Starting phenix.real_space_refine on Wed Feb 14 07:44:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvr_22511/02_2024/7jvr_22511_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvr_22511/02_2024/7jvr_22511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvr_22511/02_2024/7jvr_22511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvr_22511/02_2024/7jvr_22511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvr_22511/02_2024/7jvr_22511_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jvr_22511/02_2024/7jvr_22511_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 64 5.16 5 C 5648 2.51 5 N 1496 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 61": "NH1" <-> "NH2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8872 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2164 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 9, 'TRANS': 259} Chain breaks: 1 Chain: "A" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1807 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'08Y': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.14, per 1000 atoms: 0.58 Number of scatterers: 8872 At special positions: 0 Unit cell: (103.455, 123.31, 118.085, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 64 16.00 O 1663 8.00 N 1496 7.00 C 5648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS R 399 " - pdb=" SG CYS R 401 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.6 seconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 13 sheets defined 34.7% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'R' and resid 35 through 61 removed outlier: 3.718A pdb=" N LEU R 40 " --> pdb=" O TYR R 36 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU R 41 " --> pdb=" O TYR R 37 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU R 44 " --> pdb=" O LEU R 40 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE R 45 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA R 46 " --> pdb=" O THR R 42 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU R 54 " --> pdb=" O PHE R 50 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER R 60 " --> pdb=" O CYS R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 86 removed outlier: 4.001A pdb=" N LEU R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 97 Processing helix chain 'R' and resid 104 through 137 Processing helix chain 'R' and resid 139 through 143 Processing helix chain 'R' and resid 145 through 172 Proline residue: R 169 - end of helix removed outlier: 3.705A pdb=" N PHE R 172 " --> pdb=" O CYS R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 197 removed outlier: 3.670A pdb=" N TYR R 192 " --> pdb=" O ALA R 188 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL R 196 " --> pdb=" O TYR R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 224 Processing helix chain 'R' and resid 366 through 385 Processing helix chain 'R' and resid 387 through 399 removed outlier: 3.642A pdb=" N HIS R 393 " --> pdb=" O PHE R 389 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE R 394 " --> pdb=" O PHE R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 426 removed outlier: 3.716A pdb=" N ASN R 418 " --> pdb=" O LEU R 414 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER R 419 " --> pdb=" O GLY R 415 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA R 420 " --> pdb=" O TYR R 416 " (cutoff:3.500A) Proline residue: R 423 - end of helix Processing helix chain 'R' and resid 431 through 440 removed outlier: 3.949A pdb=" N LYS R 435 " --> pdb=" O ILE R 431 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA R 436 " --> pdb=" O GLU R 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 32 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.638A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) 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 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.785A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.840A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 351 removed outlier: 3.540A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.749A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 7.050A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 4.510A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.004A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.619A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 