Starting phenix.real_space_refine on Wed Mar 12 03:37:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8efq_28088/03_2025/8efq_28088_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efq_28088/03_2025/8efq_28088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8efq_28088/03_2025/8efq_28088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efq_28088/03_2025/8efq_28088.map" model { file = "/net/cci-nas-00/data/ceres_data/8efq_28088/03_2025/8efq_28088_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efq_28088/03_2025/8efq_28088_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 4500 2.51 5 N 1190 2.21 5 O 1295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7046 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1747 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "P" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Chain: "P" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Classifications: {'peptide': 3} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2272 Classifications: {'peptide': 283} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'ETA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.91, per 1000 atoms: 0.70 Number of scatterers: 7046 At special positions: 0 Unit cell: (79.254, 103.887, 139.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 1295 8.00 N 1190 7.00 C 4500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.02 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=1, symmetry=0 Links applied TRANS " DAL P 2 " - " TYR P 1 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 958.8 milliseconds 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL P 2 " Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 9 sheets defined 47.2% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.928A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.728A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.596A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.148A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 removed outlier: 3.753A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.057A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.891A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 352 Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.587A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.609A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.767A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 68 through 98 Processing helix chain 'R' and resid 103 through 121 removed outlier: 4.082A pdb=" N ILE R 107 " --> pdb=" O THR R 103 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 133 removed outlier: 3.734A pdb=" N VAL R 128 " --> pdb=" O PRO R 124 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN R 129 " --> pdb=" O PHE R 125 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR R 130 " --> pdb=" O GLN R 126 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU R 131 " --> pdb=" O SER R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 173 removed outlier: 3.709A pdb=" N MET R 153 " --> pdb=" O ASP R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 181 removed outlier: 3.687A pdb=" N LEU R 178 " --> pdb=" O PRO R 174 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 207 removed outlier: 4.002A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Proline residue: R 203 - end of helix Processing helix chain 'R' and resid 226 through 264 removed outlier: 3.606A pdb=" N TRP R 230 " --> pdb=" O PRO R 226 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU R 231 " --> pdb=" O THR R 227 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N MET R 245 " --> pdb=" O PHE R 241 " (cutoff:3.500A) Proline residue: R 246 - end of helix removed outlier: 3.793A pdb=" N SER R 263 " --> pdb=" O LEU R 259 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL R 264 " --> pdb=" O ARG R 260 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 308 removed outlier: 3.838A pdb=" N ASN R 276 " --> pdb=" O GLU R 272 " (cutoff:3.500A) Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 313 through 339 removed outlier: 3.580A pdb=" N THR R 317 " --> pdb=" O THR R 313 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS R 321 " --> pdb=" O THR R 317 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER R 331 " --> pdb=" O GLY R 327 " (cutoff:3.500A) Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 342 through 349 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 4.255A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP A 200 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 7.044A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 7.031A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.497A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.979A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.222A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.924A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.804A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 208 through 212 367 hydrogen bonds defined for protein. 