Starting phenix.real_space_refine on Wed Feb 12 03:59:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8efq_28088/02_2025/8efq_28088_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efq_28088/02_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_28088/02_2025/8efq_28088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efq_28088/02_2025/8efq_28088.map" model { file = "/net/cci-nas-00/data/ceres_data/8efq_28088/02_2025/8efq_28088_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efq_28088/02_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-5592/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: 4.37, per 1000 atoms: 0.62 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: 1.66 Conformation dependent library (CDL) restraints added in 986.4 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: 0.81 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: 1.97 Time building geometry restraints manager: 1.94 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: 0.010 Normalize map: mean=0, sd=1: 0.820 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.870 Find NCS groups from input model: 0.060 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.220 ------------------------------------------------------------------------------- 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 : 0.704 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: 0.2029 time to fit residues: 51.1642 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 : 0.842 ------------------------------------------------------------------------------- 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 = 82)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.156609 restraints weight = 7705.677| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.36 r_work: 0.3625 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 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 : 0.764 Fit side-chains revert: symmetry clash REVERT: A 318 GLU cc_start: 0.7632 (pm20) cc_final: 0.6994 (pt0) REVERT: B 52 ARG cc_start: 0.7420 (ttm110) cc_final: 0.7089 (mtt90) REVERT: B 155 ASN cc_start: 0.7867 (m-40) cc_final: 0.7231 (t0) REVERT: B 220 GLN cc_start: 0.8190 (mp10) cc_final: 0.7924 (mp10) REVERT: B 259 GLN cc_start: 0.7581 (pt0) cc_final: 0.7140 (tt0) REVERT: R 77 TYR cc_start: 0.7506 (m-80) cc_final: 0.7279 (m-10) REVERT: R 190 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.8022 (m-40) REVERT: R 205 MET cc_start: 0.8478 (tpp) cc_final: 0.8271 (tpp) outliers start: 18 outliers final: 13 residues processed: 150 average time/residue: 0.1784 time to fit residues: 36.2093 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 : 0.752 ------------------------------------------------------------------------------- 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: 0.6980 chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 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: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 294 ASN B 239 ASN ** R 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4270 r_free = 0.4270 target = 0.201957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.151966 restraints weight = 7685.373| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.32 r_work: 0.3569 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7185 Z= 0.235 Angle : 0.550 9.112 9725 Z= 0.291 Chirality : 0.042 0.209 1124 Planarity : 0.004 0.040 1215 Dihedral : 4.090 16.977 961 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.14 % Allowed : 11.38 % Favored : 84.48 % 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: 0.36 (0.27), residues: 877 helix: 1.70 (0.26), residues: 373 sheet: 0.06 (0.40), residues: 162 loop : -1.34 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 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 154 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 318 GLU cc_start: 0.7654 (pm20) cc_final: 0.6967 (mm-30) REVERT: B 124 TYR cc_start: 0.8877 (m-80) cc_final: 0.8126 (m-80) REVERT: B 220 GLN cc_start: 0.8148 (mp10) cc_final: 0.7772 (mp10) REVERT: B 259 GLN cc_start: 0.7610 (pt0) cc_final: 0.7060 (tt0) REVERT: R 205 MET cc_start: 0.8593 (tpp) cc_final: 0.8313 (tpp) outliers start: 32 outliers final: 23 residues processed: 143 average time/residue: 0.1698 time to fit residues: 33.5722 Evaluate side-chains 133 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 62 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 ASN R 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.202432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.157047 restraints weight = 7642.015| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.22 r_work: 0.3588 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7185 Z= 0.188 