202 removed outlier: 3.557A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 240 through 244 removed outlier: 3.693A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.463A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 45 through 52 removed outlier: 6.625A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 115 through 117 removed outlier: 6.129A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.743A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.608A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 226 through 231 removed outlier: 3.652A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1128 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: 2.75 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1441 1.32 - 1.45: 2608 1.45 - 1.59: 4912 1.59 - 1.73: 0 1.73 - 1.87: 94 Bond restraints: 9055 Sorted by residual: bond pdb=" C15 08Y R 500 " pdb=" N3 08Y R 500 " ideal model delta sigma weight residual 1.359 1.493 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C25 08Y R 500 " pdb=" C26 08Y R 500 " ideal model delta sigma weight residual 1.420 1.318 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C26 08Y R 500 " pdb=" C28 08Y R 500 " ideal model delta sigma weight residual 1.407 1.325 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C6 08Y R 500 " pdb=" C7 08Y R 500 " ideal model delta sigma weight residual 1.533 1.472 0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" C LEU R 387 " pdb=" N PRO R 388 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.38e-02 5.25e+03 5.84e+00 ... (remaining 9050 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.15: 180 106.15 - 113.13: 4925 113.13 - 120.11: 3068 120.11 - 127.10: 4012 127.10 - 134.08: 98 Bond angle restraints: 12283 Sorted by residual: angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 130.95 -9.41 1.91e+00 2.74e-01 2.43e+01 angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 123.47 130.29 -6.82 1.53e+00 4.27e-01 1.99e+01 angle pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " pdb=" CG ASN B 119 " ideal model delta sigma weight residual 112.60 117.04 -4.44 1.00e+00 1.00e+00 1.97e+01 angle pdb=" C ASP A 237 " pdb=" N GLU A 238 " pdb=" CA GLU A 238 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 123.05 128.04 -4.99 1.57e+00 4.06e-01 1.01e+01 ... (remaining 12278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.08: 5179 14.08 - 28.17: 205 28.17 - 42.25: 52 42.25 - 56.34: 13 56.34 - 70.42: 5 Dihedral angle restraints: 5454 sinusoidal: 2172 harmonic: 3282 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 161.30 -68.30 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 156.61 23.39 0 5.00e+00 4.00e-02 2.19e+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 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 5451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1148 0.061 - 0.121: 211 0.121 - 0.182: 36 0.182 - 0.242: 10 0.242 - 0.303: 2 Chirality restraints: 1407 Sorted by residual: chirality pdb=" CB ILE E 70 " pdb=" CA ILE E 70 " pdb=" CG1 ILE E 70 " pdb=" CG2 ILE E 70 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1404 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C15 08Y R 500 " -0.018 2.00e-02 2.50e+03 3.06e-02 1.17e+01 pdb=" C16 08Y R 500 " 0.030 2.00e-02 2.50e+03 pdb=" C5 08Y R 500 " 0.037 2.00e-02 2.50e+03 pdb=" N3 08Y R 500 " -0.045 2.00e-02 2.50e+03 pdb=" O5 08Y R 500 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 08Y R 500 " 0.027 2.00e-02 2.50e+03 3.02e-02 1.14e+01 pdb=" C17 08Y R 500 " -0.018 2.00e-02 2.50e+03 pdb=" C21 08Y R 500 " 0.031 2.00e-02 2.50e+03 pdb=" C22 08Y R 500 " -0.050 2.00e-02 2.50e+03 pdb=" C24 08Y R 500 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 403 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO R 404 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO R 404 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 404 " 0.033 5.00e-02 4.00e+02 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1139 2.77 - 3.30: 8502 3.30 - 3.83: 14703 3.83 - 4.37: 17177 4.37 - 4.90: 30172 Nonbonded interactions: 71693 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.235 2.440 nonbonded pdb=" OG SER A 263 " pdb=" O GLU A 318 " model vdw 2.332 2.440 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.347 2.440 