1077 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2235 1.34 - 1.46: 1370 1.46 - 1.58: 3492 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 7185 Sorted by residual: bond pdb=" O ETA P 101 " pdb=" CB ETA P 101 " ideal model delta sigma weight residual 1.413 1.460 -0.047 2.00e-02 2.50e+03 5.48e+00 bond pdb=" C THR R 296 " pdb=" N PRO R 297 " ideal model delta sigma weight residual 1.336 1.358 -0.023 1.23e-02 6.61e+03 3.43e+00 bond pdb=" CA ETA P 101 " pdb=" CB ETA P 101 " ideal model delta sigma weight residual 1.513 1.545 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C MET R 245 " pdb=" N PRO R 246 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.20e-02 6.94e+03 2.45e+00 bond pdb=" CA THR B 87 " pdb=" C THR B 87 " ideal model delta sigma weight residual 1.522 1.544 -0.022 1.51e-02 4.39e+03 2.10e+00 ... (remaining 7180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 9482 2.26 - 4.52: 206 4.52 - 6.79: 27 6.79 - 9.05: 9 9.05 - 11.31: 1 Bond angle restraints: 9725 Sorted by residual: angle pdb=" N LEU R 123 " pdb=" CA LEU R 123 " pdb=" C LEU R 123 " ideal model delta sigma weight residual 109.81 117.08 -7.27 2.21e+00 2.05e-01 1.08e+01 angle pdb=" CA LEU B 79 " pdb=" CB LEU B 79 " pdb=" CG LEU B 79 " ideal model delta sigma weight residual 116.30 127.61 -11.31 3.50e+00 8.16e-02 1.04e+01 angle pdb=" N THR B 184 " pdb=" CA THR B 184 " pdb=" C THR B 184 " ideal model delta sigma weight residual 113.02 108.59 4.43 1.49e+00 4.50e-01 8.84e+00 angle pdb=" N LYS B 78 " pdb=" CA LYS B 78 " pdb=" C LYS B 78 " ideal model delta sigma weight residual 108.69 113.91 -5.22 1.77e+00 3.19e-01 8.69e+00 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 124.31 129.21 -4.90 1.67e+00 3.59e-01 8.62e+00 ... (remaining 9720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.10: 4096 15.10 - 30.20: 149 30.20 - 45.30: 31 45.30 - 60.39: 1 60.39 - 75.49: 1 Dihedral angle restraints: 4278 sinusoidal: 1670 harmonic: 2608 Sorted by residual: dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ARG A 208 " pdb=" C ARG A 208 " pdb=" N LYS A 209 " pdb=" CA LYS A 209 " ideal model delta harmonic sigma weight residual -180.00 -163.35 -16.65 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 163.62 16.38 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 4275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 869 0.057 - 0.114: 203 0.114 - 0.171: 43 0.171 - 0.228: 6 0.228 - 0.284: 3 Chirality restraints: 1124 Sorted by residual: chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB ILE A 264 " pdb=" CA ILE A 264 " pdb=" CG1 ILE A 264 " pdb=" CG2 ILE A 264 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB ILE B 43 " pdb=" CA ILE B 43 " pdb=" CG1 ILE B 43 " pdb=" CG2 ILE B 43 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1121 not shown) Planarity restraints: 1216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO B 236 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 328 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.13e+00 pdb=" C TYR R 328 " -0.039 2.00e-02 2.50e+03 pdb=" O TYR R 328 " 0.015 2.00e-02 2.50e+03 pdb=" N THR R 329 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR R 182 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO R 183 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO R 183 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 183 " 0.030 5.00e-02 4.00e+02 ... (remaining 1213 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1926 2.82 - 3.34: 6320 3.34 - 3.86: 11205 3.86 - 4.38: 12384 4.38 - 4.90: 22326 Nonbonded interactions: 54161 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.298 3.040 nonbonded pdb=" O ALA R 325 " pdb=" OG1 THR R 329 " model vdw 2.304 3.040 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.314 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.315 3.040 nonbonded pdb=" OH TYR A 230 " pdb=" O LYS A 277 " model vdw 2.334 3.040 ... (remaining 54156 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.020 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 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 0.047 7185 Z= 0.239 Angle : 0.814 11.310 9725 Z= 0.453 Chirality : 0.053 0.284 1124 Planarity : 0.006 0.057 1215 Dihedral : 8.645 75.491 2580 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.52 (0.24), residues: 877 helix: -0.65 (0.21), residues: 367 sheet: 0.10 (0.41), residues: 159 loop : -1.85 (0.27), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 169 HIS 0.006 0.001 HIS B 183 PHE 0.016 0.002 PHE A 274 TYR 0.023 0.002 TYR R 151 ARG 0.004 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: B 155 ASN cc_start: 0.7455 (m-40) cc_final: 0.6985 (t0) REVERT: B 259 GLN cc_start: 0.7799 (pt0) cc_final: 0.7502 (tt0) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2604 time to fit residues: 66.1699 Evaluate side-chains 110 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 0.1980 chunk 22 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 119 ASN ** R 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 190 ASN R 299 HIS R 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.206204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.156471 restraints weight = 7705.676| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.39 r_work: 0.3624 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7185 Z= 0.246 Angle : 0.598 13.280 9725 Z= 0.312 Chirality : 0.042 0.202 1124 Planarity : 0.004 0.043 1215 Dihedral : 4.299 17.906 961 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.33 % Allowed : 