Angle : 0.521 8.069 9725 Z= 0.274 Chirality : 0.041 0.184 1124 Planarity : 0.003 0.040 1215 Dihedral : 3.944 16.552 961 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.92 % Allowed : 12.42 % Favored : 82.66 % 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: 0.49 (0.28), residues: 877 helix: 1.80 (0.27), residues: 381 sheet: -0.22 (0.39), residues: 160 loop : -1.13 (0.31), 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 0.002 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 156 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8401 (t80) cc_final: 0.7927 (t80) REVERT: B 124 TYR cc_start: 0.8843 (m-80) cc_final: 0.8068 (m-80) REVERT: B 198 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7387 (pp) REVERT: B 220 GLN cc_start: 0.8140 (mp10) cc_final: 0.7740 (mp10) REVERT: B 259 GLN cc_start: 0.7453 (pt0) cc_final: 0.7107 (tt0) REVERT: R 205 MET cc_start: 0.8456 (tpp) cc_final: 0.8214 (tpp) outliers start: 38 outliers final: 30 residues processed: 146 average time/residue: 0.1666 time to fit residues: 34.3396 Evaluate side-chains 138 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 306 GLN 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 84 SER 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 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 250 CYS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 23 optimal weight: 0.0050 chunk 50 optimal weight: 0.4980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 GLN R 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.206216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.167950 restraints weight = 7689.419| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 3.30 r_work: 0.3497 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7185 Z= 0.156 Angle : 0.501 7.907 9725 Z= 0.263 Chirality : 0.040 0.151 1124 Planarity : 0.003 0.041 1215 Dihedral : 3.849 15.973 961 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.27 % Allowed : 13.97 % 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: 0.65 (0.28), residues: 877 helix: 1.97 (0.27), residues: 380 sheet: -0.25 (0.39), residues: 162 loop : -1.01 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 320 HIS 0.002 0.001 HIS B 142 PHE 0.009 0.001 PHE A 189 TYR 0.017 0.001 TYR R 151 ARG 0.005 0.000 ARG B 52 *********************** 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 148 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8522 (t80) cc_final: 0.8012 (t80) REVERT: B 52 ARG cc_start: 0.7356 (ttm110) cc_final: 0.7084 (ptp90) REVERT: B 124 TYR cc_start: 0.8901 (m-80) cc_final: 0.8099 (m-80) REVERT: B 259 GLN cc_start: 0.7559 (pt0) cc_final: 0.7236 (tt0) REVERT: R 205 MET cc_start: 0.8508 (tpp) cc_final: 0.8259 (tpp) outliers start: 33 outliers final: 24 residues processed: 139 average time/residue: 0.1677 time to fit residues: 32.2832 Evaluate side-chains 133 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 ASN R 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.202367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.153912 restraints weight = 7749.977| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.41 r_work: 0.3525 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7185 Z= 0.230 Angle : 0.534 8.181 9725 Z= 0.279 Chirality : 0.041 0.151 1124 Planarity : 0.003 0.042 1215 Dihedral : 3.932 14.838 961 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % 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: 0.50 (0.29), residues: 877 helix: 1.77 (0.27), residues: 392 sheet: -0.37 (0.38), residues: 167 loop : -1.07 (0.34), residues: 318 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 0.010 0.001 PHE A 189 TYR 0.016 0.002 TYR R 151 ARG 0.006 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 147 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8456 (t80) cc_final: 0.7798 (t80) REVERT: A 317 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7534 (ptpp) REVERT: B 52 ARG cc_start: 0.7634 (ttm110) cc_final: 0.7311 (ptp90) REVERT: B 124 TYR cc_start: 0.8941 (m-80) cc_final: 0.8177 (m-80) REVERT: B 220 GLN cc_start: 0.8188 (mp10) cc_final: 0.7975 (mp10) REVERT: R 89 PHE cc_start: 0.6767 (m-80) cc_final: 0.6530 (m-80) REVERT: R 160 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7307 (mp) REVERT: R 205 MET cc_start: 0.8506 (tpp) cc_final: 0.8185 (tpp) outliers start: 33 outliers final: 27 residues processed: 140 average time/residue: 0.1771 time to fit residues: 34.1676 Evaluate side-chains 137 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 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 229 ILE Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 294 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 Chi-restraints excluded: chain R