Starting phenix.real_space_refine on Thu Mar 14 16:04:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y36_33590/03_2024/7y36_33590_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y36_33590/03_2024/7y36_33590.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/7y36_33590/03_2024/7y36_33590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y36_33590/03_2024/7y36_33590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y36_33590/03_2024/7y36_33590_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y36_33590/03_2024/7y36_33590_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= -0.000 sd= 0.002 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 58 5.16 5 C 5851 2.51 5 N 1616 2.21 5 O 1681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9206 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3053 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain breaks: 3 Chain: "P" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 288 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "A" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1858 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" 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: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' OH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.15, per 1000 atoms: 0.56 Number of scatterers: 9206 At special positions: 0 Unit cell: (124.722, 97.344, 152.1, 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 58 16.00 O 1681 8.00 N 1616 7.00 C 5851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.02 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.02 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.7 seconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 11 sheets defined 39.1% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'R' and resid 34 through 56 removed outlier: 3.522A pdb=" N ARG R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 171 No H-bonds generated for 'chain 'R' and resid 168 through 171' Processing helix chain 'R' and resid 179 through 211 removed outlier: 4.089A pdb=" N VAL R 183 " --> pdb=" O GLU R 180 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE R 184 " --> pdb=" O ARG R 181 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY R 194 " --> pdb=" O TYR R 191 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER R 198 " --> pdb=" O TYR R 195 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR R 211 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 215 No H-bonds generated for 'chain 'R' and resid 213 through 215' Processing helix chain 'R' and resid 218 through 244 Processing helix chain 'R' and resid 279 through 311 Processing helix chain 'R' and resid 317 through 329 Processing helix chain 'R' and resid 331 through 346 removed outlier: 3.566A pdb=" N THR R 345 " --> pdb=" O SER R 341 " (cutoff:3.500A) Processing helix chain 'R' and resid 361 through 390 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 401 through 417 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 421 through 423 No H-bonds generated for 'chain 'R' and resid 421 through 423' Processing helix chain 'R' and resid 435 through 460 removed outlier: 3.605A pdb=" N PHE R 450 " --> pdb=" O LEU R 446 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 464 through 479 Processing helix chain 'P' and resid 3 through 33 Processing helix chain 'A' and resid 13 through 38 removed outlier: 4.099A pdb=" N LYS A 17 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ALA A 18 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN A 31 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS A 34 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 38 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 235 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.615A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 3.883A pdb=" N ILE A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 4.013A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'R' and resid 126 through 130 Processing sheet with id= B, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.158A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.860A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.812A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.592A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 221 through 223 removed outlier: 4.302A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.591A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.422A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.641A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.522A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.514A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1062 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: 