Starting phenix.real_space_refine on Tue Sep 24 19:09:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmv_30411/09_2024/7cmv_30411_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmv_30411/09_2024/7cmv_30411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmv_30411/09_2024/7cmv_30411.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmv_30411/09_2024/7cmv_30411.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmv_30411/09_2024/7cmv_30411_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cmv_30411/09_2024/7cmv_30411_neut.cif" } resolution = 2.7 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= -0.000 sd= 0.009 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 67 5.16 5 C 5575 2.51 5 N 1489 2.21 5 O 1644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8775 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1813 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 2 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "C" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 447 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "R" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2128 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain breaks: 1 Chain: "R" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'G6O': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.37, per 1000 atoms: 0.61 Number of scatterers: 8775 At special positions: 0 Unit cell: (104.442, 129.792, 114.582, 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 67 16.00 O 1644 8.00 N 1489 7.00 C 5575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 103 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS R 355 " - pdb=" SG CYS R 358 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.1 seconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 41.0% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.816A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.265A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 4.118A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.068A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.832A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.623A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.795A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 352 removed outlier: 4.394A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.540A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.039A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'R' and resid 33 through 57 Processing helix chain 'R' and resid 62 through 82 removed outlier: 4.109A pdb=" N LEU R 67 " --> pdb=" O THR R 63 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL R 68 " --> pdb=" O THR R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 Processing helix chain 'R' and resid 99 through 134 Processing helix chain 'R' and resid 134 through 139 Processing helix chain 'R' and resid 140 through 142 No H-bonds generated for 'chain 'R' and resid 140 through 142' Processing helix chain 'R' and resid 143 through 170 removed outlier: 3.557A pdb=" N ARG R 149 " --> pdb=" O SER R 145 " (cutoff:3.500A) Proline residue: R 167 - end of helix removed outlier: 3.515A pdb=" N PHE R 170 " --> pdb=" O CYS R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 197 removed outlier: 3.917A pdb=" N ILE R 190 " --> pdb=" O PRO R 186 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TYR R 191 " --> pdb=" O ASP R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 223 Processing helix chain 'R' and resid 322 through 355 Proline residue: R 344 - end of helix Processing helix chain 'R' and resid 361 through 385 removed outlier: 3.691A pdb=" N ASN R 375 " --> pdb=" O LEU R 371 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER R 376 " --> pdb=" O GLY R 372 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA R 377 " --> pdb=" O TYR R 373 " (cutoff:3.500A) Proline residue: R 380 - end of helix Processing helix chain 'R' and resid 387 through 400 removed outlier: 3.818A pdb=" N CYS R 400 " --> pdb=" O LYS R 396 