nonbonded pdb=" OG1 THR R 69 " pdb=" OH TYR R 142 " model vdw 2.356 2.440 nonbonded pdb=" O CYS B 218 " pdb=" NE2 GLN C 18 " model vdw 2.364 2.520 ... (remaining 71688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 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: 2.150 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.440 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 0.134 9055 Z= 0.308 Angle : 0.853 10.326 12283 Z= 0.472 Chirality : 0.052 0.303 1407 Planarity : 0.006 0.060 1543 Dihedral : 8.952 70.421 3319 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.22), residues: 1110 helix: 1.15 (0.22), residues: 384 sheet: -0.83 (0.32), residues: 251 loop : -1.86 (0.23), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP E 111 HIS 0.009 0.002 HIS B 62 PHE 0.024 0.003 PHE B 151 TYR 0.026 0.002 TYR R 408 ARG 0.015 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 57 MET cc_start: 0.5462 (mtp) cc_final: 0.5188 (mtp) REVERT: R 158 ILE cc_start: 0.8055 (mt) cc_final: 0.7781 (tt) REVERT: A 189 PHE cc_start: 0.7927 (p90) cc_final: 0.7617 (p90) REVERT: A 201 VAL cc_start: 0.7929 (m) cc_final: 0.7701 (p) REVERT: A 209 LYS cc_start: 0.7902 (ttpm) cc_final: 0.7700 (ttpm) REVERT: A 225 VAL cc_start: 0.8115 (t) cc_final: 0.7883 (m) REVERT: A 259 PHE cc_start: 0.8279 (m-80) cc_final: 0.7907 (m-80) REVERT: A 273 LEU cc_start: 0.8322 (tp) cc_final: 0.8111 (tt) REVERT: A 345 LYS cc_start: 0.7957 (mttm) cc_final: 0.7752 (mptp) REVERT: B 47 THR cc_start: 0.8039 (t) cc_final: 0.6898 (p) REVERT: B 50 THR cc_start: 0.7875 (m) cc_final: 0.7638 (t) REVERT: B 110 ASN cc_start: 0.7360 (m-40) cc_final: 0.7072 (m110) REVERT: B 125 ASN cc_start: 0.8274 (t0) cc_final: 0.8008 (t0) REVERT: B 186 ASP cc_start: 0.7662 (m-30) cc_final: 0.7254 (m-30) REVERT: B 290 ASP cc_start: 0.7651 (p0) cc_final: 0.7447 (p0) REVERT: B 298 ASP cc_start: 0.7505 (t0) cc_final: 0.7227 (t70) REVERT: E 52 SER cc_start: 0.8142 (m) cc_final: 0.7938 (p) REVERT: E 116 THR cc_start: 0.8494 (m) cc_final: 0.8277 (p) REVERT: E 220 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6620 (mt-10) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.8028 time to fit residues: 251.1523 Evaluate side-chains 244 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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: 0.9990 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 0.0030 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 52 ASN R 106 HIS R 398 HIS A 188 HIS A 244 HIS A 322 HIS B 237 ASN B 239 ASN B 259 GLN B 340 ASN C 18 GLN C 44 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9055 Z= 0.212 Angle : 0.591 8.277 12283 Z= 0.303 Chirality : 0.043 0.200 1407 Planarity : 0.004 0.055 1543 Dihedral : 5.479 52.569 1300 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.29 % Allowed : 12.02 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.24), residues: 1110 helix: 2.15 (0.24), residues: 388 sheet: -0.74 (0.31), residues: 263 loop : -1.44 (0.25), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.017 0.002 PHE R 110 TYR 0.015 0.002 TYR R 408 ARG 0.006 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 255 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 57 MET cc_start: 0.5719 (mtp) cc_final: 0.5438 (mtp) REVERT: R 158 ILE cc_start: 0.7962 (mt) cc_final: 0.7735 (tt) REVERT: R 411 PHE cc_start: 0.7574 (m-10) cc_final: 0.7321 (m-10) REVERT: A 29 LYS cc_start: 0.8399 (mtpm) cc_final: 0.8168 (ttmm) REVERT: A 201 VAL cc_start: 0.8117 (m) cc_final: 0.7914 (p) REVERT: A 209 LYS cc_start: 0.7934 (ttpm) cc_final: 0.7664 (ttpm) REVERT: A 247 MET cc_start: 0.8359 (mtt) cc_final: 0.8147 (mtm) REVERT: A 318 GLU cc_start: 0.7298 (mt-10) cc_final: 0.7059 (mt-10) REVERT: B 50 THR cc_start: 0.8116 (m) cc_final: 0.7901 (t) REVERT: B 76 ASP cc_start: 0.7456 (p0) cc_final: 0.7207 (p0) REVERT: B 96 ARG cc_start: 0.7488 (mtt-85) cc_final: 0.7245 (mtt180) REVERT: B 125 ASN cc_start: 0.8361 (t0) cc_final: 0.8111 (t0) REVERT: B 161 SER cc_start: 0.7596 (m) cc_final: 0.7200 (t) REVERT: B 186 ASP cc_start: 0.7768 (m-30) cc_final: 0.7519 (p0) REVERT: B 264 TYR cc_start: 0.8465 (m-10) cc_final: 0.8249 (m-80) REVERT: E 98 ARG cc_start: 0.8040 (ppt-90) cc_final: 0.7732 (ptm160) outliers start: 32 outliers final: 11 residues processed: 270 average time/residue: 0.8752 time to fit residues: 