2.71 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1503 1.31 - 1.44: 2663 1.44 - 1.56: 5159 1.56 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 9407 Sorted by residual: bond pdb=" C GLN A 227 " pdb=" N ARG A 228 " ideal model delta sigma weight residual 1.330 1.403 -0.072 1.30e-02 5.92e+03 3.08e+01 bond pdb=" CA LEU R 174 " pdb=" C LEU R 174 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.35e-02 5.49e+03 1.98e+01 bond pdb=" CA THR R 178 " pdb=" C THR R 178 " ideal model delta sigma weight residual 1.523 1.470 0.053 1.34e-02 5.57e+03 1.59e+01 bond pdb=" N LEU R 174 " pdb=" CA LEU R 174 " ideal model delta sigma weight residual 1.459 1.410 0.049 1.23e-02 6.61e+03 1.58e+01 bond pdb=" C CYS R 170 " pdb=" O CYS R 170 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.22e-02 6.72e+03 1.42e+01 ... (remaining 9402 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.06: 215 107.06 - 113.81: 5195 113.81 - 120.56: 3832 120.56 - 127.30: 3383 127.30 - 134.05: 107 Bond angle restraints: 12732 Sorted by residual: angle pdb=" N GLU R 169 " pdb=" CA GLU R 169 " pdb=" C GLU R 169 " ideal model delta sigma weight residual 111.71 102.90 8.81 1.15e+00 7.56e-01 5.87e+01 angle pdb=" C GLN A 227 " pdb=" N ARG A 228 " pdb=" CA ARG A 228 " ideal model delta sigma weight residual 121.06 131.27 -10.21 1.88e+00 2.83e-01 2.95e+01 angle pdb=" C LEU P 24 " pdb=" N ARG P 25 " pdb=" CA ARG P 25 " ideal model delta sigma weight residual 120.44 113.12 7.32 1.36e+00 5.41e-01 2.90e+01 angle pdb=" N LEU R 174 " pdb=" CA LEU R 174 " pdb=" C LEU R 174 " ideal model delta sigma weight residual 111.33 117.63 -6.30 1.21e+00 6.83e-01 2.71e+01 angle pdb=" N LYS R 172 " pdb=" CA LYS R 172 " pdb=" C LYS R 172 " ideal model delta sigma weight residual 112.38 118.55 -6.17 1.22e+00 6.72e-01 2.56e+01 ... (remaining 12727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5106 17.75 - 35.51: 391 35.51 - 53.26: 69 53.26 - 71.01: 8 71.01 - 88.77: 5 Dihedral angle restraints: 5579 sinusoidal: 2231 harmonic: 3348 Sorted by residual: dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual -86.00 -19.11 -66.89 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CA CYS R 351 " pdb=" C CYS R 351 " pdb=" N TRP R 352 " pdb=" CA TRP R 352 " ideal model delta harmonic sigma weight residual -180.00 -150.38 -29.62 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA PHE A 238 " pdb=" C PHE A 238 " pdb=" N ASN A 239 " pdb=" CA ASN A 239 " ideal model delta harmonic sigma weight residual 180.00 152.00 28.00 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 5576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1097 0.056 - 0.111: 260 0.111 - 0.167: 40 0.167 - 0.223: 6 0.223 - 0.278: 2 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CA LEU R 174 " pdb=" N LEU R 174 " pdb=" C LEU R 174 " pdb=" CB LEU R 174 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA THR R 178 " pdb=" N THR R 178 " pdb=" C THR R 178 " pdb=" CB THR R 178 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA TYR R 191 " pdb=" N TYR R 191 " pdb=" C TYR R 191 " pdb=" CB TYR R 191 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1402 not shown) Planarity restraints: 1621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER R 168 " 0.035 2.00e-02 2.50e+03 7.17e-02 5.15e+01 pdb=" C SER R 168 " -0.124 2.00e-02 2.50e+03 pdb=" O SER R 168 " 0.048 2.00e-02 2.50e+03 pdb=" N GLU R 169 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO B 236 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.016 2.00e-02 2.50e+03 1.54e-02 4.73e+00 pdb=" CG TYR B 59 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.001 2.00e-02 2.50e+03 ... (remaining 1618 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 262 2.70 - 3.25: 8866 3.25 - 3.80: 14660 3.80 - 4.35: 19328 4.35 - 4.90: 32435 Nonbonded interactions: 75551 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.152 2.440 nonbonded pdb=" O ASP R 113 " pdb=" CG1 VAL P 31 " model vdw 2.178 3.460 nonbonded pdb=" OG1 THR R 218 " pdb=" OE2 GLU R 317 " model vdw 2.183 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.207 2.440 nonbonded pdb=" CG2 ILE R 115 " pdb=" NZ LYS P 27 " model vdw 2.229 3.540 ... (remaining 75546 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: 0.460 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: 2.880 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.660 Find NCS groups from input model: 0.240 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:10.