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.555A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.781A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.584A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.675A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.671A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.875A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.400A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.041A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.764A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.501A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.896A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN E 194 " --> pdb=" O TYR E 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.896A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1275 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: 2.62 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1470 1.32 - 1.44: 2418 1.44 - 1.57: 4969 1.57 - 1.69: 3 1.69 - 1.81: 95 Bond restraints: 8955 Sorted by residual: bond pdb=" C2 G6O R 500 " pdb=" C4 G6O R 500 " ideal model delta sigma weight residual 1.392 1.614 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C1 G6O R 500 " pdb=" C3 G6O R 500 " ideal model delta sigma weight residual 1.392 1.593 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C5 G6O R 500 " pdb=" C6 G6O R 500 " ideal model delta sigma weight residual 1.393 1.200 0.193 2.00e-02 2.50e+03 9.36e+01 bond pdb=" C10 G6O R 500 " pdb=" O2 G6O R 500 " ideal model delta sigma weight residual 1.426 1.259 0.167 2.00e-02 2.50e+03 6.98e+01 bond pdb=" C2 G6O R 500 " pdb=" O1 G6O R 500 " ideal model delta sigma weight residual 1.357 1.231 0.126 2.00e-02 2.50e+03 3.98e+01 ... (remaining 8950 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 12106 3.27 - 6.54: 29 6.54 - 9.82: 2 9.82 - 13.09: 1 13.09 - 16.36: 1 Bond angle restraints: 12139 Sorted by residual: angle pdb=" C10 G6O R 500 " pdb=" O2 G6O R 500 " pdb=" C7 G6O R 500 " ideal model delta sigma weight residual 113.23 129.59 -16.36 3.00e+00 1.11e-01 2.97e+01 angle pdb=" C2 G6O R 500 " pdb=" O1 G6O R 500 " pdb=" C8 G6O R 500 " ideal model delta sigma weight residual 117.80 130.12 -12.32 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C4 G6O R 500 " pdb=" C2 G6O R 500 " pdb=" O1 G6O R 500 " ideal model delta sigma weight residual 117.00 126.76 -9.76 3.00e+00 1.11e-01 1.06e+01 angle pdb=" N HIS R 349 " pdb=" CA HIS R 349 " pdb=" C HIS R 349 " ideal model delta sigma weight residual 111.07 107.80 3.27 1.07e+00 8.73e-01 9.33e+00 angle pdb=" C THR R 348 " pdb=" N HIS R 349 " pdb=" CA HIS R 349 " ideal model delta sigma weight residual 120.44 124.03 -3.59 1.30e+00 5.92e-01 7.64e+00 ... (remaining 12134 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4967 17.93 - 35.86: 300 35.86 - 53.79: 39 53.79 - 71.72: 15 71.72 - 89.64: 10 Dihedral angle restraints: 5331 sinusoidal: 2071 harmonic: 3260 Sorted by residual: dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 61.37 31.63 1 1.00e+01 1.00e-02 1.43e+01 dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual 180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB GLU B 10 " pdb=" CG GLU B 10 " pdb=" CD GLU B 10 " pdb=" OE1 GLU B 10 " ideal model delta sinusoidal sigma weight residual 0.00 89.64 -89.64 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 869 0.027 - 0.053: 327 0.053 - 0.080: 99 0.080 - 0.107: 57 0.107 - 0.134: 41 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA VAL E 2 " pdb=" N VAL E 2 " pdb=" C VAL E 2 " pdb=" CB VAL E 2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE E 216 " pdb=" N ILE E 216 " pdb=" C ILE E 216 " pdb=" CB ILE E 216 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 1390 not shown) Planarity restraints: 1528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 74 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.01e+00 pdb=" N PRO E 75 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS R 349 " 0.007 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C