256.9331 Evaluate side-chains 256 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 245 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 424 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 0.0670 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 34 optimal weight: 0.0010 chunk 80 optimal weight: 1.9990 overall best weight: 0.5124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN C 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9055 Z= 0.187 Angle : 0.559 7.524 12283 Z= 0.283 Chirality : 0.042 0.194 1407 Planarity : 0.004 0.049 1543 Dihedral : 5.314 49.041 1300 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.32 % Allowed : 15.01 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.24), residues: 1110 helix: 2.28 (0.25), residues: 384 sheet: -0.62 (0.31), residues: 266 loop : -1.12 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.014 0.002 PHE R 110 TYR 0.021 0.002 TYR R 142 ARG 0.007 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 246 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 48 ILE cc_start: 0.7920 (mt) cc_final: 0.7692 (mp) REVERT: R 57 MET cc_start: 0.5627 (mtp) cc_final: 0.5354 (mtp) REVERT: R 155 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6471 (mpp) REVERT: R 158 ILE cc_start: 0.7932 (mt) cc_final: 0.7697 (tt) REVERT: R 379 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6662 (tp) REVERT: R 411 PHE cc_start: 0.7570 (m-10) cc_final: 0.7305 (m-10) REVERT: A 29 LYS cc_start: 0.8389 (mtpm) cc_final: 0.8173 (ttmm) REVERT: A 201 VAL cc_start: 0.8155 (m) cc_final: 0.7859 (p) REVERT: A 209 LYS cc_start: 0.7958 (ttpm) cc_final: 0.7666 (ttpm) REVERT: A 318 GLU cc_start: 0.7269 (mt-10) cc_final: 0.7042 (mt-10) REVERT: B 76 ASP cc_start: 0.7450 (p0) cc_final: 0.7221 (p0) REVERT: B 96 ARG cc_start: 0.7549 (mtt-85) cc_final: 0.7308 (mtt180) REVERT: B 101 MET cc_start: 0.8583 (mtt) cc_final: 0.8297 (mtm) REVERT: B 125 ASN cc_start: 0.8340 (t0) cc_final: 0.8050 (t0) REVERT: B 217 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7506 (pmt) REVERT: E 98 ARG cc_start: 0.8100 (ppt-90) cc_final: 0.7705 (ptm160) outliers start: 42 outliers final: 20 residues processed: 261 average time/residue: 0.9177 time to fit residues: 259.6348 Evaluate side-chains 246 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 223 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 0.1980 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 422 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN E 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9055 Z= 0.231 Angle : 0.574 8.072 12283 Z= 0.290 Chirality : 0.042 0.184 1407 Planarity : 0.004 0.039 1543 Dihedral : 5.180 45.310 1300 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.42 % Allowed : 17.06 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1110 helix: 2.19 (0.25), residues: 395 sheet: -0.61 (0.31), residues: 273 loop : -0.93 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.019 0.002 PHE R 110 TYR 0.020 0.002 TYR R 142 ARG 0.007 0.001 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 250 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 48 ILE cc_start: 0.7929 (mt) cc_final: 0.7682 (mp) REVERT: R 57 MET cc_start: 0.5761 (mtp) cc_final: 0.5478 (mtp) REVERT: R 81 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7361 (mm) REVERT: R 117 MET cc_start: 0.6634 (mmt) cc_final: 0.6414 (mmm) REVERT: R 155 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6487 (mpp) REVERT: R 158 ILE cc_start: 0.7955 (mt) cc_final: 0.7709 (tt) REVERT: R 198 PHE cc_start: 0.8290 (t80) cc_final: 0.8037 (t80) REVERT: R 372 THR cc_start: 0.7285 (m) cc_final: 0.7028 (m) REVERT: R 411 PHE cc_start: 0.7561 (m-10) cc_final: 0.7267 (m-10) REVERT: R 418 ASN cc_start: 0.7032 (t0) cc_final: 0.6791 (t0) REVERT: A 201 VAL cc_start: 0.8160 (m) cc_final: 0.7799 (p) REVERT: A 209 LYS cc_start: 0.7953 (ttpm) cc_final: 0.7668 (ttpm) REVERT: B 19 ARG cc_start: 0.7841 (ttp80) cc_final: 0.7278 (ttp80) REVERT: B 76 ASP cc_start: 0.7617 (p0) cc_final: 0.7373 (p0) REVERT: B 96 ARG cc_start: 0.7616 (mtt-85) cc_final: 0.7357 (mtt180) REVERT: B 125 ASN cc_start: 0.8376 (t0) cc_final: 0.8050 (t0) REVERT: B 217 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7459 (pmt) REVERT: E 91 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.7977 (p) REVERT: E 98 ARG cc_start: 