Starting phenix.real_space_refine on Tue Feb 13 17:32:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy7_33513/02_2024/7xy7_33513_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy7_33513/02_2024/7xy7_33513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy7_33513/02_2024/7xy7_33513.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy7_33513/02_2024/7xy7_33513.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy7_33513/02_2024/7xy7_33513_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy7_33513/02_2024/7xy7_33513_updated.pdb" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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 47 5.16 5 C 4481 2.51 5 N 1231 2.21 5 O 1288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "R PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 217": not complete - not flipped Residue "R TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7047 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1857 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 396 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "R" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2211 Unusual residues: {'NEC': 1} Classifications: {'peptide': 283, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 271, None: 1} Not linked: pdbres="TYR R 308 " pdbres="NEC R 501 " Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 4.23, per 1000 atoms: 0.60 Number of scatterers: 7047 At special positions: 0 Unit cell: (78.72, 101.76, 134.4, 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 47 16.00 O 1288 8.00 N 1231 7.00 C 4481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 171 " 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: 2.78 Conformation dependent library (CDL) restraints added in 1.2 seconds 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 8 sheets defined 41.7% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.582A pdb=" N SER A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 285 Processing helix chain 'A' and resid 291 through 294 No H-bonds generated for 'chain 'A' and resid 291 through 294' Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 315 through 334 removed outlier: 3.631A pdb=" N ARG A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 373 Processing helix chain 'B' and resid 6 through 24 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 13 through 20 removed outlier: 3.713A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 47 removed outlier: 3.682A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA G 45 " --> pdb=" O CYS G 41 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 34 removed outlier: 4.140A pdb=" N LEU R 27 " --> pdb=" O ALA R 23 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL R 28 " --> pdb=" O GLY R 24 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS R 29 " --> pdb=" O ASN R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 69 removed outlier: 4.299A pdb=" N PHE R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU R 46 " --> pdb=" O THR R 42 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE R 61 " --> pdb=" O GLY R 57 " (cutoff:3.500A) Proline residue: R 62 - end of helix Processing helix chain 'R' and resid 76 through 108 removed outlier: 3.953A pdb=" N PHE R 80 " --> pdb=" O TYR R 76 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER R 92 " --> pdb=" O LEU R 88 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE R 93 " --> pdb=" O THR R 89 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE R 107 " --> pdb=" O ARG R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 116 No H-bonds generated for 'chain 'R' and resid 113 through 116' Processing helix chain 'R' and resid 119 through 142 removed outlier: 3.683A pdb=" N THR R 139 " --> pdb=" O GLY R 135 " (cutoff:3.500A) Proline residue: R 140 - end of helix Processing helix chain 'R' and resid 173 through 176 No H-bonds generated for 'chain 'R' and resid 173 through 176' Processing helix chain 'R' and resid 179 through 182 No H-bonds generated for 'chain 'R' and resid 179 through 182' Processing helix chain 'R' and resid 192 through 217 removed outlier: 3.641A pdb=" N PHE R 206 " --> pdb=" O TYR R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 259 removed outlier: 3.742A pdb=" N HIS R 231 " --> pdb=" O GLN R 227 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET R 238 " --> pdb=" O LYS R 234 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE R 239 " --> pdb=" O SER R 235 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL R 240 " --> pdb=" O LEU R 236 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE R 243 " --> pdb=" O ILE R 239 " (cutoff:3.500A) Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 261 through 265 Processing helix chain 'R' and resid 269 through 290 removed outlier: 3.582A pdb=" N MET R 274 " --> pdb=" O ALA R 271 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN R 282 " --> pdb=" O SER R 279 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER R 283 " --> pdb=" O HIS R 280 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL R 284 " --> pdb=" O ALA