Starting phenix.real_space_refine on Tue Jun 25 06:02:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugy_42241/06_2024/8ugy_42241_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugy_42241/06_2024/8ugy_42241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugy_42241/06_2024/8ugy_42241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugy_42241/06_2024/8ugy_42241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugy_42241/06_2024/8ugy_42241_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ugy_42241/06_2024/8ugy_42241_updated.pdb" } resolution = 3.31 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= -0.002 sd= 0.107 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 52 5.16 5 C 4503 2.51 5 N 1159 2.21 5 O 1256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 231": "OD1" <-> "OD2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 6970 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1750 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2558 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "G" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 391 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain: "R" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2110 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "R" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 161 Unusual residues: {'CLR': 5, 'WRU': 1} Classifications: {'undetermined': 6, 'water': 1} Link IDs: {None: 6} Time building chain proxies: 4.43, per 1000 atoms: 0.64 Number of scatterers: 6970 At special positions: 0 Unit cell: (76.968, 99.417, 124.004, 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 52 16.00 O 1256 8.00 N 1159 7.00 C 4503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 173 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.1 seconds 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1642 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 8 sheets defined 43.2% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 4.064A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 231 removed outlier: 4.286A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.817A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 329 through 350 Processing helix chain 'B' and resid 8 through 25 removed outlier: 4.225A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 14 through 23 Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'R' and resid 21 through 49 removed outlier: 3.571A pdb=" N THR R 37 " --> pdb=" O THR R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 74 Processing helix chain 'R' and resid 76 through 84 Processing helix chain 'R' and resid 94 through 125 removed outlier: 3.890A pdb=" N ILE R 110 " --> pdb=" O CYS R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 133 removed outlier: 4.308A pdb=" N ARG R 132 " --> pdb=" O ILE R 128 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS R 133 " --> pdb=" O GLU R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 152 Processing helix chain 'R' and resid 156 through 159 No H-bonds generated for 'chain 'R' and resid 156 through 159' Processing helix chain 'R' and resid 180 through 190 Processing helix chain 'R' and resid 192 through 214 Processing helix chain 'R' and resid 284 through 315 removed outlier: 3.625A pdb=" N PHE R 300 " --> pdb=" O ILE R 296 " (cutoff:3.500A) Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 323 through 345 removed outlier: 4.134A pdb=" N ASN R 336 " --> pdb=" O LEU R 332 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER R 337 " --> pdb=" O GLY R 333 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU R 338 " --> pdb=" O TYR R 334 " (cutoff:3.500A) Proline residue: R 341 - end of helix Processing helix chain 'R' and resid 349 through 357 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.714A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 49 through 52 Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.968A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.676A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.867A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.530A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.809A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.632A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 978 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: 1.98 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2185 1.35 - 1.47: 1700 1.47 - 1.59: 3161 1.59 - 1.71: 0 1.71 - 1.83: 74 Bond restraints: 7120 Sorted by residual: bond pdb=" C3 CLR R 404 " pdb=" O1 CLR R 