt) REVERT: B 22 ARG cc_start: 0.7209 (mtt90) cc_final: 0.6905 (mtt90) REVERT: B 74 SER cc_start: 0.8417 (m) cc_final: 0.8141 (t) REVERT: B 129 ARG cc_start: 0.7204 (mmp80) cc_final: 0.6737 (mmp80) REVERT: B 135 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8195 (m) REVERT: B 137 ARG cc_start: 0.7926 (mmt-90) cc_final: 0.7691 (mmt180) REVERT: B 168 LEU cc_start: 0.8010 (tp) cc_final: 0.7575 (tp) REVERT: B 188 MET cc_start: 0.8221 (mmm) cc_final: 0.7856 (mmm) REVERT: B 205 ASP cc_start: 0.7457 (p0) cc_final: 0.7040 (p0) REVERT: B 219 ARG cc_start: 0.7883 (mmt180) cc_final: 0.7471 (mmt90) REVERT: B 232 ILE cc_start: 0.8687 (tt) cc_final: 0.8358 (tt) REVERT: B 239 ASN cc_start: 0.7900 (m-40) cc_final: 0.7569 (m-40) REVERT: B 258 ASP cc_start: 0.7849 (t70) cc_final: 0.7336 (t0) REVERT: B 275 SER cc_start: 0.8293 (t) cc_final: 0.7993 (m) REVERT: B 277 SER cc_start: 0.8278 (t) cc_final: 0.7680 (m) REVERT: B 298 ASP cc_start: 0.7923 (t70) cc_final: 0.7710 (t70) REVERT: B 301 LYS cc_start: 0.8509 (mmmt) cc_final: 0.8304 (mtpp) REVERT: B 312 ASP cc_start: 0.6798 (t0) cc_final: 0.6469 (t70) REVERT: B 331 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.8151 (p) REVERT: B 333 ASP cc_start: 0.7062 (m-30) cc_final: 0.6596 (m-30) REVERT: D 98 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8235 (m-40) REVERT: D 154 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8152 (p) REVERT: H 60 TYR cc_start: 0.8171 (m-80) cc_final: 0.7822 (m-80) REVERT: H 93 MET cc_start: 0.7754 (ttm) cc_final: 0.7528 (ttm) REVERT: H 172 THR cc_start: 0.8569 (m) cc_final: 0.8211 (p) REVERT: H 173 TYR cc_start: 0.8628 (m-80) cc_final: 0.8308 (m-80) REVERT: H 215 THR cc_start: 0.7725 (m) cc_final: 0.7365 (p) REVERT: H 243 THR cc_start: 0.8692 (m) cc_final: 0.8294 (p) outliers start: 29 outliers final: 16 residues processed: 269 average time/residue: 0.2006 time to fit residues: 76.2863 Evaluate side-chains 274 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 254 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 42 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS B 88 ASN D 77 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.141465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.124254 restraints weight = 12200.855| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.02 r_work: 0.3461 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9024 Z= 0.129 Angle : 0.541 7.091 12242 Z= 0.282 Chirality : 0.042 0.134 1410 Planarity : 0.004 0.047 1537 Dihedral : 4.774 25.829 1235 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.50 % Allowed : 17.48 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.74 (0.26), residues: 1127 helix: 1.79 (0.26), residues: 410 sheet: -0.34 (0.29), residues: 300 loop : -0.03 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.003 0.001 HIS G 44 PHE 0.019 0.002 PHE D 218 TYR 0.024 0.001 TYR D 179 ARG 0.004 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 474) hydrogen bonds : angle 4.71022 ( 1317) SS BOND : bond 0.00520 ( 2) SS BOND : angle 1.81599 ( 4) covalent geometry : bond 0.00285 ( 9022) covalent geometry : angle 0.53984 (12238) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 256 time to evaluate : 0.860 Fit side-chains REVERT: A 14 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7384 (tm-30) REVERT: A 29 LYS cc_start: 0.7680 (ttpt) cc_final: 0.7294 (ttpt) REVERT: A 33 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7106 (mt-10) REVERT: A 197 LYS cc_start: 0.8281 (mtmt) cc_final: 