0.8167 (ppt-90) cc_final: 0.7966 (ptt-90) REVERT: E 140 MET cc_start: 0.8193 (tpt) cc_final: 0.7903 (mmt) outliers start: 43 outliers final: 21 residues processed: 268 average time/residue: 0.9179 time to fit residues: 266.6117 Evaluate side-chains 252 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 227 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN B 62 HIS B 88 ASN B 230 ASN B 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9055 Z= 0.247 Angle : 0.571 8.590 12283 Z= 0.291 Chirality : 0.042 0.190 1407 Planarity : 0.004 0.081 1543 Dihedral : 5.018 41.419 1300 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 5.55 % Allowed : 17.27 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1110 helix: 2.24 (0.25), residues: 392 sheet: -0.60 (0.31), residues: 275 loop : -0.85 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS E 232 PHE 0.023 0.002 PHE R 110 TYR 0.021 0.002 TYR R 142 ARG 0.007 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 250 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: R 48 ILE cc_start: 0.7949 (mt) cc_final: 0.7697 (mp) REVERT: R 57 MET cc_start: 0.5713 (mtp) cc_final: 0.5442 (mtp) REVERT: R 81 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7367 (mm) REVERT: R 155 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6544 (mpp) REVERT: R 158 ILE cc_start: 0.7942 (mt) cc_final: 0.7629 (tt) REVERT: R 372 THR cc_start: 0.7289 (m) cc_final: 0.7038 (m) REVERT: R 411 PHE cc_start: 0.7543 (m-10) cc_final: 0.7287 (m-10) REVERT: A 201 VAL cc_start: 0.8067 (m) cc_final: 0.7705 (p) REVERT: A 209 LYS cc_start: 0.7958 (ttpm) cc_final: 0.7674 (ttpm) REVERT: A 316 THR cc_start: 0.8288 (p) cc_final: 0.8051 (p) REVERT: B 19 ARG cc_start: 0.7873 (ttp80) cc_final: 0.7516 (ttp80) REVERT: B 76 ASP cc_start: 0.7641 (p0) cc_final: 0.7301 (p0) REVERT: B 125 ASN cc_start: 0.8410 (t0) cc_final: 0.8084 (t0) REVERT: B 136 SER cc_start: 0.8303 (m) cc_final: 0.8089 (p) REVERT: B 170 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7949 (t0) REVERT: B 217 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7323 (pmt) REVERT: B 314 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7569 (ptt180) REVERT: E 91 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.8069 (p) REVERT: E 117 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7966 (tt) REVERT: E 140 MET cc_start: 0.8209 (tpt) cc_final: 0.7957 (mmt) REVERT: E 192 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7715 (ptp) outliers start: 54 outliers final: 30 residues processed: 273 average time/residue: 0.9340 time to fit residues: 276.4900 Evaluate side-chains 269 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 231 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 394 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 0.0040 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 88 ASN B 119 ASN B 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9055 Z= 0.231 Angle : 0.573 8.216 12283 Z= 0.291 Chirality : 0.042 0.181 1407 Planarity : 0.004 0.058 1543 Dihedral : 4.939 40.703 1300 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.34 % Allowed : 19.22 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.25), residues: 1110 helix: 2.22 (0.25), residues: 397 sheet: -0.54 (0.31), residues: 273 loop : -0.70 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.007 0.001 HIS A 188 PHE 0.023 0.002 PHE R 110 TYR 0.024 0.002 TYR E 50 ARG 0.007 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 236 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 48 ILE cc_start: 0.7948 (mt) cc_final: 0.7706 (mp) REVERT: R 57 MET cc_start: 0.5680 (mtp) cc_final: 0.5434 (mtp) REVERT: R 117 MET cc_start: 0.6527 (mmt) cc_final: 0.6229 (mmm) REVERT: R 140 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6584 (mmt) REVERT: R 155 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6544 (mpp) REVERT: R 158 ILE cc_start: 0.7993 (mt) cc_final: 0.7717 (tt) REVERT: R 372 THR cc_start: 0.7233 (m) cc_final: 0.6952 (m) REVERT: R 411 PHE cc_start: 0.7659 (m-10) cc_final: 0.7353 (m-10) REVERT: A 10 LYS cc_start: 0.8394 (ttmm) cc_final: 0.8138 (mtpp) REVERT: A 197 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7857 (mttp) REVERT: A 248 LYS cc_start: 0.8323 (tttt) cc_final: 0.7736 (mmmm) REVERT: A 308 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.6791 (mp0) REVERT: A 316 THR cc_start: 0.8332 (p) cc_final: 0.8090 (p) REVERT: B 19 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7634 (ttp80) REVERT: B 125 ASN cc_start: 0.8406 (t0) cc_final: 0.8045 (t0) REVERT: B 136 SER cc_start: 0.8278 (m) cc_final: 0.8056 (p) REVERT: B 217 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7301 (pmt) REVERT: B 258 ASP cc_start: 0.7558 (t0) cc_final: 0.6843 (t0) REVERT: E 91 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8110 (p) REVERT: E 140 MET cc_start: 0.8207 (tpt) cc_final: 0.7943 (tpp) outliers start: 52 outliers final: 29 residues processed: 256 average time/residue: 0.9087 time to fit residues: 252.6486 Evaluate side-chains 268 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 233 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 140 MET Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 383 ILE Chi-restraints excluded: chain R residue 394 ILE Chi-restraints excluded: chain R residue 427 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN C 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9055 Z= 0.303 Angle : 0.618 8.775 12283 Z= 0.311 Chirality : 0.044 0.216 1407 Planarity : 0.004 0.047 1543 Dihedral : 4.935 38.730 1300 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 5.55 % Allowed : 19.32 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1110 helix: 2.20 (0.25), residues: 398 sheet: -0.53 (0.30), residues: 277 loop : -0.64 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.005 0.001 HIS E 232 PHE 0.031 0.002 PHE R 198 TYR 0.028 0.002 TYR E 50 ARG 0.008 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 239 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 48 ILE cc_start: 0.7942 (mt) cc_final: 0.7690 (mp) REVERT: R 57 MET cc_start: 0.5749 (mtp) cc_final: 0.5516 (mtp) REVERT: R 82 LEU cc_start: 0.6944 (mp) cc_final: 0.6523 (mp) REVERT: R 117 MET cc_start: 0.6528 (mmt) cc_final: 0.6075 (mmm) REVERT: R 140 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6625 (mmt) REVERT: R 155 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.6547 (mpp) REVERT: R 158 ILE cc_start: 0.8087 (mt) cc_final: 0.7752 (tt) REVERT: R 372 THR cc_start: 0.7271 (m) cc_final: 0.7012 (m) REVERT: R 411 PHE cc_start: 0.7685 (m-10) cc_final: 0.7407 (m-10) REVERT: R 427 THR cc_start: 0.7833 (OUTLIER) cc_final: 0.7598 (m) REVERT: A 10 LYS cc_start: 0.8402 (ttmm) cc_final: 0.8147 (mtpm) REVERT: A 209 LYS cc_start: 0.7934 (ttpm) cc_final: 0.7685 (ttpm) REVERT: A 248 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7749 (mmmm) REVERT: A 308 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6719 (mp0) REVERT: A 316 THR cc_start: 0.8321 (p) cc_final: 0.8064 (p) REVERT: B 19 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7525 (ttp80) REVERT: B 93 ILE cc_start: 0.8213 (mp) cc_final: 0.7999 (mp) REVERT: B 125 ASN cc_start: 0.8433 (t0) cc_final: 0.8175 (t0) REVERT: B 136 SER cc_start: 0.8334 (m) cc_final: 0.8096 (p) REVERT: B 217 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7457 (pmt) REVERT: B 258 ASP cc_start: 0.7563 (t0) cc_final: 0.7022 (t0) REVERT: E 91 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8173 (p) REVERT: E 140 MET cc_start: 0.8348 (tpt) cc_final: 0.8081 (mmt) REVERT: E 230 MET cc_start: 0.7948 (ttp) cc_final: 0.7708 (ttm) outliers start: 54 outliers final: 32 residues processed: 260 average time/residue: 0.8169 time to fit residues: 232.6463 Evaluate side-chains 280 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 241 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 140 MET Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 186 ASN Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 383 ILE Chi-restraints excluded: chain R residue 394 ILE Chi-restraints excluded: chain R residue 427 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN B 176 GLN B 237 ASN B 239 ASN C 18 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9055 Z= 0.236 Angle : 0.601 8.390 12283 Z= 0.302 Chirality : 0.043 0.193 1407 Planarity : 0.003 0.040 1543 Dihedral : 4.866 39.029 1300 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.93 % Allowed : 20.35 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1110 helix: 2.31 (0.25), residues: 397 sheet: -0.55 (0.30), residues: 285 loop : -0.55 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.028 0.002 