404 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C3 CLR R 403 " pdb=" O1 CLR R 403 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.16e+00 bond pdb=" C3 CLR R 405 " pdb=" O1 CLR R 405 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.14e+00 bond pdb=" C3 CLR R 402 " pdb=" O1 CLR R 402 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.12e+00 bond pdb=" C3 CLR R 401 " pdb=" O1 CLR R 401 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.07e+00 ... (remaining 7115 not shown) Histogram of bond angle deviations from ideal: 97.40 - 104.73: 93 104.73 - 112.06: 3688 112.06 - 119.38: 2383 119.38 - 126.71: 3405 126.71 - 134.04: 103 Bond angle restraints: 9672 Sorted by residual: angle pdb=" N GLU A 308 " pdb=" CA GLU A 308 " pdb=" CB GLU A 308 " ideal model delta sigma weight residual 110.39 114.73 -4.34 1.66e+00 3.63e-01 6.83e+00 angle pdb=" C PHE A 307 " pdb=" N GLU A 308 " pdb=" CA GLU A 308 " ideal model delta sigma weight residual 120.72 116.59 4.13 1.67e+00 3.59e-01 6.12e+00 angle pdb=" C VAL R 115 " pdb=" CA VAL R 115 " pdb=" CB VAL R 115 " ideal model delta sigma weight residual 112.16 108.22 3.94 1.63e+00 3.76e-01 5.83e+00 angle pdb=" N MET R 155 " pdb=" CA MET R 155 " pdb=" C MET R 155 " ideal model delta sigma weight residual 109.81 114.96 -5.15 2.21e+00 2.05e-01 5.44e+00 angle pdb=" N PRO R 156 " pdb=" CA PRO R 156 " pdb=" C PRO R 156 " ideal model delta sigma weight residual 110.70 113.54 -2.84 1.22e+00 6.72e-01 5.40e+00 ... (remaining 9667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.48: 4236 24.48 - 48.96: 223 48.96 - 73.43: 22 73.43 - 97.91: 2 97.91 - 122.39: 7 Dihedral angle restraints: 4490 sinusoidal: 1963 harmonic: 2527 Sorted by residual: dihedral pdb=" CB CYS R 95 " pdb=" SG CYS R 95 " pdb=" SG CYS R 173 " pdb=" CB CYS R 173 " ideal model delta sinusoidal sigma weight residual 93.00 179.63 -86.63 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" C1 CLR R 405 " pdb=" C2 CLR R 405 " pdb=" C3 CLR R 405 " pdb=" O1 CLR R 405 " ideal model delta sinusoidal sigma weight residual 180.04 57.65 122.39 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" N1 WRU R 406 " pdb=" C11 WRU R 406 " pdb=" C12 WRU R 406 " pdb=" N2 WRU R 406 " ideal model delta sinusoidal sigma weight residual -58.38 62.28 -120.66 1 3.00e+01 1.11e-03 1.61e+01 ... (remaining 4487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 748 0.037 - 0.074: 284 0.074 - 0.111: 79 0.111 - 0.148: 19 0.148 - 0.185: 2 Chirality restraints: 1132 Sorted by residual: chirality pdb=" C9 CLR R 402 " pdb=" C10 CLR R 402 " pdb=" C11 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.45 -2.26 -0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 1129 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET R 155 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO R 156 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO R 156 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 156 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C13 WRU R 406 " -0.005 2.00e-02 2.50e+03 1.20e-02 2.90e+00 pdb=" C14 WRU R 406 " 0.009 2.00e-02 2.50e+03 pdb=" C15 WRU R 406 " 0.011 2.00e-02 2.50e+03 pdb=" C16 WRU R 406 " -0.001 2.00e-02 2.50e+03 pdb=" C17 WRU R 406 " -0.014 2.00e-02 2.50e+03 pdb=" C18 WRU R 406 " -0.012 2.00e-02 2.50e+03 pdb=" C2 WRU R 406 " 0.022 2.00e-02 2.50e+03 pdb=" N2 WRU R 406 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO G 55 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " 0.019 5.00e-02 4.00e+02 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 136 2.69 - 3.24: 6820 3.24 - 3.80: 11032 3.80 - 4.35: 14768 4.35 - 4.90: 24943 Nonbonded interactions: 57699 Sorted by model distance: nonbonded pdb=" O PRO R 341 " pdb=" OG1 THR R 345 " model vdw 2.138 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.220 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.273 2.440 nonbonded pdb=" NE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 2.274 2.520 nonbonded pdb=" OD1 ASP A 341 " pdb=" NZ LYS A 345 " model vdw 2.288 2.520 ... (remaining 57694 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 3.700 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.690 Find NCS groups from input model: 0.180 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 0.003 0.032 7120 Z= 0.209 Angle : 0.560 6.713 9672 Z= 0.290 Chirality : 0.043 0.185 1132 Planarity : 0.003 0.056 1170 Dihedral : 14.646 122.390 2842 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.71 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.29), residues: 848 helix: 1.66 (0.28), residues: 372 sheet: -0.64 (0.39), residues: 167 loop : -0.96 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.001 0.000 HIS R 177 PHE 0.012 0.001 PHE A 189 TYR 0.014 0.001 TYR R 203 ARG 0.007 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.788 Fit side-chains REVERT: A 349 LYS cc_start: 0.8582 (ttpt) cc_final: 0.8030 (ttmt) REVERT: R 338 LEU cc_start: 0.8846 (tp) cc_final: 0.8571 (tp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2247 time to fit residues: 36.4110 Evaluate side-chains 109 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 0.0470 chunk 77 optimal weight: 0.7980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.0625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7120 Z= 0.214 Angle : 0.530 7.205 9672 Z= 0.268 Chirality : 0.041 0.151 1132 Planarity : 0.003 0.055 1170 Dihedral : 5.722 57.614 1274 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.48 % Favored : 97.41 % Rotamer: Outliers : 1.22 % Allowed : 8.51 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.29), residues: 848 helix: 1.97 (0.28), residues: 373 sheet: -0.68 (0.39), residues: 169 loop : -0.96 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS B 142 PHE 0.014 0.001 PHE R 300 TYR 0.012 0.001 TYR R 203 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 0.789 Fit side-chains REVERT: A 255 ASN cc_start: 0.8823 (m110) cc_final: 0.8469 (m-40) REVERT: R 124 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8096 (mt) outliers start: 9 outliers final: 5 residues processed: 119 average time/residue: 0.2100 time to fit residues: 32.5688 Evaluate side-chains 120 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 155 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7120 Z= 0.233 Angle : 0.493 6.140 9672 Z= 0.260 Chirality : 0.041 0.148 1132 Planarity : 0.003 0.056 1170 Dihedral : 5.083 58.116 1274 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.59 % Favored : 97.29 % Rotamer: Outliers : 1.89 % Allowed : 11.22 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.29), residues: 848 helix: 2.03 (0.28), residues: 373 sheet: -0.68 (0.39), residues: 169 loop : -0.91 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS R 207 PHE 0.014 0.001 PHE R 300 TYR 0.013 0.001 TYR R 182 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 0.706 Fit side-chains REVERT: A 255 ASN cc_start: 0.8836 (m110) cc_final: 0.8492 (m-40) REVERT: A 308 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: B 153 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.7917 (p0) REVERT: R 124 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8071 (mt) REVERT: R 338 LEU cc_start: 0.8829 (tp) cc_final: 0.8587 (tp) outliers start: 14 outliers final: 9 residues processed: 123 average time/residue: 0.2046 time to fit residues: 33.0352 Evaluate side-chains 128 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 155 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 0.0370 chunk 40 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7120 Z= 0.166 Angle : 0.459 6.019 9672 Z= 0.242 Chirality : 0.040 0.139 1132 Planarity : 0.003 0.055 1170 Dihedral : 5.029 57.328 1274 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.24 % Favored : 97.64 % Rotamer: Outliers : 2.43 % Allowed : 13.11 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.29), residues: 848 helix: 2.15 (0.28), residues: 373 sheet: -0.58 (0.38), residues: 170 loop : -0.86 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.002 0.001 HIS R 207 PHE 0.013 0.001 PHE R 300 TYR 0.013 0.001 TYR R 182 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 0.773 Fit side-chains REVERT: A 255 ASN cc_start: 0.8830 (m110) cc_final: 0.8477 (m-40) REVERT: A 308 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: G 19 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7926 (tt) REVERT: R 124 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8126 (mt) REVERT: R 212 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6539 (mp) REVERT: R 338 LEU cc_start: 0.8816 (tp) cc_final: 0.8500 (tp) outliers start: 18 outliers final: 12 residues processed: 130 average time/residue: 0.2128 time to fit residues: 36.4846 Evaluate side-chains 132 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 321 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7120 Z= 0.290 Angle : 0.527 6.147 9672 Z= 0.276 Chirality : 0.042 0.150 1132 Planarity : 0.003 0.055 1170 Dihedral : 5.298 56.340 1274 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 3.38 % Allowed : 13.51 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.29), residues: 