Starting phenix.real_space_refine on Fri Mar 15 09:06:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgx_31979/03_2024/7vgx_31979_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgx_31979/03_2024/7vgx_31979.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgx_31979/03_2024/7vgx_31979_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgx_31979/03_2024/7vgx_31979_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgx_31979/03_2024/7vgx_31979_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgx_31979/03_2024/7vgx_31979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgx_31979/03_2024/7vgx_31979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgx_31979/03_2024/7vgx_31979_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgx_31979/03_2024/7vgx_31979_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.035 sd= 0.132 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2157 atoms to isotropic. 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 66 5.16 5 C 5763 2.51 5 N 1540 2.21 5 O 1675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 26": "OD1" <-> "OD2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 89": "OE1" <-> "OE2" Residue "S PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9044 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2257 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 268} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 200 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain breaks: 1 Chain: "A" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1806 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "S" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 4.91, per 1000 atoms: 0.54 Number of scatterers: 9044 At special positions: 0 Unit cell: (93.42, 121.965, 140.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1675 8.00 N 1540 7.00 C 5763 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 113 " - pdb=" SG CYS R 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.05 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 2.94 Conformation dependent library (CDL) restraints added in 1.6 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 13 sheets defined 33.6% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'R' and resid 37 through 67 removed outlier: 3.634A pdb=" N PHE R 41 " --> pdb=" O LEU R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 102 removed outlier: 3.950A pdb=" N LEU R 94 " --> pdb=" O ALA R 90 " (cutoff:3.500A) Proline residue: R 95 - end of helix removed outlier: 3.797A pdb=" N PHE R 98 " --> pdb=" O LEU R 94 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL R 99 " --> pdb=" O PRO R 95 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU R 102 " --> pdb=" O PHE R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 143 removed outlier: 4.120A pdb=" N ASN R 116 " --> pdb=" O CYS R 113 " (cutoff:3.500A) Proline residue: R 117 - end of helix removed outlier: 3.828A pdb=" N VAL R 126 " --> pdb=" O SER R 123 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU R 141 " --> pdb=" O ARG R 138 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE R 142 " --> pdb=" O HIS R 139 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE R 143 " --> pdb=" O GLN R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 174 removed outlier: 4.119A pdb=" N TYR R 156 " --> pdb=" O ASN R 152 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER R 170 " --> pdb=" O ALA R 166 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU R 171 " --> pdb=" O VAL R 167 " (cutoff:3.500A) Proline residue: R 172 - end of helix Processing helix chain 'R' and resid 205 through 219 Processing helix chain 'R' and resid 221 through 244 removed outlier: 4.080A pdb=" N CYS R 225 " --> pdb=" O PHE R 221 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG R 240 " --> pdb=" O ILE R 236 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG R 241 " --> pdb=" O ARG R 237 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASN R 242 " --> pdb=" O LEU R 238 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ASN R 243 " --> pdb=" O LYS R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 275 removed outlier: 3.685A pdb=" N ARG R 260 " --> pdb=" O SER R 256 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 288 Processing helix chain 'R' and resid 298 through 320 removed outlier: 5.070A pdb=" N SER R 312 " --> pdb=" O THR R 308 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N THR R 313 " --> pdb=" O ALA R 309 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N CYS R 314 " --> pdb=" O MET R 310 " (cutoff:3.500A) Proline residue: R 317 - end of helix Processing helix chain 'L' and resid 21 through 31 Processing helix chain 'A' and resid 7 through 32 removed outlier: 4.432A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 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 