PHE R 110 TYR 0.033 0.002 TYR E 50 ARG 0.007 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 237 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 48 ILE cc_start: 0.7935 (mt) cc_final: 0.7660 (mp) REVERT: R 57 MET cc_start: 0.5745 (mtp) cc_final: 0.5532 (mtp) REVERT: R 81 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7293 (mm) REVERT: R 117 MET cc_start: 0.6457 (mmt) cc_final: 0.6090 (mmm) REVERT: R 155 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6547 (mpp) REVERT: R 158 ILE cc_start: 0.8085 (mt) cc_final: 0.7775 (tt) REVERT: R 372 THR cc_start: 0.7196 (m) cc_final: 0.6968 (m) REVERT: R 411 PHE cc_start: 0.7675 (m-10) cc_final: 0.7386 (m-10) REVERT: A 10 LYS cc_start: 0.8400 (ttmm) cc_final: 0.8140 (mtpm) REVERT: A 209 LYS cc_start: 0.7930 (ttpm) cc_final: 0.7665 (ttpm) REVERT: A 248 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7744 (mmmm) REVERT: A 308 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.6706 (mp0) REVERT: A 316 THR cc_start: 0.8315 (p) cc_final: 0.8065 (p) REVERT: B 55 LEU cc_start: 0.8349 (mt) cc_final: 0.8103 (mp) REVERT: B 125 ASN cc_start: 0.8415 (t0) cc_final: 0.7986 (t0) REVERT: B 156 GLN cc_start: 0.8284 (mt0) cc_final: 0.8018 (mt0) REVERT: B 217 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7416 (pmt) REVERT: B 237 ASN cc_start: 0.7299 (t0) cc_final: 0.7055 (t0) REVERT: B 258 ASP cc_start: 0.7693 (t0) cc_final: 0.7152 (t0) REVERT: B 297 TRP cc_start: 0.8687 (m100) cc_final: 0.8441 (m100) REVERT: E 91 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8152 (p) REVERT: E 140 MET cc_start: 0.8130 (tpt) cc_final: 0.7909 (mmt) outliers start: 48 outliers final: 33 residues processed: 256 average time/residue: 0.8306 time to fit residues: 232.0664 Evaluate side-chains 272 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 233 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 186 ASN Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 383 ILE Chi-restraints excluded: chain R residue 394 ILE Chi-restraints excluded: chain R residue 427 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9055 Z= 0.261 Angle : 0.609 9.273 12283 Z= 0.306 Chirality : 0.043 0.199 1407 Planarity : 0.004 0.039 1543 Dihedral : 4.856 38.449 1300 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.83 % Allowed : 20.35 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1110 helix: 2.32 (0.25), residues: 397 sheet: -0.60 (0.30), residues: 282 loop : -0.58 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.032 0.002 PHE R 198 TYR 0.021 0.002 TYR R 142 ARG 0.008 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 244 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: R 48 ILE cc_start: 0.7934 (mt) cc_final: 0.7653 (mp) REVERT: R 81 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7277 (mm) REVERT: R 82 LEU cc_start: 0.6884 (mp) cc_final: 0.6441 (mp) REVERT: R 117 MET cc_start: 0.6511 (mmt) cc_final: 0.6089 (mmm) REVERT: R 140 MET cc_start: 0.6978 (mmt) cc_final: 0.6639 (mmt) REVERT: R 155 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6549 (mpp) REVERT: R 158 ILE cc_start: 0.8063 (mt) cc_final: 0.7697 (tt) REVERT: R 372 THR cc_start: 0.7355 (m) cc_final: 0.7105 (m) REVERT: R 411 PHE cc_start: 0.7664 (m-10) cc_final: 0.7363 (m-10) REVERT: R 427 THR cc_start: 0.7891 (OUTLIER) cc_final: 0.7670 (m) REVERT: A 10 LYS cc_start: 0.8393 (ttmm) cc_final: 0.8134 (mtpm) REVERT: A 209 LYS cc_start: 0.7933 (ttpm) cc_final: 0.7661 (ttpm) REVERT: A 248 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7746 (mmmm) REVERT: A 308 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: A 316 THR cc_start: 0.8266 (p) cc_final: 0.8021 (p) REVERT: B 19 ARG cc_start: 0.7878 (ttp80) cc_final: 0.7287 (ttp80) REVERT: B 55 LEU cc_start: 0.8363 (mt) cc_final: 0.8125 (mp) REVERT: B 125 ASN cc_start: 0.8434 (t0) cc_final: 0.8128 (t0) REVERT: B 136 SER cc_start: 0.8447 (t) cc_final: 0.8095 (p) REVERT: B 156 GLN cc_start: 0.8292 (mt0) cc_final: 0.8040 (mt0) REVERT: B 217 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7390 (pmt) REVERT: B 237 ASN cc_start: 0.7309 (t0) cc_final: 0.6768 (t0) REVERT: B 239 ASN cc_start: 0.8157 (m-40) cc_final: 0.7377 (m-40) REVERT: B 258 ASP cc_start: 0.7725 (t0) cc_final: 0.7213 (t0) REVERT: B 297 TRP cc_start: 0.8713 (m100) cc_final: 0.8463 (m100) REVERT: E 140 MET cc_start: 