HIS R 349 " -0.027 2.00e-02 2.50e+03 pdb=" O HIS R 349 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL R 350 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 13 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.09e+00 pdb=" C ARG C 13 " -0.025 2.00e-02 2.50e+03 pdb=" O ARG C 13 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS C 14 " 0.008 2.00e-02 2.50e+03 ... (remaining 1525 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 99 2.61 - 3.18: 7597 3.18 - 3.75: 13212 3.75 - 4.33: 18737 4.33 - 4.90: 32082 Nonbonded interactions: 71727 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.032 3.040 nonbonded pdb=" OG1 THR E 150 " pdb=" OE1 GLU E 153 " model vdw 2.091 3.040 nonbonded pdb=" O PHE E 29 " pdb=" NH2 ARG E 72 " model vdw 2.161 3.120 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.162 3.120 nonbonded pdb=" OD1 ASP A 315 " pdb=" N THR A 316 " model vdw 2.207 3.120 ... (remaining 71722 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.910 Find NCS groups from input model: 0.080 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:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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 : 0.005 0.222 8955 Z= 0.395 Angle : 0.487 16.359 12139 Z= 0.260 Chirality : 0.039 0.134 1393 Planarity : 0.002 0.056 1528 Dihedral : 12.439 89.644 3218 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 2.95 (0.26), residues: 1105 helix: 3.91 (0.25), residues: 374 sheet: 1.44 (0.31), residues: 269 loop : 0.65 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 85 HIS 0.002 0.000 HIS A 188 PHE 0.009 0.001 PHE R 345 TYR 0.004 0.000 TYR R 212 ARG 0.007 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.100 Fit side-chains REVERT: B 19 ARG cc_start: 0.7451 (ttt-90) cc_final: 0.6718 (ttm110) REVERT: B 47 THR cc_start: 0.8744 (t) cc_final: 0.8494 (m) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 1.2004 time to fit residues: 226.2007 Evaluate side-chains 131 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 244 HIS B 62 HIS B 75 GLN B 175 GLN E 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8955 Z= 0.301 Angle : 0.631 10.266 12139 Z= 0.333 Chirality : 0.046 0.183 1393 Planarity : 0.004 0.050 1528 Dihedral : 4.307 23.860 1239 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.22 % Allowed : 8.21 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 2.25 (0.25), residues: 1105 helix: 3.12 (0.25), residues: 392 sheet: 1.12 (0.30), residues: 278 loop : 0.24 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.008 0.002 HIS R 349 PHE 0.017 0.002 PHE R 345 TYR 0.014 0.001 TYR R 383 ARG 0.009 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 0.982 Fit side-chains REVERT: A 26 ASP cc_start: 0.7928 (m-30) cc_final: 0.7692 (m-30) REVERT: B 19 ARG cc_start: 0.7533 (ttt-90) cc_final: 0.6767 (ttm110) REVERT: B 22 ARG cc_start: 0.6934 (OUTLIER) cc_final: 0.6021 (mtt180) REVERT: B 258 ASP cc_start: 0.8186 (t0) cc_final: 0.7109 (t0) REVERT: E 113 GLN cc_start: 0.7950 (mm110) cc_final: 0.7663 (mm110) REVERT: R 58 ARG cc_start: 0.6977 (tmt-80) cc_final: 0.5493 (mmt180) REVERT: R 212 TYR cc_start: 0.7247 (t80) cc_final: 0.6994 (t80) outliers start: 31 outliers final: 13 residues processed: 161 average time/residue: 1.1755 time to fit residues: 201.9954 Evaluate side-chains 141 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8955 Z= 0.197 Angle : 0.532 8.602 12139 Z= 0.282 Chirality : 0.042 0.169 1393 Planarity : 0.004 0.045 1528 Dihedral : 4.135 23.832 1239 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.70 % Allowed : 11.12 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 2.06 (0.25), residues: 1105 helix: 3.19 (0.25), residues: 390 sheet: 0.95 (0.31), residues: 271 loop : -0.01 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS R 349 PHE 0.014 0.001 PHE R 345 TYR 0.009 0.001 TYR R 383 ARG 0.012 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 0.991 Fit side-chains REVERT: A 318 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7096 (tt0) REVERT: B 19 ARG cc_start: 0.7538 (ttt-90) cc_final: 0.6769 (ttm110) REVERT: B 258 ASP cc_start: 0.8304 (t0) cc_final: 0.7970 (t0) REVERT: B 303 ASP cc_start: 0.7774 (m-30) cc_final: 0.7541 (m-30) REVERT: B 322 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8179 (m-30) REVERT: E 113 GLN cc_start: 0.7954 (mm110) cc_final: 0.7697 (mm110) REVERT: R 58 ARG cc_start: 0.6982 (tmt-80) cc_final: 0.5590 (mmt180) REVERT: R 219 ARG cc_start: 0.5906 (tpm170) cc_final: 0.5627 (tpm170) outliers start: 26 outliers final: 12 residues processed: 146 average time/residue: 1.3934 time to fit residues: 215.6820 Evaluate side-chains 136 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 67 optimal weight: 0.0060 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 75 GLN B 175 GLN E 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8955 Z= 0.133 Angle : 0.478 7.352 12139 Z= 0.255 Chirality : 0.041 0.147 1393 Planarity : 0.003 0.047 1528 Dihedral : 3.875 21.656 1239 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.60 % Allowed : 13.10 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 2.15 (0.25), residues: 1105 helix: 3.36 (0.25), residues: 388 sheet: 1.07 (0.31), residues: 263 loop : -0.09 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.003 0.001 HIS R 349 PHE 0.012 0.001 PHE R 345 TYR 0.007 0.001 TYR E 60 ARG 0.012 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 1.016 Fit side-chains REVERT: A 273 LEU cc_start: 0.7814 (tt) cc_final: 0.7314 (mp) REVERT: B 19 ARG cc_start: 0.7528 (ttt-90) cc_final: 0.6699 (ttm110) REVERT: B 260 GLU cc_start: 0.7848 (tt0) cc_final: 0.7433 (tt0) REVERT: B 303 ASP cc_start: 0.7784 (m-30) cc_final: 0.7549 (m-30) REVERT: E 18 ARG cc_start: 0.8273 (tpp-160) cc_final: 0.7988 (tpp-160) REVERT: E 113 GLN cc_start: 0.7889 (mm110) cc_final: 0.7611 (mm110) REVERT: R 58 ARG cc_start: 0.6988 (tmt-80) cc_final: 0.5575 (mmt180) outliers start: 25 outliers final: 9 residues processed: 156 average time/residue: 0.9656 time to fit residues: 160.8394 Evaluate side-chains 145 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 8955 Z= 0.411 Angle : 0.665 10.283 12139 Z= 0.348 Chirality : 0.047 0.220 1393 Planarity : 0.005 0.045 1528 Dihedral : 4.673 27.911 1239 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.85 % Allowed : 13.62 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.56 (0.25), residues: 1105 helix: 2.82 (0.25), residues: 384 sheet: 0.71 (0.31), residues: 279 loop : -0.35 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.007 0.002 HIS R 349 PHE 0.019 0.002 PHE R 345 TYR 0.014 0.002 TYR E 59 ARG 0.012 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 128 time to evaluate : 0.950 Fit side-chains REVERT: A 9 ASP cc_start: 0.7305 (m-30) cc_final: 0.7084 (m-30) REVERT: B 19 ARG cc_start: 0.7385 (ttt-90) cc_final: 0.6687 (ttp80) REVERT: B 260 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: B 303 ASP cc_start: 0.7823 (m-30) cc_final: 0.7580 (m-30) REVERT: B 322 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8283 (m-30) REVERT: E 43 LYS cc_start: 0.8247 (mppt) cc_final: 0.7885 (mppt) REVERT: E 113 GLN cc_start: 0.8030 (mm110) cc_final: 0.7728 (mm110) REVERT: R 58 ARG cc_start: 0.7165 (tmt-80) cc_final: 0.5729 (mmt180) REVERT: R 139 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.5971 (tt0) REVERT: R 212 TYR cc_start: 0.7406 (t80) cc_final: 0.7203 (t80) outliers start: 37 outliers final: 16 residues processed: 155 average time/residue: 1.0966 time to fit residues: 181.3698 Evaluate side-chains 143 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 139 GLN Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 364 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 0.0170 chunk 102 optimal weight: 6.