9.57 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.00 (0.27), residues: 877 helix: 1.25 (0.26), residues: 371 sheet: 0.18 (0.40), residues: 156 loop : -1.47 (0.29), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.012 0.001 PHE B 241 TYR 0.019 0.002 TYR R 229 ARG 0.004 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 318 GLU cc_start: 0.7636 (pm20) cc_final: 0.6997 (pt0) REVERT: B 52 ARG cc_start: 0.7418 (ttm110) cc_final: 0.7087 (mtt90) REVERT: B 155 ASN cc_start: 0.7871 (m-40) cc_final: 0.7230 (t0) REVERT: B 220 GLN cc_start: 0.8191 (mp10) cc_final: 0.7925 (mp10) REVERT: B 259 GLN cc_start: 0.7580 (pt0) cc_final: 0.7141 (tt0) REVERT: R 77 TYR cc_start: 0.7490 (m-80) cc_final: 0.7261 (m-10) REVERT: R 190 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.8018 (m-40) REVERT: R 205 MET cc_start: 0.8479 (tpp) cc_final: 0.8270 (tpp) outliers start: 18 outliers final: 13 residues processed: 150 average time/residue: 0.1770 time to fit residues: 36.0297 Evaluate side-chains 131 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 190 ASN Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 336 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 17 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 294 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 ASN ** R 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.201012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.154937 restraints weight = 7686.182| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.44 r_work: 0.3559 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7185 Z= 0.251 Angle : 0.559 8.917 9725 Z= 0.295 Chirality : 0.043 0.216 1124 Planarity : 0.004 0.040 1215 Dihedral : 4.121 16.942 961 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.66 % Allowed : 11.13 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.33 (0.27), residues: 877 helix: 1.67 (0.26), residues: 373 sheet: -0.07 (0.39), residues: 165 loop : -1.30 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.012 0.001 PHE B 241 TYR 0.020 0.002 TYR R 151 ARG 0.004 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 318 GLU cc_start: 0.7671 (pm20) cc_final: 0.6988 (mm-30) REVERT: B 124 TYR cc_start: 0.8893 (m-80) cc_final: 0.7243 (m-80) REVERT: B 220 GLN cc_start: 0.8150 (mp10) cc_final: 0.7766 (mp10) REVERT: B 259 GLN cc_start: 0.7594 (pt0) cc_final: 0.7037 (tt0) REVERT: R 205 MET cc_start: 0.8603 (tpp) cc_final: 0.8304 (tpp) outliers start: 36 outliers final: 27 residues processed: 145 average time/residue: 0.1582 time to fit residues: 31.8565 Evaluate side-chains 137 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 111 ASN Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 336 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 27 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 62 optimal weight: 0.0070 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 18 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN R 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.203156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.159488 restraints weight = 7628.662| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.17 r_work: 0.3601 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7185 Z= 0.161 Angle : 0.511 8.016 9725 Z= 0.268 Chirality : 0.040 0.178 1124 Planarity : 0.003 0.040 1215 Dihedral : 3.908 16.633 961 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.27 % Allowed : 13.20 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.52 (0.28), residues: 877 helix: 1.83 (0.27), residues: 381 sheet: -0.21 (0.39), residues: 160 loop : -1.10 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.010 0.001 PHE A 189 TYR 0.018 0.001 TYR R 151 ARG 0.005 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8345 (t80) cc_final: 0.7835 (t80) REVERT: B 124 TYR cc_start: 0.8798 (m-80) cc_final: 0.8027 (m-80) REVERT: B 198 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7377 (pp) REVERT: B 220 GLN cc_start: 0.8123 (mp10) cc_final: 0.7917 (mp10) REVERT: B 246 ASP cc_start: 0.8047 (m-30) cc_final: 0.7845 (m-30) REVERT: B 259 GLN cc_start: 0.7437 (pt0) cc_final: 0.7091 (tt0) REVERT: R 205 MET cc_start: 0.8458 (tpp) cc_final: 0.8211 (tpp) REVERT: R 330 ASN cc_start: 0.7395 (t0) cc_final: 0.6917 (t0) outliers start: 33 outliers final: 25 residues processed: 143 average time/residue: 0.1666 time to fit residues: 33.1665 Evaluate side-chains 138 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 111 ASN Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 293 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.203224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.151227 restraints weight = 7699.556| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.43 r_work: 0.3540 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7185 Z= 0.217 Angle : 0.524 7.297 9725 Z= 0.276 Chirality : 0.041 0.150 1124 Planarity : 0.003 0.042 1215 Dihedral : 3.934 15.454 961 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.66 % Allowed : 13.58 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.57 (0.28), residues: 877 helix: 1.81 (0.27), residues: 388 sheet: -0.33 (0.39), residues: 167 loop : -0.99 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.003 0.001 HIS B 62 PHE 0.010 0.001 PHE A 189 TYR 0.017 0.002 