0.8180 (tpt) cc_final: 0.7911 (tpp) outliers start: 47 outliers final: 32 residues processed: 261 average time/residue: 0.9213 time to fit residues: 261.1499 Evaluate side-chains 276 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 238 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 186 ASN Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 383 ILE Chi-restraints excluded: chain R residue 394 ILE Chi-restraints excluded: chain R residue 427 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.256 9055 Z= 0.365 Angle : 1.022 59.199 12283 Z= 0.608 Chirality : 0.050 0.611 1407 Planarity : 0.005 0.142 1543 Dihedral : 4.967 38.468 1300 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.43 % Favored : 97.48 % Rotamer: Outliers : 4.42 % Allowed : 21.58 % Favored : 74.00 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1110 helix: 2.33 (0.25), residues: 397 sheet: -0.60 (0.30), residues: 282 loop : -0.61 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.033 0.002 PHE E 239 TYR 0.022 0.002 TYR E 50 ARG 0.008 0.001 ARG B 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 233 time to evaluate : 1.111 Fit side-chains REVERT: R 48 ILE cc_start: 0.7934 (mt) cc_final: 0.7654 (mp) REVERT: R 81 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7275 (mm) REVERT: R 82 LEU cc_start: 0.6864 (mp) cc_final: 0.6426 (mp) REVERT: R 117 MET cc_start: 0.6507 (mmt) cc_final: 0.6101 (mmm) REVERT: R 140 MET cc_start: 0.6979 (mmt) cc_final: 0.6637 (mmt) REVERT: R 155 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6549 (mpp) REVERT: R 158 ILE cc_start: 0.8061 (mt) cc_final: 0.7689 (tt) REVERT: R 372 THR cc_start: 0.7357 (m) cc_final: 0.7106 (m) REVERT: R 411 PHE cc_start: 0.7663 (m-10) cc_final: 0.7361 (m-10) REVERT: R 427 THR cc_start: 0.7891 (OUTLIER) cc_final: 0.7669 (m) REVERT: A 10 LYS cc_start: 0.8380 (ttmm) cc_final: 0.8142 (mtpm) REVERT: A 209 LYS cc_start: 0.7929 (ttpm) cc_final: 0.7658 (ttpm) REVERT: A 248 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7747 (mmmm) REVERT: A 308 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: A 316 THR cc_start: 0.8266 (p) cc_final: 0.8022 (p) REVERT: B 19 ARG cc_start: 0.7878 (ttp80) cc_final: 0.7304 (ttp80) REVERT: B 55 LEU cc_start: 0.8364 (mt) cc_final: 0.8129 (mp) REVERT: B 125 ASN cc_start: 0.8435 (t0) cc_final: 0.8125 (t0) REVERT: B 136 SER cc_start: 0.8447 (t) cc_final: 0.8096 (p) REVERT: B 156 GLN cc_start: 0.8304 (mt0) cc_final: 0.8027 (mt0) REVERT: B 217 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7401 (pmt) REVERT: B 237 ASN cc_start: 0.7309 (t0) cc_final: 0.6762 (t0) REVERT: B 239 ASN cc_start: 0.8159 (m-40) cc_final: 0.7371 (m-40) REVERT: B 258 ASP cc_start: 0.7699 (t0) cc_final: 0.7213 (t0) REVERT: B 297 TRP cc_start: 0.8709 (m100) cc_final: 0.8492 (m100) REVERT: E 140 MET cc_start: 0.8179 (tpt) cc_final: 0.7912 (tpp) outliers start: 43 outliers final: 32 residues processed: 251 average time/residue: 0.9281 time to fit residues: 253.0882 Evaluate side-chains 270 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 232 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 186 ASN Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 383 ILE Chi-restraints excluded: chain R residue 394 ILE Chi-restraints excluded: chain R residue 397 ILE Chi-restraints excluded: chain R residue 427 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.0670 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.152538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.129909 restraints weight = 11352.969| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.03 r_work: 0.3611 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.256 9055 Z= 0.365 Angle : 1.022 59.199 12283 Z= 0.608 Chirality : 0.050 0.611 1407 Planarity : 0.005 0.142 1543 Dihedral : 4.967 38.468 1300 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.43 % Favored : 97.48 % Rotamer: Outliers : 4.01 % Allowed : 22.10 % Favored : 73.90 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1110 helix: 2.33 (0.25), residues: 397 sheet: -0.60 (0.30), residues: 282 loop : -0.61 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.033 0.002 PHE E 239 TYR 0.022 0.002 TYR E 50 ARG 0.008 0.001 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4304.08 seconds wall clock time: 76 minutes 54.68 seconds (4614.68 seconds total)