848 helix: 1.94 (0.28), residues: 379 sheet: -0.76 (0.39), residues: 171 loop : -0.81 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS R 207 PHE 0.016 0.002 PHE R 307 TYR 0.011 0.001 TYR R 182 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 0.811 Fit side-chains REVERT: A 255 ASN cc_start: 0.8857 (m110) cc_final: 0.8500 (m-40) REVERT: A 308 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: A 349 LYS cc_start: 0.8495 (ttpt) cc_final: 0.7916 (ttmt) REVERT: G 19 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7973 (tt) REVERT: R 124 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8179 (mt) REVERT: R 212 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6652 (mp) outliers start: 25 outliers final: 14 residues processed: 133 average time/residue: 0.1965 time to fit residues: 34.5019 Evaluate side-chains 133 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 321 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7120 Z= 0.197 Angle : 0.491 7.079 9672 Z= 0.256 Chirality : 0.040 0.139 1132 Planarity : 0.003 0.054 1170 Dihedral : 5.235 55.817 1274 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.59 % Favored : 97.29 % Rotamer: Outliers : 3.24 % Allowed : 15.14 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.29), residues: 848 helix: 2.06 (0.28), residues: 374 sheet: -0.66 (0.38), residues: 172 loop : -0.73 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS R 207 PHE 0.013 0.001 PHE R 300 TYR 0.012 0.001 TYR R 182 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 0.716 Fit side-chains REVERT: A 255 ASN cc_start: 0.8750 (m110) cc_final: 0.8517 (m-40) REVERT: A 349 LYS cc_start: 0.8484 (ttpt) cc_final: 0.7912 (ttmt) REVERT: G 19 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7920 (tt) REVERT: R 124 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8164 (mt) REVERT: R 212 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6469 (mp) REVERT: R 338 LEU cc_start: 0.8833 (tp) cc_final: 0.8464 (tp) outliers start: 24 outliers final: 17 residues processed: 129 average time/residue: 0.1994 time to fit residues: 33.8293 Evaluate side-chains 134 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 321 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 49 optimal weight: 0.0270 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7120 Z= 0.210 Angle : 0.505 7.386 9672 Z= 0.263 Chirality : 0.040 0.140 1132 Planarity : 0.003 0.054 1170 Dihedral : 5.242 55.158 1274 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 2.97 % Allowed : 15.95 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.29), residues: 848 helix: 1.99 (0.28), residues: 380 sheet: -0.62 (0.39), residues: 172 loop : -0.72 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS B 54 PHE 0.014 0.001 PHE R 300 TYR 0.011 0.001 TYR R 182 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 0.772 Fit side-chains REVERT: A 255 ASN cc_start: 0.8738 (m110) cc_final: 0.8534 (m-40) REVERT: A 306 GLN cc_start: 0.7393 (tt0) cc_final: 0.7102 (mt0) REVERT: A 349 LYS cc_start: 0.8488 (ttpt) cc_final: 0.7904 (ttmt) REVERT: B 234 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8972 (m-80) REVERT: G 19 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7929 (tt) REVERT: R 124 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8170 (mt) REVERT: R 212 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6469 (mp) REVERT: R 338 LEU cc_start: 0.8832 (tp) cc_final: 0.8426 (tp) outliers start: 22 outliers final: 16 residues processed: 131 average time/residue: 0.2286 time to fit residues: 39.0133 Evaluate side-chains 137 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 321 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.1980 chunk 24 optimal weight: 0.0020 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 0.0970 chunk 64 optimal weight: 0.0070 chunk 74 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 overall best weight: 0.