0.8068 (mtpp) REVERT: A 210 LYS cc_start: 0.7865 (mmmt) cc_final: 0.7566 (mmtt) REVERT: A 251 ASP cc_start: 0.7728 (t0) cc_final: 0.7453 (t0) REVERT: A 261 ASP cc_start: 0.7718 (t0) cc_final: 0.7508 (t0) REVERT: A 309 ASP cc_start: 0.6974 (m-30) cc_final: 0.6580 (m-30) REVERT: A 330 LYS cc_start: 0.7701 (mmtt) cc_final: 0.7090 (mmtt) REVERT: B 22 ARG cc_start: 0.7233 (mtt90) cc_final: 0.6859 (mtt90) REVERT: B 74 SER cc_start: 0.8420 (m) cc_final: 0.8165 (t) REVERT: B 129 ARG cc_start: 0.7249 (mmp80) cc_final: 0.6769 (mmp80) REVERT: B 135 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8206 (m) REVERT: B 137 ARG cc_start: 0.7888 (mmt-90) cc_final: 0.7647 (mmt180) REVERT: B 188 MET cc_start: 0.8278 (mmm) cc_final: 0.7811 (mmm) REVERT: B 205 ASP cc_start: 0.7461 (p0) cc_final: 0.7100 (p0) REVERT: B 219 ARG cc_start: 0.7917 (mmt180) cc_final: 0.7504 (mmt90) REVERT: B 232 ILE cc_start: 0.8712 (tt) cc_final: 0.8353 (tt) REVERT: B 258 ASP cc_start: 0.7821 (t70) cc_final: 0.7198 (t0) REVERT: B 275 SER cc_start: 0.8304 (t) cc_final: 0.8055 (t) REVERT: B 277 SER cc_start: 0.8384 (t) cc_final: 0.7777 (m) REVERT: B 298 ASP cc_start: 0.7941 (t70) cc_final: 0.7708 (t70) REVERT: B 312 ASP cc_start: 0.6877 (t0) cc_final: 0.6562 (t70) REVERT: B 331 SER cc_start: 0.8457 (OUTLIER) cc_final: 0.8191 (p) REVERT: B 333 ASP cc_start: 0.7035 (m-30) cc_final: 0.6647 (m-30) REVERT: D 98 ASN cc_start: 0.8499 (m110) cc_final: 0.8226 (m-40) REVERT: D 154 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8168 (p) REVERT: G 21 MET cc_start: 0.6458 (tpp) cc_final: 0.6240 (tpp) REVERT: H 60 TYR cc_start: 0.8149 (m-80) cc_final: 0.7826 (m-80) REVERT: H 93 MET cc_start: 0.7796 (ttm) cc_final: 0.7542 (ttm) REVERT: H 172 THR cc_start: 0.8580 (m) cc_final: 0.8164 (p) REVERT: H 173 TYR cc_start: 0.8646 (m-80) cc_final: 0.8335 (m-80) REVERT: H 178 LEU cc_start: 0.8549 (tp) cc_final: 0.8302 (tt) REVERT: H 215 THR cc_start: 0.7705 (OUTLIER) cc_final: 0.7351 (p) REVERT: H 243 THR cc_start: 0.8711 (m) cc_final: 0.8277 (p) outliers start: 33 outliers final: 23 residues processed: 268 average time/residue: 0.1961 time to fit residues: 73.2764 Evaluate side-chains 275 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 248 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.1980 chunk 91 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.141749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.124615 restraints weight = 12216.929| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.02 r_work: 0.3462 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9024 Z= 0.121 Angle : 0.533 7.168 12242 Z= 0.276 Chirality : 0.041 0.133 1410 Planarity : 0.004 0.044 1537 Dihedral : 4.662 25.721 1235 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.97 % Allowed : 19.17 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.79 (0.26), residues: 1127 helix: 1.88 (0.26), residues: 417 sheet: -0.29 (0.29), residues: 288 loop : -0.13 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.003 0.001 HIS A 213 PHE 0.015 0.002 PHE D 212 TYR 0.022 0.001 TYR D 179 ARG 0.006 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.03262 ( 474) hydrogen bonds : angle 4.67839 ( 1317) SS BOND : bond 0.00514 ( 2) SS BOND : angle 1.61172 ( 4) covalent geometry : bond 0.00270 ( 9022) covalent geometry : angle 0.53230 (12238) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 250 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7607 (ttpt) cc_final: 0.7213 (ttpt) REVERT: A 33 