TYR A 302 ARG 0.009 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8437 (t80) cc_final: 0.7685 (t80) REVERT: A 317 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7728 (ptpp) REVERT: B 52 ARG cc_start: 0.7510 (ttm110) cc_final: 0.7195 (ptp90) REVERT: B 124 TYR cc_start: 0.8931 (m-80) cc_final: 0.8176 (m-80) REVERT: B 198 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7434 (pp) REVERT: B 220 GLN cc_start: 0.8166 (mp10) cc_final: 0.7924 (mp10) REVERT: R 89 PHE cc_start: 0.6623 (m-80) cc_final: 0.6388 (m-80) REVERT: R 205 MET cc_start: 0.8483 (tpp) cc_final: 0.8186 (tpp) outliers start: 36 outliers final: 28 residues processed: 140 average time/residue: 0.1673 time to fit residues: 32.5135 Evaluate side-chains 138 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 111 ASN Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 336 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 13 optimal weight: 0.4980 chunk 57 optimal weight: 4.9990 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 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.200432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.153533 restraints weight = 7673.940| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.43 r_work: 0.3545 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7185 Z= 0.197 Angle : 0.514 8.165 9725 Z= 0.270 Chirality : 0.041 0.148 1124 Planarity : 0.003 0.042 1215 Dihedral : 3.929 14.376 961 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.27 % Allowed : 14.36 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.55 (0.29), residues: 877 helix: 1.79 (0.27), residues: 393 sheet: -0.36 (0.38), residues: 165 loop : -1.03 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.002 0.001 HIS B 62 PHE 0.010 0.001 PHE A 189 TYR 0.017 0.002 TYR R 151 ARG 0.007 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8502 (t80) cc_final: 0.8093 (t80) REVERT: A 306 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7456 (mp10) REVERT: A 317 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7722 (ptpp) REVERT: B 52 ARG cc_start: 0.7572 (ttm110) cc_final: 0.7327 (ptp90) REVERT: B 124 TYR cc_start: 0.8884 (m-80) cc_final: 0.8075 (m-80) REVERT: B 198 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7495 (pp) REVERT: B 220 GLN cc_start: 0.8151 (mp10) cc_final: 0.7903 (mp10) REVERT: R 160 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7425 (mp) REVERT: R 205 MET cc_start: 0.8500 (tpp) cc_final: 0.8211 (tpp) REVERT: R 301 TYR cc_start: 0.7358 (t80) cc_final: 0.6939 (t80) outliers start: 33 outliers final: 24 residues processed: 142 average time/residue: 0.1636 time to fit residues: 32.2292 Evaluate side-chains 136 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 293 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 84 optimal weight: 0.1980 chunk 39 optimal weight: 0.0980 chunk 67 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 59 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.202599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.152312 restraints weight = 7496.981| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.34 r_work: 0.3576 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7185 Z= 0.146 Angle : 0.495 8.593 9725 Z= 0.261 Chirality : 0.040 0.144 1124 Planarity : 0.003 0.041 1215 Dihedral : 3.782 14.158 961 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.88 % Allowed : 15.39 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.77 (0.29), residues: 877 helix: 2.01 (0.27), residues: 387 sheet: -0.29 (0.39), residues: 161 loop : -0.87 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.002 0.001 HIS B 311 PHE 0.012 0.001 PHE R 89 TYR 0.017 0.001 TYR R 151 ARG 0.007 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8486 (t80) cc_final: 0.7760 (t80) REVERT: A 317 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7920 (ptpp) REVERT: B 124 TYR cc_start: 0.8796 (m-80) cc_final: 0.7933 (m-80) REVERT: B 220 GLN cc_start: 0.8152 (mp10) cc_final: 0.7884 (mp10) REVERT: R 160 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7474 (mp) REVERT: R 205 MET cc_start: 0.8530 (tpp) cc_final: 0.8229 (tpp) REVERT: R 330 ASN cc_start: 0.7226 (t0) cc_final: 0.7025 (t0) outliers start: 30 outliers final: 23 residues processed: 135 average time/residue: 0.1669 time to fit residues: 31.5896 Evaluate side-chains 132 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 111 ASN Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 292 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 32 optimal weight: 0.0870 chunk 64 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN R 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.201077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.162615 restraints weight = 7975.924| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 3.55 r_work: 0.3418 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7185 Z= 0.177 Angle : 0.514 9.073 9725 Z= 0.269 Chirality : 0.040 0.146 1124 Planarity : 0.003 0.041 1215 Dihedral : 3.792 13.553 961 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.14 % Allowed : 16.17 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.29), residues: 877 helix: 1.97 (0.27), residues: 387 sheet: -0.31 (0.38), residues: 166 loop : -0.86 