removed outlier: 3.679A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 241 through 254 removed outlier: 4.803A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.650A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (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 310 removed outlier: 4.021A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 43 removed outlier: 4.339A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.600A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 269 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.122A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.809A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.885A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 202 removed outlier: 3.917A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 262 through 265 removed outlier: 4.721A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.743A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.612A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.879A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR S 50 " --> pdb=" O TYR S 59 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.590A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'S' and resid 225 through 231 removed outlier: 3.788A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1029 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 3.22 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: 2919 1.35 - 1.47: 2284 1.47 - 1.60: 3935 1.60 - 1.72: 0 1.72 - 1.85: 96 Bond restraints: 9234 Sorted by residual: bond pdb=" C TYC L 36 " pdb=" NXT TYC L 36 " ideal model delta sigma weight residual 1.451 1.336 0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" N VAL B 71 " pdb=" CA VAL B 71 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.15e-02 7.56e+03 1.01e+01 bond pdb=" N ILE B 80 " pdb=" CA ILE B 80 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.93e+00 bond pdb=" N ARG B 150 " pdb=" CA ARG B 150 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.23e-02 6.61e+03 9.70e+00 bond pdb=" N VAL R 122 " pdb=" CA VAL R 122 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.80e+00 ... (remaining 9229 not shown) Histogram of bond angle deviations from ideal: 99.86 - 106.72: 208 106.72 - 113.58: 5042 113.58 - 120.44: 3580 120.44 - 127.30: 3586 127.30 - 134.15: 90 Bond angle restraints: 12506 Sorted by residual: angle pdb=" N MET S 192 " pdb=" CA MET S 192 " pdb=" CB MET S 192 " ideal model delta sigma weight residual 114.17 109.67 4.50 1.14e+00 7.69e-01 1.56e+01 angle pdb=" N MET R 179 " pdb=" CA MET R 179 " pdb=" C MET R 179 " ideal model delta sigma weight residual 113.88 109.52 4.36 1.23e+00 6.61e-01 1.26e+01 angle pdb=" CA TRP B 339 " pdb=" C TRP B 339 " pdb=" O TRP B 339 " ideal model delta sigma weight residual 121.56 117.89 3.67 1.09e+00 8.42e-01 1.13e+01 angle pdb=" CA LEU A 36 " pdb=" C LEU A 36 " pdb=" O LEU A 36 " ideal model delta sigma weight residual 121.58 117.70 3.88 1.16e+00 7.43e-01 1.12e+01 angle pdb=" N GLY B 77 " pdb=" CA GLY B 77 " pdb=" C GLY B 77 " ideal model delta sigma weight residual 115.63 110.85 4.78 1.49e+00 4.50e-01 1.03e+01 ... (remaining 12501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.19: 4959 16.19 - 32.39: 425 32.39 - 48.58: 86 48.58 - 64.78: 11 64.78 - 80.97: 7 Dihedral angle restraints: 5488 sinusoidal: 2146 harmonic: 3342 Sorted by residual: dihedral pdb=" CB CYS R 113 " pdb=" SG CYS R 113 " pdb=" SG CYS R 198 " pdb=" CB CYS R 198 " ideal model delta sinusoidal sigma weight residual -86.00 -154.34 68.34 1 1.00e+01 1.00e-02 6.06e+01 dihedral pdb=" CA THR R 180 " pdb=" C THR R 180 " pdb=" N ASP R 181 " pdb=" CA ASP R 181 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA TYR S 101 " pdb=" C TYR S 101 " pdb=" N TYR S 102 " pdb=" CA TYR S 102 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 5485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1149 0.054 - 0.108: 219 0.108 - 0.162: 41 0.162 - 0.216: 5 0.216 - 0.270: 2 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA LEU A 36 " pdb=" N LEU A 36 " pdb=" C LEU A 36 " pdb=" CB LEU A 36 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE A 222 " pdb=" CA ILE A 222 " pdb=" CG1 ILE A 222 " pdb=" CG2 ILE A 222 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1413 not shown) Planarity restraints: 1583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO B 236 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 35 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO R 36 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO R 36 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 36 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE S 68 " 0.004 2.00e-02 2.50e+03 9.53e-03 1.59e+00 pdb=" CG PHE S 68 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE S 68 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE S 68 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE S 68 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE S 68 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE S 68 " -0.000 2.00e-02 2.50e+03 ... (remaining 1580 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1909 2.78 - 3.31: 8106 3.31 - 3.84: 13770 3.84 - 4.37: 15661 4.37 - 4.90: 28668 Nonbonded interactions: 68114 Sorted by model distance: nonbonded pdb=" OG SER A 293 " pdb=" OE1 GLU A 298 " model vdw 2.255 2.440 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.289 2.440 nonbonded pdb=" NH2 ARG B 256 " pdb=" OD2 ASP G 36 " model vdw 2.289 2.520 nonbonded pdb=" NE2 GLN G 18 " pdb=" OE2 GLU G 22 " model vdw 2.302 2.520 nonbonded pdb=" O THR B 34 " pdb=" NZ LYS B 301 " model vdw 2.325 2.520 ... (remaining 68109 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 13.280 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 25.830 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 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 0.115 9234 Z= 0.262 Angle : 0.665 9.595 12506 Z= 0.387 Chirality : 0.046 0.270 1416 Planarity : 0.003 0.039 1583 Dihedral : 12.583 80.973 3319 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.12 (0.25), residues: 1126 helix: 2.00 (0.28), residues: 368 sheet: -0.33 (0.32), residues: 254 loop : -1.15 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.009 0.001 HIS B 142 PHE 0.019 0.001 PHE S 68 TYR 0.014 0.001 TYR S 59 ARG 0.006 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: R 103 MET cc_start: 0.7710 (mtm) cc_final: 0.7407 (mtt) REVERT: A 29 LYS cc_start: 0.7969 (tmtt) cc_final: 0.7730 (tttm) REVERT: B 312 ASP cc_start: 0.7539 (t70) cc_final: 0.7336 (t0) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2708 time to fit residues: 53.8626 Evaluate side-chains 125 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 45 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 316 ASN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9234 Z= 0.217 Angle : 0.547 6.248 12506 Z= 0.286 Chirality : 0.042 0.167 1416 Planarity : 0.004 0.038 1583 Dihedral : 4.077 19.847 1246 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.52 % Allowed : 8.21 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.25), residues: 1126 helix: 1.85 (0.27), residues: 370 sheet: -0.17 (0.32), residues: 255 loop : -1.19 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.010 0.001 HIS B 142 PHE 0.013 0.001 PHE R 272 TYR 0.011 0.001 TYR S 175 ARG 0.004 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.035 Fit side-chains REVERT: R 103 MET cc_start: 0.7671 (mtm) cc_final: 0.7371 (mtt) REVERT: A 29 LYS cc_start: 0.8050 (tmtt) cc_final: 0.7810 (tttm) REVERT: B 17 GLN cc_start: 0.7564 (tm-30) cc_final: 0.6434 (tt0) outliers start: 15 outliers final: 12 residues processed: 135 average time/residue: 0.2952 time to fit residues: 51.3017 Evaluate side-chains 131 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 275 CYS Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 315 VAL Chi-restraints excluded: chain R residue 316 ASN Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 69 optimal weight: 0.0980 chunk 28 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9234 Z= 0.202 Angle : 0.520 7.276 12506 Z= 0.273 Chirality : 0.041 0.141 1416 Planarity : 0.004 0.037 1583 Dihedral : 3.981 17.520 1246 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.33 % Allowed : 10.74 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.13 (0.25), residues: 1126 helix: 1.83 (0.28), residues: 373 sheet: -0.10 (0.32), residues: 263 loop : -1.20 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.009 0.001 HIS B 142 PHE 0.013 0.001 PHE R 272 TYR 0.020 0.001 TYR S 190 ARG 0.005 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.035 Fit side-chains REVERT: R 103 MET cc_start: 0.7663 (mtm) cc_final: 0.7329 (mtt) REVERT: A 29 LYS cc_start: 0.8114 (tmtt) cc_final: 0.7782 (tttm) REVERT: B 17 GLN cc_start: 0.7560 (tm-30) cc_final: 0.6469 (tt0) REVERT: B 285 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8117 (pt) outliers start: 23 outliers final: 17 residues processed: 137 average time/residue: 0.2616 time to fit residues: 47.0756 Evaluate side-chains 132 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 275 CYS Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 310 MET Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.9990 chunk 77 optimal weight: 0.1980 chunk 53 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 69 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9234 Z= 0.164 Angle : 0.486 7.323 12506 Z= 0.255 Chirality : 0.040 0.133 1416 Planarity : 0.003 0.036 1583 Dihedral : 3.820 17.273 1246 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.23 % Allowed : 13.78 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.29 (0.25), residues: 