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7146 (mt-10) REVERT: A 210 LYS cc_start: 0.7922 (mmmt) cc_final: 0.7588 (mmtt) REVERT: A 251 ASP cc_start: 0.7715 (t0) cc_final: 0.7421 (t0) REVERT: A 261 ASP cc_start: 0.7675 (t0) cc_final: 0.7442 (t0) REVERT: A 309 ASP cc_start: 0.6957 (m-30) cc_final: 0.6603 (m-30) REVERT: A 330 LYS cc_start: 0.7717 (mmtt) cc_final: 0.7112 (mmtt) REVERT: A 333 GLN cc_start: 0.7856 (tp40) cc_final: 0.7319 (tp-100) REVERT: B 22 ARG cc_start: 0.7275 (mtt90) cc_final: 0.6904 (mtt90) REVERT: B 43 ILE cc_start: 0.8752 (mt) cc_final: 0.8541 (mt) REVERT: B 74 SER cc_start: 0.8437 (m) cc_final: 0.8180 (t) REVERT: B 129 ARG cc_start: 0.7214 (mmp80) cc_final: 0.6722 (mmp80) REVERT: B 135 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.8277 (m) REVERT: B 137 ARG cc_start: 0.7833 (mmt-90) cc_final: 0.7605 (mmt180) REVERT: B 188 MET cc_start: 0.8247 (mmm) cc_final: 0.8042 (mmm) REVERT: B 219 ARG cc_start: 0.7912 (mmt180) cc_final: 0.7515 (mmt90) REVERT: B 232 ILE cc_start: 0.8729 (tt) cc_final: 0.8391 (tt) REVERT: B 239 ASN cc_start: 0.7860 (m-40) cc_final: 0.7543 (m-40) REVERT: B 258 ASP cc_start: 0.7811 (t0) cc_final: 0.7160 (t0) REVERT: B 275 SER cc_start: 0.8312 (t) cc_final: 0.8059 (t) REVERT: B 277 SER cc_start: 0.8240 (t) cc_final: 0.7684 (m) REVERT: B 298 ASP cc_start: 0.7933 (t70) cc_final: 0.7598 (t70) REVERT: B 312 ASP cc_start: 0.6851 (t0) cc_final: 0.6544 (t70) REVERT: B 331 SER cc_start: 0.8450 (t) cc_final: 0.8172 (p) REVERT: B 333 ASP cc_start: 0.7032 (m-30) cc_final: 0.6648 (m-30) REVERT: D 154 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8203 (p) REVERT: H 60 TYR cc_start: 0.8106 (m-80) cc_final: 0.7783 (m-80) REVERT: H 93 MET cc_start: 0.7780 (ttm) cc_final: 0.7522 (ttm) REVERT: H 115 THR cc_start: 0.8260 (t) cc_final: 0.8027 (t) REVERT: H 138 ILE cc_start: 0.8136 (mm) cc_final: 0.7933 (mm) REVERT: H 172 THR cc_start: 0.8590 (m) cc_final: 0.8154 (p) REVERT: H 178 LEU cc_start: 0.8536 (tp) cc_final: 0.8317 (tt) REVERT: H 243 THR cc_start: 0.8725 (m) cc_final: 0.8248 (p) outliers start: 28 outliers final: 23 residues processed: 262 average time/residue: 0.1893 time to fit residues: 69.6659 Evaluate side-chains 272 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 247 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 11 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.140798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.123334 restraints weight = 12334.578| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.04 r_work: 0.3442 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9024 Z= 0.153 Angle : 0.563 7.624 12242 Z= 0.290 Chirality : 0.043 0.168 1410 Planarity : 0.004 0.045 1537 Dihedral : 4.730 27.104 1235 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.50 % Allowed : 18.11 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.80 (0.26), residues: 1127 helix: 1.92 (0.26), residues: 410 sheet: -0.34 (0.29), residues: 292 loop : -0.08 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 111 HIS 0.004 0.001 HIS A 213 PHE 0.025 0.002 PHE H 68 TYR 0.020 0.001 TYR D 179 ARG 0.004 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 474) hydrogen bonds : angle 4.79363 ( 1317) SS BOND : bond 0.00638 ( 2) SS BOND : angle 1.93801 ( 4) covalent geometry : bond 0.00343 ( 9022) covalent geometry : angle 0.56155 (12238) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 254 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7922 (mttt) cc_final: 0.7715 (mmmm) REVERT: A 29 LYS cc_start: 0.7618 (ttpt) cc_final: 0.7240 (ttpt) REVERT: A 33 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7193 (mt-10) REVERT: A 210 LYS cc_start: 0.7899 (mmmt) cc_final: 0.7585 (mmtt) REVERT: A 251 ASP cc_start: 0.7729 (t0) cc_final: 0.7455 (t0) REVERT: A 309 ASP cc_start: 0.6990 (m-30) cc_final: 0.6688 (m-30) REVERT: A 330 LYS cc_start: 0.7760 (mmtt) cc_final: 0.7179 (mmtt) REVERT: A 333 GLN cc_start: 0.7951 (tp40) cc_final: 0.7398 (tp40) REVERT: B 22 ARG cc_start: 0.7310 (mtt90) cc_final: 0.7034 (mtt90) REVERT: B 74 SER cc_start: 0.8423 (m) cc_final: 0.8192 (t) REVERT: B 129 ARG cc_start: 0.7261 (mmp80) cc_final: 0.6754 (mmp80) REVERT: B 135 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8391 (m) REVERT: B 137 ARG cc_start: 0.7839 (mmt-90) cc_final: 0.7624 (mmt180) REVERT: B 205 ASP cc_start: 0.7432 (p0) cc_final: 0.7172 (p0) REVERT: B 219 ARG cc_start: 0.8051 (mmt180) cc_final: 0.7682 (mmt90) REVERT: B 239 ASN cc_start: 0.7851 (m-40) cc_final: 0.7553 (m-40) REVERT: B 258 ASP cc_start: 0.7806 (t0) cc_final: 0.7131 (t0) REVERT: B 275 SER cc_start: 0.8310 (t) cc_final: 0.8052 (t) REVERT: B 277 SER cc_start: 0.8373 (t) cc_final: 0.7804 (m) REVERT: B 298 ASP cc_start: 0.7970 (t70) cc_final: 0.7585 (t70) REVERT: B 312 ASP cc_start: 0.6905 (t0) cc_final: 0.6634 (t70) REVERT: B 333 ASP cc_start: 0.7075 (m-30) cc_final: 0.6815 (m-30) REVERT: D 102 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7794 (t0) REVERT: D 121 MET cc_start: 0.7306 (mtm) cc_final: 0.7100 (mtp) REVERT: D 154 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8216 (p) REVERT: D 162 ILE cc_start: 0.7728 (mt) cc_final: 0.7384 (tt) REVERT: H 93 MET cc_start: 0.7796 (ttm) cc_final: 0.7522 (ttm) REVERT: H 115 THR cc_start: 0.8257 (t) cc_final: 0.8016 (t) REVERT: H 172 THR cc_start: 0.8584 (m) cc_final: 0.8119 (p) outliers start: 33 outliers final: 26 residues processed: 267 average time/residue: 0.1973 time to fit residues: 74.1716 Evaluate side-chains 274 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 245 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 153 GLN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 14 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 94 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.141426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.124044 restraints weight = 12433.303| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.05 r_work: 0.3451 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9024 Z= 0.135 Angle : 0.558 7.816 12242 Z= 0.286 Chirality : 0.043 0.186 1410 Planarity : 0.004 0.044 1537 Dihedral : 4.668 28.515 1235 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.07 % Allowed : 19.81 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.82 (0.26), residues: 1127 helix: 2.01 (0.26), residues: 408 sheet: -0.30 (0.30), residues: 289 loop : -0.16 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 111 HIS 0.004 0.001 HIS B 142 PHE 0.023 0.002 PHE D 218 TYR 0.022 0.001 TYR D 179 ARG 0.004 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 474) hydrogen bonds : angle 4.71601 ( 1317) SS BOND : bond 0.00593 ( 2) SS BOND : angle 1.77412 ( 4) covalent geometry : bond 0.00303 ( 9022) covalent geometry : angle 0.55730 (12238) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 250 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7906 (mttt) cc_final: 0.7702 (mmmm) REVERT: A 29 LYS cc_start: 0.7620 (ttpt) cc_final: 0.7233 (ttpt) REVERT: A 33 