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.002 0.001 HIS B 62 PHE 0.010 0.001 PHE A 189 TYR 0.016 0.001 TYR R 151 ARG 0.006 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8587 (t80) cc_final: 0.8166 (t80) REVERT: A 306 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7395 (mp10) REVERT: A 317 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7570 (ptpp) REVERT: B 124 TYR cc_start: 0.8906 (m-80) cc_final: 0.8077 (m-80) REVERT: B 220 GLN cc_start: 0.8187 (mp10) cc_final: 0.7945 (mp10) REVERT: R 89 PHE cc_start: 0.7043 (m-80) cc_final: 0.6767 (m-80) REVERT: R 160 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7672 (mp) REVERT: R 205 MET cc_start: 0.8546 (tpp) cc_final: 0.8233 (tpp) outliers start: 32 outliers final: 25 residues processed: 136 average time/residue: 0.1642 time to fit residues: 31.2945 Evaluate side-chains 142 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 111 ASN Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 293 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 78 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.201286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.163392 restraints weight = 8024.250| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 3.56 r_work: 0.3434 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7185 Z= 0.172 Angle : 0.519 9.336 9725 Z= 0.271 Chirality : 0.040 0.146 1124 Planarity : 0.003 0.041 1215 Dihedral : 3.775 13.452 961 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.53 % Allowed : 16.04 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.62 (0.29), residues: 877 helix: 1.90 (0.27), residues: 391 sheet: -0.36 (0.38), residues: 156 loop : -1.00 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 169 HIS 0.002 0.001 HIS B 62 PHE 0.009 0.001 PHE A 189 TYR 0.016 0.001 TYR R 151 ARG 0.008 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8567 (t80) cc_final: 0.7879 (t80) REVERT: A 317 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7498 (ptpp) REVERT: B 124 TYR cc_start: 0.8896 (m-80) cc_final: 0.8046 (m-80) REVERT: B 220 GLN cc_start: 0.8163 (mp10) cc_final: 0.7884 (mp10) REVERT: B 262 MET cc_start: 0.7936 (tpp) cc_final: 0.7678 (ttt) REVERT: R 89 PHE cc_start: 0.7044 (m-80) cc_final: 0.6806 (m-80) REVERT: R 160 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7602 (mp) REVERT: R 205 MET cc_start: 0.8555 (tpp) cc_final: 0.8212 (tpp) outliers start: 35 outliers final: 26 residues processed: 138 average time/residue: 0.1669 time to fit residues: 32.1084 Evaluate side-chains 143 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 111 ASN Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 293 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.197315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.162495 restraints weight = 8020.450| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 3.26 r_work: 0.3446 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7185 Z= 0.191 Angle : 0.532 9.514 9725 Z= 0.277 Chirality : 0.040 0.146 1124 Planarity : 0.003 0.042 1215 Dihedral : 3.812 13.727 961 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.49 % Allowed : 17.21 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.62 (0.29), residues: 877 helix: 1.98 (0.27), residues: 384 sheet: -0.39 (0.39), residues: 151 loop : -1.02 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 169 HIS 0.003 0.001 HIS B 62 PHE 0.010 0.001 PHE A 189 TYR 0.016 0.001 TYR R 151 ARG 0.009 0.000 ARG A 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8572 (t80) cc_final: 0.8139 (t80) REVERT: A 306 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7351 (mp10) REVERT: A 317 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7434 (ptpp) REVERT: B 124 TYR cc_start: 0.8926 (m-80) cc_final: 0.8102 (m-80) REVERT: B 220 GLN cc_start: 0.8163 (mp10) cc_final: 0.7899 (mp10) REVERT: R 89 PHE cc_start: 0.7022 (m-80) cc_final: 0.6813 (m-80) REVERT: R 160 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7593 (mp) REVERT: R 205 MET cc_start: 0.8573 (tpp) cc_final: 0.8241 (tpp) outliers start: 27 outliers final: 24 residues processed: 134 average time/residue: 0.1619 time to fit residues: 30.1400 Evaluate side-chains 142 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 111 ASN Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 164 SER Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 293 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.195956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.145296 restraints weight = 7822.094| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.38 r_work: 0.3490 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7185 Z= 0.227 Angle : 0.556 9.363 9725 Z= 0.289 Chirality : 0.041 0.150 1124 Planarity : 0.004 0.042 1215 Dihedral : 3.892 14.295 961 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.62 % Allowed : 17.46 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.55 (0.29), residues: 877 helix: 1.89 (0.27), residues: 385 sheet: -0.39 (0.40), residues: 149 loop : -1.05 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.003 0.001 HIS B 62 PHE 0.011 0.001 PHE A 189 TYR 0.015 0.002 TYR R 151 ARG 0.009 0.000 ARG A 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3829.10 seconds wall clock time: 66 minutes 50.55 seconds (4010.55 seconds total)