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 186 GLN E 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8955 Z= 0.139 Angle : 0.495 7.918 12139 Z= 0.262 Chirality : 0.041 0.151 1393 Planarity : 0.003 0.044 1528 Dihedral : 4.026 22.985 1239 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.60 % Allowed : 15.18 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.86 (0.25), residues: 1105 helix: 3.19 (0.26), residues: 386 sheet: 0.86 (0.31), residues: 271 loop : -0.29 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.003 0.001 HIS R 349 PHE 0.014 0.001 PHE R 345 TYR 0.007 0.001 TYR E 60 ARG 0.011 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 1.196 Fit side-chains REVERT: B 19 ARG cc_start: 0.7376 (ttt-90) cc_final: 0.6585 (ttp80) REVERT: B 258 ASP cc_start: 0.8363 (t0) cc_final: 0.8135 (t0) REVERT: B 262 MET cc_start: 0.8149 (ttm) cc_final: 0.7844 (ttm) REVERT: B 303 ASP cc_start: 0.7764 (m-30) cc_final: 0.7515 (m-30) REVERT: E 43 LYS cc_start: 0.8210 (mppt) cc_final: 0.7901 (mppt) REVERT: E 113 GLN cc_start: 0.7919 (mm110) cc_final: 0.7660 (mm110) REVERT: R 58 ARG cc_start: 0.7068 (tmt-80) cc_final: 0.5635 (mmt180) outliers start: 25 outliers final: 10 residues processed: 146 average time/residue: 1.2299 time to fit residues: 191.7021 Evaluate side-chains 139 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 59 optimal weight: 0.2980 chunk 106 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8955 Z= 0.228 Angle : 0.553 8.861 12139 Z= 0.289 Chirality : 0.043 0.156 1393 Planarity : 0.004 0.063 1528 Dihedral : 4.236 24.318 1239 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.91 % Allowed : 15.38 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.74 (0.25), residues: 1105 helix: 3.02 (0.26), residues: 390 sheet: 0.91 (0.31), residues: 266 loop : -0.40 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS R 349 PHE 0.016 0.001 PHE R 345 TYR 0.012 0.001 TYR E 59 ARG 0.016 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 1.063 Fit side-chains REVERT: A 9 ASP cc_start: 0.7284 (m-30) cc_final: 0.7035 (m-30) REVERT: B 19 ARG cc_start: 0.7379 (ttt-90) cc_final: 0.6687 (ttp80) REVERT: B 118 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7554 (p0) REVERT: B 258 ASP cc_start: 0.8421 (t0) cc_final: 0.8158 (t0) REVERT: B 262 MET cc_start: 0.8134 (ttm) cc_final: 0.7893 (ttm) REVERT: B 303 ASP cc_start: 0.7797 (m-30) cc_final: 0.7550 (m-30) REVERT: E 43 LYS cc_start: 0.8228 (mppt) cc_final: 0.7870 (mppt) REVERT: E 113 GLN cc_start: 0.7953 (mm110) cc_final: 0.7697 (mm110) REVERT: R 58 ARG cc_start: 0.7008 (tmt-80) cc_final: 0.5567 (mmt180) REVERT: R 139 GLN cc_start: 0.6955 (OUTLIER) cc_final: 0.6082 (tt0) outliers start: 28 outliers final: 16 residues processed: 149 average time/residue: 1.1694 time to fit residues: 186.2496 Evaluate side-chains 147 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 139 GLN Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 96 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 13 GLN E 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8955 Z= 0.192 Angle : 0.532 8.231 12139 Z= 0.279 Chirality : 0.042 0.157 1393 Planarity : 0.004 0.071 1528 Dihedral : 4.158 23.675 1239 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.70 % Allowed : 16.01 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.74 (0.25), residues: 1105 helix: 3.05 (0.26), residues: 391 sheet: 0.84 (0.32), residues: 266 loop : -0.38 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS R 349 PHE 0.014 0.001 PHE R 345 TYR 0.008 0.001 TYR R 383 ARG 0.018 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 1.053 Fit side-chains REVERT: A 9 ASP cc_start: 0.7264 (m-30) cc_final: 0.7020 (m-30) REVERT: A 229 ASP cc_start: 0.7283 (m-30) cc_final: 0.7012 (m-30) REVERT: B 19 ARG cc_start: 0.7352 (ttt-90) cc_final: 0.6689 (ttp80) REVERT: B 118 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7517 (p0) REVERT: B 258 ASP cc_start: 0.8383 (t0) cc_final: 0.8128 (t0) REVERT: B 262 MET cc_start: 0.8040 (ttm) cc_final: 0.7830 (ttm) REVERT: B 267 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7539 (t0) REVERT: B 303 ASP cc_start: 0.7798 (m-30) cc_final: 0.7553 (m-30) REVERT: E 43 LYS cc_start: 0.8279 (mppt) cc_final: 0.8063 (mppt) REVERT: E 113 GLN cc_start: 0.7923 (mm110) cc_final: 0.7666 (mm110) REVERT: R 139 GLN cc_start: 0.6927 (OUTLIER) cc_final: 0.6025 (tt0) outliers start: 26 outliers final: 14 residues processed: 141 average time/residue: 1.1902 time to fit residues: 179.0255 Evaluate side-chains 141 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 139 GLN Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 13 GLN E 194 ASN ** R 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8955 Z= 0.148 Angle : 0.506 8.136 12139 Z= 0.266 Chirality : 0.041 0.160 1393 Planarity : 0.004 0.077 1528 Dihedral : 3.983 21.515 1239 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.39 % Allowed : 16.01 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.84 (0.25), residues: 1105 helix: 3.20 (0.26), residues: 388 sheet: 0.93 (0.32), residues: 262 loop : -0.39 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS R 349 PHE 0.013 0.001 PHE R 345 TYR 0.007 0.001 TYR E 95 ARG 0.018 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 1.077 Fit side-chains REVERT: B 19 ARG cc_start: 0.7385 (ttt-90) cc_final: 0.6623 (ttp80) REVERT: B 118 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7458 (p0) REVERT: B 258 ASP cc_start: 0.8315 (t0) cc_final: 0.8082 (t0) REVERT: B 303 ASP cc_start: 0.7819 (m-30) cc_final: 0.7567 (m-30) REVERT: E 43 LYS cc_start: 0.8289 (mppt) cc_final: 0.8060 (mppt) REVERT: E 113 GLN cc_start: 0.7886 (mm110) cc_final: 0.7640 (mm110) REVERT: R 330 MET cc_start: 0.7747 (tpp) cc_final: 0.7428 (mmt) outliers start: 23 outliers final: 15 residues processed: 153 average time/residue: 1.1624 time to fit residues: 190.0061 Evaluate side-chains 142 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 87 optimal weight: 0.0670 chunk 9 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** R 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8955 Z= 0.138 Angle : 0.499 7.686 12139 Z= 0.262 Chirality : 0.041 0.160 1393 Planarity : 0.004 0.080 1528 Dihedral : 3.906 20.430 1239 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.66 % Allowed : 17.05 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.87 (0.25), residues: 1105 helix: 3.22 (0.25), residues: 388 sheet: 0.97 (0.32), residues: 262 loop : -0.38 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 244 PHE 0.012 0.001 PHE A 189 TYR 0.006 0.001 TYR E 95 ARG 0.019 0.000 ARG A 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.017 Fit side-chains REVERT: A 273 LEU cc_start: 0.7777 (tt) cc_final: 0.7381 (mp) REVERT: B 19 ARG cc_start: 0.7371 (ttt-90) cc_final: 0.6621 (ttp80) REVERT: B 118 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7439 (p0) REVERT: B 258 ASP cc_start: 0.8283 (t0) cc_final: 0.8067 (t0) REVERT: B 303 ASP cc_start: 0.7780 (m-30) cc_final: 0.7566 (m-30) REVERT: E 43 LYS cc_start: 0.8272 (mppt) cc_final: 0.8053 (mppt) REVERT: E 113 GLN cc_start: 0.7835 (mm110) cc_final: 0.7575 (mm110) outliers start: 16 outliers final: 14 residues processed: 140 average time/residue: 1.1906 time to fit residues: 177.8555 Evaluate side-chains 145 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 63 optimal weight: 0.2980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** R 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.159998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.119364 restraints weight = 9308.466| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.46 r_work: 0.3019 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8955 Z= 0.217 Angle : 0.552 8.499 12139 Z= 0.289 Chirality : 0.042 0.161 1393 Planarity : 0.004 0.078 1528 Dihedral : 4.181 22.909 1239 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.39 % Allowed : 16.63 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.71 (0.25), residues: 1105 helix: 2.99 (0.26), residues: 392 sheet: 0.90 (0.32), residues: 266 loop : -0.43 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS C 44 PHE 0.014 0.001 PHE R 345 TYR 0.008 0.001 TYR R 383 ARG 0.018 0.000 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3762.77 seconds wall clock time: 69 minutes 30.50 seconds (4170.50 seconds total)