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7188 (mt-10) REVERT: A 210 LYS cc_start: 0.7905 (mmmt) cc_final: 0.7569 (mmtt) REVERT: A 251 ASP cc_start: 0.7716 (t0) cc_final: 0.7454 (t0) REVERT: A 309 ASP cc_start: 0.6964 (m-30) cc_final: 0.6716 (m-30) REVERT: A 330 LYS cc_start: 0.7772 (mmtt) cc_final: 0.7173 (mmtt) REVERT: A 333 GLN cc_start: 0.7982 (tp40) cc_final: 0.7277 (tp40) REVERT: A 337 ASP cc_start: 0.7740 (t0) cc_final: 0.7515 (t0) REVERT: B 22 ARG cc_start: 0.7321 (mtt90) cc_final: 0.7025 (mtt90) REVERT: B 40 VAL cc_start: 0.8434 (p) cc_final: 0.8222 (t) REVERT: B 74 SER cc_start: 0.8388 (m) cc_final: 0.8179 (t) REVERT: B 129 ARG cc_start: 0.7274 (mmp80) cc_final: 0.6760 (mmp80) REVERT: B 132 ASN cc_start: 0.8465 (p0) cc_final: 0.8235 (p0) REVERT: B 135 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8274 (m) REVERT: B 137 ARG cc_start: 0.7821 (mmt-90) cc_final: 0.7620 (mmt180) REVERT: B 188 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7762 (mmm) REVERT: B 205 ASP cc_start: 0.7413 (p0) cc_final: 0.7188 (p0) REVERT: B 219 ARG cc_start: 0.8060 (mmt180) cc_final: 0.7696 (mmt90) REVERT: B 239 ASN cc_start: 0.7795 (m-40) cc_final: 0.7512 (m-40) REVERT: B 258 ASP cc_start: 0.7825 (t0) cc_final: 0.7112 (t0) REVERT: B 275 SER cc_start: 0.8307 (t) cc_final: 0.8051 (t) REVERT: B 277 SER cc_start: 0.8367 (t) cc_final: 0.7811 (m) REVERT: B 291 ASP cc_start: 0.7425 (p0) cc_final: 0.7014 (p0) REVERT: B 298 ASP cc_start: 0.7997 (t70) cc_final: 0.7589 (t70) REVERT: B 312 ASP cc_start: 0.6927 (t0) cc_final: 0.6649 (t70) REVERT: B 333 ASP cc_start: 0.7054 (m-30) cc_final: 0.6839 (m-30) REVERT: D 95 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7665 (mtm) REVERT: D 154 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8218 (p) REVERT: D 162 ILE cc_start: 0.7713 (mt) cc_final: 0.7389 (tt) REVERT: H 59 TYR cc_start: 0.8010 (m-80) cc_final: 0.7745 (m-10) REVERT: H 67 ARG cc_start: 0.7949 (ttp80) cc_final: 0.7543 (ttp80) REVERT: H 93 MET cc_start: 0.7792 (ttm) cc_final: 0.7541 (ttm) REVERT: H 172 THR cc_start: 0.8595 (m) cc_final: 0.8133 (p) REVERT: H 226 VAL cc_start: 0.7947 (t) cc_final: 0.7585 (m) outliers start: 29 outliers final: 21 residues processed: 261 average time/residue: 0.1921 time to fit residues: 70.7773 Evaluate side-chains 270 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 245 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.140076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.123022 restraints weight = 12616.927| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.05 r_work: 0.3440 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9024 Z= 0.128 Angle : 0.558 8.426 12242 Z= 0.286 Chirality : 0.043 0.205 1410 Planarity : 0.004 0.043 1537 Dihedral : 4.641 30.205 1235 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.18 % Allowed : 20.13 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.84 (0.26), residues: 1127 helix: 2.05 (0.26), residues: 408 sheet: -0.23 (0.30), residues: 284 loop : -0.24 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 111 HIS 0.003 0.001 HIS B 142 PHE 0.022 0.002 PHE D 218 TYR 0.020 0.001 TYR D 179 ARG 0.003 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03298 ( 474) hydrogen bonds : angle 4.72620 ( 1317) SS BOND : bond 0.00550 ( 2) SS BOND : angle 1.73363 ( 4) covalent geometry : bond 0.00287 ( 9022) covalent geometry : angle 0.55722 (12238) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 243 time to evaluate : 0.911 Fit side-chains REVERT: A 29 LYS cc_start: 