R 281 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN R 286 " --> pdb=" O SER R 283 " (cutoff:3.500A) Proline residue: R 287 - end of helix removed outlier: 3.594A pdb=" N TYR R 290 " --> pdb=" O PRO R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 307 Processing sheet with id= A, first strand: chain 'A' and resid 269 through 275 removed outlier: 4.204A pdb=" N ALA A 236 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 37 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N LEU A 36 " --> pdb=" O ASN A 211 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N HIS A 213 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU A 38 " --> pdb=" O HIS A 213 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE A 215 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.886A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.254A 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: 6.749A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.090A 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: 7.121A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.600A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.926A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.598A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 308 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 327 through 330 removed outlier: 3.658A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 852 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: 1.82 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2296 1.34 - 1.46: 1024 1.46 - 1.57: 3805 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 7190 Sorted by residual: bond pdb=" C4 NEC R 501 " pdb=" C5 NEC R 501 " ideal model delta sigma weight residual 1.385 1.471 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C5 NEC R 501 " pdb=" C6 NEC R 501 " ideal model delta sigma weight residual 1.407 1.482 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C8 NEC R 501 " pdb=" N7 NEC R 501 " ideal model delta sigma weight residual 1.302 1.357 -0.055 2.00e-02 2.50e+03 7.65e+00 bond pdb=" C3' NEC R 501 " pdb=" O3' NEC R 501 " ideal model delta sigma weight residual 1.393 1.433 -0.040 2.00e-02 2.50e+03 4.03e+00 bond pdb=" C2' NEC R 501 " pdb=" O2' NEC R 501 " ideal model delta sigma weight residual 1.400 1.434 -0.034 2.00e-02 2.50e+03 2.89e+00 ... (remaining 7185 not shown) Histogram of bond angle deviations from ideal: 100.03 - 107.26: 190 107.26 - 114.49: 4228 114.49 - 121.72: 3764 121.72 - 128.95: 1515 128.95 - 136.18: 55 Bond angle restraints: 9752 Sorted by residual: angle pdb=" C2 NEC R 501 " pdb=" N3 NEC R 501 " pdb=" C4 NEC R 501 " ideal model delta sigma weight residual 111.54 120.89 -9.35 3.00e+00 1.11e-01 9.71e+00 angle pdb=" CA LEU B 198 " pdb=" CB LEU B 198 " pdb=" CG LEU B 198 " ideal model delta sigma weight residual 116.30 126.02 -9.72 3.50e+00 8.16e-02 7.70e+00 angle pdb=" C5 NEC R 501 " pdb=" C4 NEC R 501 " pdb=" N3 NEC R 501 " ideal model delta sigma weight residual 126.75 118.68 8.07 3.00e+00 1.11e-01 7.23e+00 angle pdb=" CA GLN B 17 " pdb=" CB GLN B 17 " pdb=" CG GLN B 17 " ideal model delta sigma weight residual 114.10 119.35 -5.25 2.00e+00 2.50e-01 6.89e+00 angle pdb=" CB ARG A 339 " pdb=" CG ARG A 339 " pdb=" CD ARG A 339 " ideal model delta sigma weight residual 111.30 117.23 -5.93 2.30e+00 1.89e-01 6.64e+00 ... (remaining 9747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 4180 35.44 - 70.87: 112 70.87 - 106.31: 4 106.31 - 141.74: 0 141.74 - 177.18: 1 Dihedral angle restraints: 4297 sinusoidal: 1686 harmonic: 2611 Sorted by residual: dihedral pdb=" CB CYS R 78 " pdb=" SG CYS R 78 " pdb=" SG CYS R 171 " pdb=" CB CYS R 171 " ideal model delta sinusoidal sigma weight residual 93.00 162.51 -69.51 1 1.00e+01 1.00e-02 6.24e+01 dihedral pdb=" CB GLU R 217 " pdb=" CG GLU R 217 " pdb=" CD GLU R 217 " pdb=" OE1 GLU R 217 " ideal model delta sinusoidal sigma weight residual 0.00 177.18 -177.18 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA CYS R 171 " pdb=" C CYS R 171 " pdb=" N LEU R 172 " pdb=" CA LEU R 172 " ideal model delta harmonic sigma weight residual 180.00 161.32 18.68 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 4294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 767 0.037 - 0.074: 260 0.074 - 0.111: 67 0.111 - 0.149: 23 0.149 - 0.186: 1 Chirality restraints: 1118 Sorted by residual: chirality pdb=" C2' NEC R 501 " pdb=" C1' NEC R 501 " pdb=" C3' NEC R 501 " pdb=" O2' NEC R 501 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CA PRO R 249 " pdb=" N PRO R 249 " pdb=" C PRO R 249 " pdb=" CB PRO R 249 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ASP B 163 " pdb=" N ASP B 163 " pdb=" C ASP B 163 " pdb=" CB ASP B 163 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 1115 not shown) Planarity restraints: 1239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 193 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO R 194 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO R 194 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 194 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 