1126 helix: 1.95 (0.28), residues: 372 sheet: 0.11 (0.32), residues: 257 loop : -1.15 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.008 0.001 HIS B 142 PHE 0.011 0.001 PHE R 272 TYR 0.015 0.001 TYR S 190 ARG 0.006 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 1.064 Fit side-chains REVERT: R 103 MET cc_start: 0.7593 (mtm) cc_final: 0.7271 (mtt) REVERT: A 29 LYS cc_start: 0.8075 (tmtt) cc_final: 0.7739 (tttm) REVERT: B 17 GLN cc_start: 0.7525 (tm-30) cc_final: 0.6486 (tt0) REVERT: B 285 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8143 (pt) outliers start: 22 outliers final: 9 residues processed: 134 average time/residue: 0.2624 time to fit residues: 46.4132 Evaluate side-chains 121 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 275 CYS Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 243 ASN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9234 Z= 0.360 Angle : 0.615 8.577 12506 Z= 0.320 Chirality : 0.044 0.144 1416 Planarity : 0.004 0.040 1583 Dihedral : 4.335 17.825 1246 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.26 % Allowed : 13.58 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.02 (0.25), residues: 1126 helix: 1.63 (0.28), residues: 372 sheet: 0.02 (0.32), residues: 259 loop : -1.33 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.014 0.002 HIS B 142 PHE 0.014 0.002 PHE B 151 TYR 0.015 0.002 TYR S 190 ARG 0.006 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 121 time to evaluate : 1.093 Fit side-chains REVERT: L 30 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6803 (mp) REVERT: B 285 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8123 (pt) outliers start: 42 outliers final: 29 residues processed: 152 average time/residue: 0.2414 time to fit residues: 48.8880 Evaluate side-chains 149 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 118 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 275 CYS Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 315 VAL Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9234 Z= 0.233 Angle : 0.538 8.138 12506 Z= 0.282 Chirality : 0.041 0.139 1416 Planarity : 0.004 0.038 1583 Dihedral : 4.121 17.588 1246 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.65 % Allowed : 14.79 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.07 (0.25), residues: 1126 helix: 1.71 (0.28), residues: 372 sheet: 0.08 (0.33), residues: 253 loop : -1.26 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.011 0.001 HIS B 142 PHE 0.012 0.001 PHE A 189 TYR 0.014 0.001 TYR S 190 ARG 0.005 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 1.034 Fit side-chains REVERT: L 30 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6777 (mp) REVERT: B 17 GLN cc_start: 0.7452 (tm-30) cc_final: 0.6378 (tt0) REVERT: B 134 ARG cc_start: 0.8288 (ttp80) cc_final: 0.7857 (ttp80) REVERT: B 285 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8150 (pt) outliers start: 36 outliers final: 27 residues processed: 144 average time/residue: 0.2442 time to fit residues: 46.7998 Evaluate side-chains 145 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 275 CYS Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 108 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 67 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9234 Z= 0.186 Angle : 0.499 6.908 12506 Z= 0.262 Chirality : 0.040 0.133 1416 Planarity : 0.003 0.037 1583 Dihedral : 3.931 17.367 1246 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.34 % Allowed : 15.70 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.14 (0.25), residues: 1126 helix: 1.91 (0.28), residues: 366 sheet: -0.00 (0.32), residues: 263 loop : -1.27 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.009 0.001 HIS B 142 PHE 0.012 0.001 PHE R 272 TYR 0.013 0.001 TYR S 190 ARG 0.005 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 120 time to evaluate : 1.084 Fit side-chains REVERT: R 103 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7027 (mtt) REVERT: L 30 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6759 (mp) REVERT: B 17 GLN cc_start: 0.7443 (tm-30) cc_final: 0.6419 (tt0) REVERT: B 134 ARG cc_start: 0.8264 (ttp80) cc_final: 0.7859 (ttp80) REVERT: B 285 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8156 (pt) outliers start: 33 outliers final: 26 residues processed: 140 average time/residue: 0.2449 time to fit residues: 45.9098 Evaluate side-chains 147 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 MET Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain R residue 236 ILE Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 275 CYS Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9234 Z= 0.245 Angle : 0.538 6.635 12506 Z= 0.283 Chirality : 0.042 0.141 1416 Planarity : 0.004 0.037 1583 Dihedral : 4.093 17.610 1246 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.95 % Allowed : 