0.7609 (ttpt) cc_final: 0.7209 (ttpt) REVERT: A 33 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7157 (mt-10) REVERT: A 198 MET cc_start: 0.8346 (ttm) cc_final: 0.8140 (ttm) REVERT: A 210 LYS cc_start: 0.7908 (mmmt) cc_final: 0.7571 (mmtt) REVERT: A 251 ASP cc_start: 0.7749 (t0) cc_final: 0.7477 (t0) REVERT: A 318 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7193 (mm-30) REVERT: A 330 LYS cc_start: 0.7792 (mmtt) cc_final: 0.7344 (mmtt) REVERT: B 22 ARG cc_start: 0.7381 (mtt90) cc_final: 0.7089 (mtt90) REVERT: B 74 SER cc_start: 0.8366 (m) cc_final: 0.8152 (t) REVERT: B 129 ARG cc_start: 0.7347 (mmp80) cc_final: 0.6830 (mmp80) REVERT: B 135 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8331 (m) REVERT: B 188 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7570 (mmm) REVERT: B 205 ASP cc_start: 0.7548 (p0) cc_final: 0.7332 (p0) REVERT: B 219 ARG cc_start: 0.8025 (mmt180) cc_final: 0.7690 (mmt90) REVERT: B 239 ASN cc_start: 0.7755 (m-40) cc_final: 0.7388 (m-40) REVERT: B 258 ASP cc_start: 0.7818 (t0) cc_final: 0.7115 (t0) REVERT: B 275 SER cc_start: 0.8311 (t) cc_final: 0.8050 (t) REVERT: B 277 SER cc_start: 0.8440 (t) cc_final: 0.7893 (m) REVERT: B 298 ASP cc_start: 0.8037 (t70) cc_final: 0.7548 (t70) REVERT: B 312 ASP cc_start: 0.6897 (t0) cc_final: 0.6643 (t70) REVERT: D 95 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7609 (mtm) REVERT: D 154 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8162 (p) REVERT: D 162 ILE cc_start: 0.7785 (mt) cc_final: 0.7444 (tt) REVERT: H 59 TYR cc_start: 0.8002 (m-80) cc_final: 0.7733 (m-10) REVERT: H 67 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7602 (ttp80) REVERT: H 93 MET cc_start: 0.7712 (ttm) cc_final: 0.7440 (ttm) REVERT: H 172 THR cc_start: 0.8568 (m) cc_final: 0.8129 (p) outliers start: 30 outliers final: 25 residues processed: 253 average time/residue: 0.1928 time to fit residues: 68.3785 Evaluate side-chains 274 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 245 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 153 GLN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 82 optimal weight: 0.0670 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 109 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN D 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.140263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.123308 restraints weight = 12652.001| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.05 r_work: 0.3442 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9024 Z= 0.125 Angle : 0.569 10.374 12242 Z= 0.289 Chirality : 0.042 0.195 1410 Planarity : 0.004 0.043 1537 Dihedral : 4.645 31.099 1235 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.07 % Allowed : 20.44 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.81 (0.26), residues: 1127 helix: 2.05 (0.26), residues: 408 sheet: -0.33 (0.30), residues: 288 loop : -0.22 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 111 HIS 0.004 0.001 HIS A 213 PHE 0.034 0.002 PHE A 336 TYR 0.019 0.001 TYR D 179 ARG 0.009 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 474) hydrogen bonds : angle 4.72103 ( 1317) SS BOND : bond 0.00512 ( 2) SS BOND : angle 1.64637 ( 4) covalent geometry : bond 0.00279 ( 9022) covalent geometry : angle 0.56825 (12238) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 0.881 Fit side-chains REVERT: A 29 LYS cc_start: 0.7628 (ttpt) cc_final: 0.7236 (ttpt) REVERT: A 33 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7198 (mt-10) REVERT: A 197 LYS cc_start: 0.8473 (mtpp) cc_final: 0.8210 (ttmm) REVERT: A 198 MET cc_start: 0.8378 (ttm) cc_final: 0.8165 (ttm) REVERT: A 210 LYS cc_start: 0.7899 (mmmt) cc_final: 0.7561 (mmtt) REVERT: A 251 ASP cc_start: 0.7753 (t0) cc_final: 0.7482 (t0) REVERT: A 309 ASP cc_start: 0.6786 (m-30) cc_final: 0.6510 (m-30) REVERT: A 318 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7168 (mm-30) REVERT: A 330 LYS cc_start: 0.7773 (mmtt) cc_final: 0.7316 (mmtt) REVERT: B 22 ARG cc_start: 0.7386 (mtt90) cc_final: 0.7088 (mtt90) REVERT: B 74 SER cc_start: 0.8353 (m) cc_final: 0.8134 (t) REVERT: B 129 ARG cc_start: 0.7358 (mmp80) cc_final: 0.6845 (mmp80) REVERT: B 135 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8325 (m) REVERT: B 188 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7558 (mmm) REVERT: B 219 ARG cc_start: 0.8027 (mmt180) cc_final: 0.7680 (mmt90) REVERT: B 239 ASN cc_start: 0.7732 (m-40) cc_final: 0.7348 (m-40) REVERT: B 256 ARG cc_start: 0.8323 (mpp80) cc_final: 0.7837 (mtm180) REVERT: B 258 ASP cc_start: 0.7825 (t0) cc_final: 0.7116 (t0) REVERT: B 275 SER cc_start: 0.8322 (t) cc_final: 0.8059 (t) REVERT: B 277 SER cc_start: 0.8418 (t) cc_final: 0.7889 (m) REVERT: B 298 ASP cc_start: 0.8042 (t70) cc_final: 0.7546 (t70) REVERT: B 312 ASP cc_start: 0.6889 (t0) cc_final: 0.6653 (t70) REVERT: D 95 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7602 (mtm) REVERT: D 154 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8155 (p) REVERT: D 162 ILE cc_start: 0.7772 (mt) cc_final: 0.7439 (tt) REVERT: G 50 LEU cc_start: 0.8657 (mt) cc_final: 0.8408 (mp) REVERT: H 59 TYR cc_start: 0.7985 (m-80) cc_final: 0.7719 (m-10) REVERT: H 67 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7603 (ttp80) REVERT: H 93 MET cc_start: 0.7731 (ttm) cc_final: 0.7453 (ttm) REVERT: H 172 THR cc_start: 0.8554 (m) cc_final: 0.8139 (p) REVERT: H 230 MET cc_start: 0.7999 (ttp) cc_final: 0.7792 (ttm) outliers start: 29 outliers final: 24 residues processed: 250 average time/residue: 0.1974 time to fit residues: 69.1450 Evaluate side-chains 272 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 153 GLN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 106 optimal weight: 0.0470 chunk 32 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 89 optimal weight: 0.0170 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.140608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.123716 restraints weight = 12605.387| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.05 r_work: 0.3447 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9024 Z= 0.123 Angle : 0.566 10.015 12242 Z= 0.289 Chirality : 0.042 0.183 1410 Planarity : 0.004 0.043 1537 Dihedral : 4.615 31.927 1235 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.97 % Allowed : 20.76 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.81 (0.26), residues: 1127 helix: 2.07 (0.26), residues: 408 sheet: -0.31 (0.30), residues: 288 loop : -0.24 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 111 HIS 0.004 0.001 HIS A 213 PHE 0.032 0.002 PHE A 336 TYR 0.019 0.001 TYR D 179 ARG 0.013 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03294 ( 474) hydrogen bonds : angle 4.70734 ( 1317) SS BOND : bond 0.00494 ( 2) SS BOND : angle 1.62491 ( 4) covalent geometry : bond 0.00273 ( 9022) covalent geometry : angle 0.56578 (12238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5142.68 seconds wall clock time: 88 minutes 48.39 seconds (5328.39 seconds total)