314 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.83e+00 pdb=" N PRO A 315 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 315 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 315 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 118 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" CG ASP B 118 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASP B 118 " 0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP B 118 " 0.008 2.00e-02 2.50e+03 ... (remaining 1236 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 142 2.69 - 3.24: 6519 3.24 - 3.80: 10502 3.80 - 4.35: 13097 4.35 - 4.90: 22292 Nonbonded interactions: 52552 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.141 2.440 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.258 2.440 nonbonded pdb=" OG1 THR B 173 " pdb=" OE1 GLN B 175 " model vdw 2.259 2.440 nonbonded pdb=" OG SER A 6 " pdb=" OE1 GLU A 8 " model vdw 2.260 2.440 nonbonded pdb=" O ALA A 41 " pdb=" OG SER A 44 " model vdw 2.276 2.440 ... (remaining 52547 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: 1.170 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: 0.000 Extract box with map and model: 5.180 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.560 Find NCS groups from input model: 0.200 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 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 0.086 7190 Z= 0.215 Angle : 0.576 9.715 9752 Z= 0.307 Chirality : 0.042 0.186 1118 Planarity : 0.004 0.041 1239 Dihedral : 15.857 177.175 2600 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.40 % Allowed : 17.72 % Favored : 81.88 % 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: 1.03 (0.29), residues: 881 helix: 1.98 (0.28), residues: 369 sheet: 0.61 (0.43), residues: 168 loop : -0.72 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS B 54 PHE 0.020 0.001 PHE A 215 TYR 0.008 0.001 TYR R 104 ARG 0.007 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 0.821 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 171 average time/residue: 0.2688 time to fit residues: 56.6967 Evaluate side-chains 166 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.0870 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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: 0.7548 moved from start: 0.0659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7190 Z= 0.242 Angle : 0.493 7.567 9752 Z= 0.266 Chirality : 0.042 0.129 1118 Planarity : 0.004 0.045 1239 Dihedral : 4.235 25.185 1003 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.57 % Allowed : 15.61 % Favored : 80.82 % 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: 1.17 (0.29), residues: 881 helix: 2.03 (0.28), residues: 376 sheet: 0.67 (0.43), residues: 161 loop : -0.58 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS G 44 PHE 0.012 0.002 PHE B 199 TYR 0.010 0.001 TYR R 104 ARG 0.005 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 173 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 ARG cc_start: 0.7319 (ttm-80) cc_final: 0.7068 (ttm170) REVERT: B 239 ASN cc_start: 0.7557 (m-40) cc_final: 0.7334 (m-40) outliers start: 27 outliers final: 20 residues processed: 177 average time/residue: 0.3052 time to fit residues: 65.0488 Evaluate side-chains 190 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 170 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 80 optimal weight: 0.5980 chunk 86 optimal weight: 0.0970 chunk 71 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7190 Z= 0.238 Angle : 0.478 8.068 9752 Z= 0.259 Chirality : 0.041 0.129 1118 Planarity : 0.004 0.046 1239 Dihedral : 3.971 16.723 999 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.63 % Allowed : 15.34 % Favored : 80.03 % 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: 1.18 (0.29), residues: 881 helix: 2.12 (0.27), residues: 377 sheet: 0.66 (0.44), residues: 156 loop : -0.66 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS G 44 PHE 0.014 0.002 PHE B 235 TYR 0.009 0.001 TYR A 322 ARG 0.005 0.000 ARG R 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8179 (tppp) cc_final: 0.7768 (mttt) REVERT: A 330 ARG cc_start: 0.7352 (ttm-80) cc_final: 0.7091 (ttm170) REVERT: A 339 ARG cc_start: 0.7111 (mpp80) cc_final: 0.6731 (mpp80) REVERT: B 249 THR cc_start: 0.8346 (p) cc_final: 0.8126 (p) REVERT: B 298 ASP cc_start: 0.7636 (t70) cc_final: 0.7114 (t70) outliers start: 35 outliers final: 30 residues processed: 189 average time/residue: 0.2938 time to fit residues: 66.9181 Evaluate side-chains 208 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 178 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.2980 chunk 60 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 22 optimal weight: 0.0020 chunk 70 optimal weight: 1.