residue 336 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 84 optimal weight: 0.0470 chunk 39 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 75 optimal weight: 0.7980 chunk 35 optimal weight: 0.0670 chunk 34 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** B 239 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 = 0.4266 r_free = 0.4266 target = 0.201765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.156301 restraints weight = 7460.873| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.14 r_work: 0.3588 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3827 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= 0.144 Angle : 0.505 8.757 9725 Z= 0.264 Chirality : 0.040 0.145 1124 Planarity : 0.003 0.042 1215 Dihedral : 3.853 14.789 961 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.14 % Allowed : 15.52 % Favored : 80.34 % 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: 0.67 (0.29), residues: 877 helix: 1.96 (0.27), residues: 387 sheet: -0.39 (0.38), residues: 166 loop : -0.94 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 82 HIS 0.002 0.001 HIS B 311 PHE 0.009 0.001 PHE A 189 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 148 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8446 (t80) cc_final: 0.7881 (t80) REVERT: A 317 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7230 (ptpp) REVERT: B 47 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8221 (t) REVERT: B 52 ARG cc_start: 0.7336 (ttm110) cc_final: 0.7130 (ptp90) REVERT: B 124 TYR cc_start: 0.8809 (m-80) cc_final: 0.7964 (m-80) REVERT: B 155 ASN cc_start: 0.7268 (t0) cc_final: 0.7008 (t0) REVERT: B 220 GLN cc_start: 0.8199 (mp10) cc_final: 0.7961 (mp10) REVERT: R 89 PHE cc_start: 0.6724 (m-80) cc_final: 0.6502 (m-80) REVERT: R 205 MET cc_start: 0.8490 (tpp) cc_final: 0.8224 (tpp) REVERT: R 301 TYR cc_start: 0.7282 (t80) cc_final: 0.6898 (t80) outliers start: 32 outliers final: 25 residues processed: 138 average time/residue: 0.1688 time to fit residues: 32.3397 Evaluate side-chains 136 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 327 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 THR 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 160 SER 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 5 optimal weight: 0.0070 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 = 0.4272 r_free = 0.4272 target = 0.203146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.162502 restraints weight = 7663.071| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 3.35 r_work: 0.3485 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7185 Z= 0.178 Angle : 0.514 9.217 9725 Z= 0.268 Chirality : 0.040 0.144 1124 Planarity : 0.003 0.042 1215 Dihedral : 3.822 13.701 961 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.14 % Allowed : 16.43 % 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: 0.69 (0.29), residues: 877 helix: 1.96 (0.27), residues: 387 sheet: -0.34 (0.38), residues: 166 loop : -0.93 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 0.007 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 148 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 306 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7747 (mt0) REVERT: A 317 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7379 (ptmt) REVERT: A 327 THR cc_start: 0.7146 (OUTLIER) cc_final: 0.6738 (p) REVERT: B 124 TYR cc_start: 0.8937 (m-80) cc_final: 0.8139 (m-80) REVERT: B 154 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.7037 (m-30) REVERT: B 220 GLN cc_start: 0.8276 (mp10) cc_final: 0.7998 (mp10) REVERT: B 262 MET cc_start: 0.8086 (tpp) cc_final: 0.7742 (ttt) REVERT: R 160 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7555 (mp) REVERT: R 205 MET cc_start: 0.8553 (tpp) cc_final: 0.8233 (tpp) outliers start: 32 outliers final: 25 residues processed: 136 average time/residue: 0.1724 time to fit residues: 32.4528 Evaluate side-chains 143 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 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 154 ASP 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 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 Chi-restraints excluded: chain R residue 336 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 20 optimal weight: 0.5980 chunk 78 optimal weight: 0.0020 chunk 26 optimal weight: 0.6980 overall best weight: 0.4566 ------------------------------------------------------------------------------- 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 = 0.4228 r_free = 0.4228 target = 0.198316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.161257 restraints weight = 7819.966| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 3.13 r_work: 0.3471 