15.40 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.01 (0.25), residues: 1126 helix: 1.71 (0.28), residues: 373 sheet: -0.03 (0.33), residues: 258 loop : -1.32 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.008 0.001 HIS B 142 PHE 0.012 0.001 PHE R 272 TYR 0.012 0.001 TYR S 190 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 119 time to evaluate : 1.011 Fit side-chains REVERT: L 30 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6771 (mp) REVERT: B 17 GLN cc_start: 0.7449 (tm-30) cc_final: 0.6435 (tt0) REVERT: B 134 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7861 (ttp80) REVERT: B 285 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8153 (pt) REVERT: B 312 ASP cc_start: 0.7694 (t70) cc_final: 0.7176 (t0) outliers start: 39 outliers final: 32 residues processed: 146 average time/residue: 0.2430 time to fit residues: 47.6438 Evaluate side-chains 151 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 117 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 236 ILE Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 275 CYS Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 104 optimal weight: 0.0670 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 91 optimal weight: 0.0050 chunk 95 optimal weight: 0.0670 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 overall best weight: 0.2870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 243 ASN A 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9234 Z= 0.128 Angle : 0.464 6.756 12506 Z= 0.244 Chirality : 0.040 0.137 1416 Planarity : 0.003 0.035 1583 Dihedral : 3.710 16.981 1246 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.53 % Allowed : 17.22 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.34 (0.25), residues: 1126 helix: 2.08 (0.28), residues: 365 sheet: 0.23 (0.32), residues: 263 loop : -1.23 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS G 44 PHE 0.009 0.001 PHE B 199 TYR 0.012 0.001 TYR S 190 ARG 0.005 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: B 17 GLN cc_start: 0.7438 (tm-30) cc_final: 0.6439 (tt0) REVERT: B 134 ARG cc_start: 0.8232 (ttp80) cc_final: 0.7843 (ttp80) REVERT: B 312 ASP cc_start: 0.7642 (t70) cc_final: 0.7200 (t0) outliers start: 25 outliers final: 18 residues processed: 137 average time/residue: 0.2503 time to fit residues: 45.3849 Evaluate side-chains 138 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain R residue 236 ILE Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 275 CYS Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.0970 chunk 74 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 71 optimal weight: 0.0870 chunk 95 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 243 ASN A 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9234 Z= 0.141 Angle : 0.471 6.933 12506 Z= 0.246 Chirality : 0.039 0.132 1416 Planarity : 0.003 0.035 1583 Dihedral : 3.657 16.676 1246 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.03 % Allowed : 17.53 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.25), residues: 1126 helix: 2.11 (0.28), residues: 364 sheet: 0.12 (0.32), residues: 269 loop : -1.19 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.011 0.001 PHE A 189 TYR 0.012 0.001 TYR S 190 ARG 0.004 0.000 ARG A 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: R 103 MET cc_start: 0.7300 (mtp) cc_final: 0.6889 (mtt) REVERT: B 17 GLN cc_start: 0.7466 (tm-30) cc_final: 0.6499 (tt0) REVERT: B 134 ARG cc_start: 0.8219 (ttp80) cc_final: 0.7835 (ttp80) REVERT: B 312 ASP cc_start: 0.7642 (t70) cc_final: 0.7202 (t0) outliers start: 20 outliers final: 20 residues processed: 132 average time/residue: 0.2648 time to fit residues: 46.2057 Evaluate side-chains 138 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain R residue 236 ILE Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 275 CYS Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.6980 chunk 13 optimal weight: 0.0010 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.115267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.090256 restraints weight = 15029.667| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.09 r_work: 0.3070 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9234 Z= 0.345 Angle : 0.608 7.630 12506 Z= 0.316 Chirality : 0.044 0.144 1416 Planarity : 0.004 0.038 1583 Dihedral : 4.236 17.814 1246 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.94 % Allowed : 16.41 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.01 (0.25), residues: 1126 helix: 1.67 (0.28), residues: 378 sheet: -0.05 (0.32), residues: 272 loop : -1.36 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.009 0.002 HIS B 142 PHE 0.015 0.002 PHE A 189 TYR 0.010 0.002 TYR S 190 ARG 0.005 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2350.02 seconds wall clock time: 42 minutes 44.33 seconds (2564.33 seconds total)