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7190 Z= 0.190 Angle : 0.466 8.430 9752 Z= 0.248 Chirality : 0.041 0.129 1118 Planarity : 0.003 0.045 1239 Dihedral : 3.828 16.057 999 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.89 % Allowed : 18.12 % Favored : 76.98 % 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: 1.17 (0.29), residues: 881 helix: 2.20 (0.28), residues: 376 sheet: 0.53 (0.42), residues: 163 loop : -0.72 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.002 0.001 HIS G 44 PHE 0.023 0.001 PHE A 215 TYR 0.008 0.001 TYR A 322 ARG 0.004 0.000 ARG R 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 169 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 ARG cc_start: 0.7140 (mpp80) cc_final: 0.6800 (mpp80) REVERT: B 298 ASP cc_start: 0.7595 (t70) cc_final: 0.7080 (t70) outliers start: 37 outliers final: 30 residues processed: 182 average time/residue: 0.2823 time to fit residues: 62.7824 Evaluate side-chains 198 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 168 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 279 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 58 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7190 Z= 0.173 Angle : 0.456 9.083 9752 Z= 0.244 Chirality : 0.040 0.129 1118 Planarity : 0.003 0.044 1239 Dihedral : 3.735 15.027 999 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 5.03 % Allowed : 18.92 % Favored : 76.06 % 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: 1.23 (0.29), residues: 881 helix: 2.29 (0.28), residues: 374 sheet: 0.57 (0.43), residues: 163 loop : -0.73 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.002 0.000 HIS G 44 PHE 0.023 0.001 PHE A 215 TYR 0.008 0.001 TYR A 322 ARG 0.004 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 168 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8671 (ttpt) cc_final: 0.8466 (mtpt) REVERT: A 339 ARG cc_start: 0.7164 (mpp80) cc_final: 0.6949 (mpp80) REVERT: B 245 SER cc_start: 0.8408 (p) cc_final: 0.8102 (m) REVERT: B 298 ASP cc_start: 0.7609 (t70) cc_final: 0.7106 (t70) outliers start: 38 outliers final: 35 residues processed: 179 average time/residue: 0.2686 time to fit residues: 59.6645 Evaluate side-chains 203 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 168 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 279 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 0.0270 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 82 optimal weight: 0.4980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7190 Z= 0.189 Angle : 0.456 8.455 9752 Z= 0.245 Chirality : 0.041 0.129 1118 Planarity : 0.003 0.044 1239 Dihedral : 3.708 14.745 999 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.23 % Allowed : 19.18 % Favored : 76.59 % 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: 1.21 (0.29), residues: 881 helix: 2.26 (0.28), residues: 376 sheet: 0.54 (0.43), residues: 163 loop : -0.73 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.002 0.000 HIS G 44 PHE 0.021 0.001 PHE A 215 TYR 0.008 0.001 TYR A 322 ARG 0.004 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 168 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8685 (ttpt) cc_final: 0.8476 (mtpt) REVERT: A 339 ARG cc_start: 0.7178 (mpp80) cc_final: 0.6947 (mpp80) REVERT: B 245 SER cc_start: 0.8395 (p) cc_final: 0.8086 (m) REVERT: B 298 ASP cc_start: 0.7618 (t70) cc_final: 0.7106 (t70) outliers start: 32 outliers final: 31 residues processed: 178 average time/residue: 0.2631 time to fit residues: 57.6228 Evaluate side-chains 198 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 167 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 279 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.0770 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 71 optimal weight: 0.4980 chunk 47 optimal weight: 0.4980 chunk 84 optimal weight: 0.0570 chunk 53 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- 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: 0.7523 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7190 Z= 0.155 Angle : 0.435 6.026 9752 Z= 0.237 Chirality : 0.040 0.131 1118 Planarity : 0.003 0.043 1239 Dihedral : 3.620 14.417 999 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.89 % Allowed : 18.25 % Favored : 76.85 % 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: 1.27 (0.29), residues: 881 helix: 2.32 (0.28), residues: 375 sheet: 0.59 (0.43), residues: 163 loop : -0.71 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.002 0.000 HIS G 44 PHE 0.018 0.001 PHE A 215 TYR 0.007 0.001 TYR A 322 ARG 0.004 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 165 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7757 (ttp-170) cc_final: 0.7299 (ttp-170) REVERT: A 321 LYS cc_start: 0.8647 (ttpt) cc_final: 0.8439 (mtpt) REVERT: A 339 ARG cc_start: 0.7192 (mpp80) cc_final: 0.6943 (mpp80) REVERT: B 86 THR cc_start: 0.8281 (p) cc_final: 0.8054 (p) REVERT: B 298 ASP cc_start: 0.7609 (t70) cc_final: 0.7110 (t70) outliers start: 37 outliers final: 32 residues processed: 178 average time/residue: 0.2334 time to fit residues: 52.7377 Evaluate side-chains 193 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 279 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 16 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 0.2980 chunk 66 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7190 Z= 0.176 Angle : 0.454 5.856 9752 Z= 0.245 