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4057 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= 0.160 Angle : 0.513 9.345 9725 Z= 0.268 Chirality : 0.040 0.144 1124 Planarity : 0.003 0.041 1215 Dihedral : 3.769 13.556 961 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.75 % Allowed : 16.82 % 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: 0.60 (0.29), residues: 877 helix: 1.85 (0.27), residues: 394 sheet: -0.37 (0.39), residues: 156 loop : -0.99 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 169 HIS 0.002 0.001 HIS B 311 PHE 0.018 0.001 PHE R 89 TYR 0.027 0.001 TYR A 302 ARG 0.009 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 145 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8595 (t80) cc_final: 0.7897 (t80) REVERT: A 317 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7303 (ptmt) REVERT: A 327 THR cc_start: 0.6943 (OUTLIER) cc_final: 0.6568 (p) REVERT: B 124 TYR cc_start: 0.8862 (m-80) cc_final: 0.7993 (m-80) REVERT: B 154 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.7080 (m-30) REVERT: B 220 GLN cc_start: 0.8212 (mp10) cc_final: 0.7892 (mp10) REVERT: B 262 MET cc_start: 0.7859 (tpp) cc_final: 0.7564 (ttt) REVERT: R 205 MET cc_start: 0.8551 (tpp) cc_final: 0.8218 (tpp) REVERT: R 330 ASN cc_start: 0.7220 (t0) cc_final: 0.6989 (t0) outliers start: 29 outliers final: 23 residues processed: 137 average time/residue: 0.1560 time to fit residues: 30.4133 Evaluate side-chains 139 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 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 154 ASP 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 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 293 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 0.0770 chunk 21 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.4229 r_free = 0.4229 target = 0.198674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.162025 restraints weight = 8018.549| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 3.37 r_work: 0.3434 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4124 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= 0.187 Angle : 0.535 9.504 9725 Z= 0.279 Chirality : 0.041 0.178 1124 Planarity : 0.003 0.041 1215 Dihedral : 3.810 13.505 961 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.75 % Allowed : 17.34 % 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: 0.63 (0.29), residues: 877 helix: 1.94 (0.27), residues: 386 sheet: -0.46 (0.38), residues: 156 loop : -0.94 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 169 HIS 0.002 0.001 HIS B 62 PHE 0.010 0.001 PHE A 189 TYR 0.024 0.002 TYR A 302 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 145 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8641 (t80) cc_final: 0.7961 (t80) REVERT: A 317 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7333 (ptmt) REVERT: A 327 THR cc_start: 0.6786 (OUTLIER) cc_final: 0.6449 (p) REVERT: B 124 TYR cc_start: 0.8922 (m-80) cc_final: 0.8081 (m-80) REVERT: B 154 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.7123 (m-30) REVERT: B 220 GLN cc_start: 0.8217 (mp10) cc_final: 0.7890 (mp10) REVERT: B 262 MET cc_start: 0.7884 (tpp) cc_final: 0.7538 (ttt) REVERT: R 205 MET cc_start: 0.8574 (tpp) cc_final: 0.8234 (tpp) outliers start: 29 outliers final: 24 residues processed: 135 average time/residue: 0.1644 time to fit residues: 31.0109 Evaluate side-chains 141 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 327 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP 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 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 293 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 0.0370 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 62 optimal weight: 0.2980 chunk 69 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.4232 r_free = 0.4232 target = 0.199089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.163347 restraints weight = 7802.461| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.62 r_work: 0.3525 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7185 Z= 0.170 Angle : 0.547 9.395 9725 Z= 0.287 Chirality : 0.040 0.149 1124 Planarity : 0.003 0.041 1215 Dihedral : 3.771 13.439 961 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.88 % Allowed : 17.59 % Favored : 78.53 % 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: 0.66 (0.29), residues: 877 helix: 1.99 (0.27), residues: 385 sheet: -0.47 (0.39), residues: 156 loop : -0.94 (0.34), residues: 336 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 0.022 0.001 TYR A 302 ARG 0.008 0.000 ARG A 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3800.87 seconds wall clock time: 68 minutes 46.68 seconds (4126.68 seconds total)