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7120 Z= 0.121 Angle : 0.461 6.312 9672 Z= 0.243 Chirality : 0.039 0.136 1132 Planarity : 0.003 0.054 1170 Dihedral : 5.029 54.588 1274 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.48 % Favored : 97.41 % Rotamer: Outliers : 2.43 % Allowed : 17.16 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.30), residues: 848 helix: 2.14 (0.28), residues: 379 sheet: -0.49 (0.39), residues: 173 loop : -0.70 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS B 54 PHE 0.010 0.001 PHE A 189 TYR 0.011 0.001 TYR R 182 ARG 0.007 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 0.669 Fit side-chains REVERT: A 349 LYS cc_start: 0.8482 (ttpt) cc_final: 0.7914 (ttmt) REVERT: B 153 ASP cc_start: 0.8351 (p0) cc_final: 0.7990 (p0) REVERT: B 234 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8718 (m-80) REVERT: G 19 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7893 (tt) REVERT: R 124 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8127 (mt) REVERT: R 212 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6396 (mp) REVERT: R 338 LEU cc_start: 0.8839 (tp) cc_final: 0.8623 (tp) outliers start: 18 outliers final: 12 residues processed: 132 average time/residue: 0.1965 time to fit residues: 34.2311 Evaluate side-chains 138 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 321 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.0570 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7120 Z= 0.190 Angle : 0.503 7.075 9672 Z= 0.263 Chirality : 0.040 0.137 1132 Planarity : 0.003 0.053 1170 Dihedral : 5.073 53.864 1274 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.42 % Favored : 96.46 % Rotamer: Outliers : 2.43 % Allowed : 17.70 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.30), residues: 848 helix: 2.10 (0.28), residues: 379 sheet: -0.50 (0.39), residues: 172 loop : -0.73 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 54 PHE 0.013 0.001 PHE A 189 TYR 0.012 0.001 TYR R 182 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 0.705 Fit side-chains REVERT: A 349 LYS cc_start: 0.8493 (ttpt) cc_final: 0.7918 (ttmt) REVERT: B 234 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8785 (m-80) REVERT: G 19 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7907 (tt) REVERT: R 124 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8168 (mt) REVERT: R 212 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6430 (mp) REVERT: R 338 LEU cc_start: 0.8841 (tp) cc_final: 0.8629 (tp) outliers start: 18 outliers final: 12 residues processed: 132 average time/residue: 0.2005 time to fit residues: 34.8085 Evaluate side-chains 135 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 321 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7120 Z= 0.309 Angle : 0.566 8.820 9672 Z= 0.293 Chirality : 0.043 0.153 1132 Planarity : 0.003 0.053 1170 Dihedral : 5.406 51.722 1274 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.30 % Favored : 96.58 % Rotamer: Outliers : 2.57 % Allowed : 17.70 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.29), residues: 848 helix: 1.94 (0.28), residues: 379 sheet: -0.70 (0.39), residues: 171 loop : -0.75 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS A 188 PHE 0.017 0.002 PHE A 189 TYR 0.011 0.001 TYR R 202 ARG 0.006 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 0.777 Fit side-chains REVERT: A 306 GLN cc_start: 0.7447 (tt0) cc_final: 0.7177 (mt0) REVERT: A 349 LYS cc_start: 0.8498 (ttpt) cc_final: 0.7928 (ttmt) REVERT: B 198 LEU cc_start: 0.9090 (mp) cc_final: 0.8800 (mp) REVERT: B 234 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.9007 (m-80) REVERT: G 19 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7877 (tt) REVERT: R 124 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8068 (mp) REVERT: R 212 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6492 (mp) REVERT: R 338 LEU cc_start: 0.8825 (tp) cc_final: 0.8538 (tp) outliers start: 19 outliers final: 14 residues processed: 131 average time/residue: 0.2041 time to fit residues: 35.1846 Evaluate side-chains 135 residues out of total 748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 321 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 69 optimal weight: 0.0770 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.144355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.105392 restraints weight = 7583.616| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.08 r_work: 0.2939 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7120 Z= 0.181 Angle : 0.504 7.725 9672 Z= 0.262 Chirality : 0.040 0.136 1132 Planarity : 0.003 0.054 1170 Dihedral : 5.221 49.940 1274 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.07 % Favored : 96.82 % Rotamer: Outliers : 2.43 % Allowed : 18.11 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.29), residues: 848 helix: 2.05 (0.28), residues: 378 sheet: -0.58 (0.39), residues: 172 loop : -0.79 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS R 207 PHE 0.012 0.001 PHE A 189 TYR 0.011 0.001 TYR R 182 ARG 0.006 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1865.58 seconds wall clock time: 34 minutes 19.34 seconds (2059.34 seconds total)