Chirality : 0.041 0.140 1118 Planarity : 0.003 0.044 1239 Dihedral : 3.601 14.083 999 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.76 % Allowed : 18.52 % Favored : 76.72 % 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: 1.29 (0.29), residues: 881 helix: 2.31 (0.28), residues: 377 sheet: 0.63 (0.43), residues: 162 loop : -0.71 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.002 0.000 HIS G 44 PHE 0.024 0.001 PHE A 215 TYR 0.007 0.001 TYR A 322 ARG 0.002 0.000 ARG R 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 160 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7757 (ttp-170) cc_final: 0.7285 (ttp-170) REVERT: A 339 ARG cc_start: 0.7205 (mpp80) cc_final: 0.6940 (mpp80) REVERT: B 190 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7694 (pp) REVERT: B 197 ARG cc_start: 0.7506 (tpp80) cc_final: 0.7280 (tpp80) REVERT: B 249 THR cc_start: 0.8292 (p) cc_final: 0.8080 (p) REVERT: B 298 ASP cc_start: 0.7624 (t70) cc_final: 0.7156 (t70) REVERT: R 272 MET cc_start: 0.8115 (mmm) cc_final: 0.7418 (tmm) outliers start: 36 outliers final: 33 residues processed: 171 average time/residue: 0.2326 time to fit residues: 50.6452 Evaluate side-chains 194 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 160 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 279 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 0.0170 chunk 71 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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: 0.7534 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7190 Z= 0.191 Angle : 0.458 5.786 9752 Z= 0.249 Chirality : 0.041 0.134 1118 Planarity : 0.003 0.044 1239 Dihedral : 3.619 14.087 999 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.37 % Allowed : 19.18 % Favored : 76.46 % 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: 1.29 (0.29), residues: 881 helix: 2.31 (0.28), residues: 377 sheet: 0.61 (0.42), residues: 162 loop : -0.70 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.002 0.000 HIS G 44 PHE 0.024 0.001 PHE A 215 TYR 0.009 0.001 TYR A 322 ARG 0.002 0.000 ARG R 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 158 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7762 (ttp-170) cc_final: 0.7294 (ttp-170) REVERT: A 255 ASP cc_start: 0.8124 (t0) cc_final: 0.7919 (t70) REVERT: A 339 ARG cc_start: 0.7213 (mpp80) cc_final: 0.6928 (mpp80) REVERT: B 197 ARG cc_start: 0.7540 (tpp80) cc_final: 0.7294 (tpp80) REVERT: B 245 SER cc_start: 0.8474 (p) cc_final: 0.8130 (m) REVERT: B 298 ASP cc_start: 0.7656 (t70) cc_final: 0.7183 (t70) outliers start: 33 outliers final: 33 residues processed: 170 average time/residue: 0.2373 time to fit residues: 50.9307 Evaluate side-chains 190 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 224 THR Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 279 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 74 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7190 Z= 0.233 Angle : 0.481 5.811 9752 Z= 0.261 Chirality : 0.042 0.135 1118 Planarity : 0.003 0.044 1239 Dihedral : 3.770 14.536 999 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.50 % Allowed : 19.05 % Favored : 76.46 % 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: 1.24 (0.29), residues: 881 helix: 2.22 (0.27), residues: 378 sheet: 0.69 (0.43), residues: 160 loop : -0.72 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS G 44 PHE 0.027 0.002 PHE A 215 TYR 0.010 0.001 TYR B 289 ARG 0.003 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 169 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 ASP cc_start: 0.8150 (t0) cc_final: 0.7948 (t70) REVERT: A 339 ARG cc_start: 0.7245 (mpp80) cc_final: 0.6930 (mpp80) REVERT: B 190 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7784 (pp) REVERT: B 245 SER cc_start: 0.8378 (p) cc_final: 0.8069 (m) REVERT: B 298 ASP cc_start: 0.7631 (t70) cc_final: 0.7254 (t70) outliers start: 34 outliers final: 31 residues processed: 181 average time/residue: 0.2535 time to fit residues: 56.8460 Evaluate side-chains 201 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 169 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 279 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.131169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.112581 restraints weight = 10432.693| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.40 r_work: 0.3312 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7190 Z= 0.239 Angle : 0.483 5.782 9752 Z= 0.261 Chirality : 0.042 0.126 1118 Planarity : 0.004 0.044 1239 Dihedral : 3.798 14.540 999 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.10 % Allowed : 19.71 % Favored : 76.19 % 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: 1.22 (0.29), residues: 881 helix: 2.21 (0.27), residues: 378 sheet: 0.65 (0.43), residues: 160 loop : -0.72 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.003 0.001 HIS G 44 PHE 0.027 0.002 PHE A 215 TYR 0.010 0.001 TYR A 322 ARG 0.002 0.000 ARG R 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2102.24 seconds wall clock time: 38 minutes 32.05 seconds (2312.05 seconds total)