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5207 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 : 0.007 0.072 9407 Z= 0.426 Angle : 0.732 10.207 12732 Z= 0.445 Chirality : 0.049 0.278 1405 Planarity : 0.005 0.072 1621 Dihedral : 12.892 88.766 3395 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.22), residues: 1127 helix: -0.23 (0.22), residues: 449 sheet: -0.68 (0.31), residues: 227 loop : -1.41 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 99 HIS 0.008 0.001 HIS A 357 PHE 0.021 0.002 PHE R 335 TYR 0.038 0.002 TYR B 59 ARG 0.009 0.001 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 310 average time/residue: 1.0824 time to fit residues: 359.2652 Evaluate side-chains 162 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 458 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 140 HIS R 463 ASN A 14 ASN A 41 HIS ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 119 ASN B 176 GLN B 266 HIS B 313 ASN N 77 ASN N 82 GLN N 84 ASN N 123 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.7077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 9407 Z= 0.367 Angle : 0.817 12.283 12732 Z= 0.436 Chirality : 0.048 0.177 1405 Planarity : 0.006 0.057 1621 Dihedral : 5.325 31.485 1261 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.56 % Allowed : 15.05 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.24), residues: 1127 helix: 0.22 (0.23), residues: 451 sheet: -0.17 (0.33), residues: 230 loop : -0.99 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.014 0.002 HIS B 183 PHE 0.036 0.003 PHE R 335 TYR 0.048 0.003 TYR R 191 ARG 0.008 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 288 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 211 TRP cc_start: 0.6312 (OUTLIER) cc_final: 0.4567 (m-10) outliers start: 55 outliers final: 14 residues processed: 316 average time/residue: 1.0739 time to fit residues: 363.3053 Evaluate side-chains 203 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 188 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 0.0570 chunk 101 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 220 ASN R 440 GLN P 6 GLN P 9 HIS P 32 HIS A 236 GLN B 62 HIS B 75 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 295 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.9233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9407 Z= 0.249 Angle : 0.677 8.876 12732 Z= 0.359 Chirality : 0.044 0.157 1405 Planarity : 0.005 0.047 1621 Dihedral : 4.785 28.238 1259 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 6.46 % Allowed : 21.11 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1127 helix: 0.68 (0.24), residues: 449 sheet: 0.18 (0.33), residues: 228 loop : -0.65 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.006 0.001 HIS R 420 PHE 0.032 0.002 PHE R 335 TYR 0.022 0.002 TYR R 191 ARG 0.009 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 242 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LEU cc_start: 0.7987 (mt) cc_final: 0.7507 (tp) REVERT: N 73 ASP cc_start: 0.6071 (p0) cc_final: 0.5702 (p0) REVERT: N 87 LYS cc_start: 0.8710 (ptpp) cc_final: 0.8459 (ptpp) outliers start: 64 outliers final: 28 residues processed: 281 average time/residue: 1.1427 time to fit residues: 343.2214 Evaluate side-chains 213 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 185 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 431 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 124 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 chunk 29 optimal weight: 0.0070 chunk 90 optimal weight: 5.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 6 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 142 HIS B 230 ASN B 266 HIS ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.9937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9407 Z= 0.214 Angle : 0.646 10.105 12732 Z= 0.341 Chirality : 0.043 0.181 1405 Planarity : 0.005 0.034 1621 Dihedral : 4.515 26.210 1259 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 6.06 % Allowed : 24.44 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1127 helix: 0.81 (0.25), residues: 443 sheet: 0.14 (0.33), residues: 225 loop : -0.37 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS R 420 PHE 0.026 0.001 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.008 0.001 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 212 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 30 residues processed: 254 average time/residue: 1.1389 time to fit residues: 308.8712 Evaluate side-chains 215 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 185 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 214 ARG Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 348 ASN B 75 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 1.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9407 Z= 0.232 Angle : 0.642 8.913 12732 Z= 0.341 Chirality : 0.043 0.211 1405 Planarity : 0.005 0.034 1621 Dihedral : 4.513 24.314 1259 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 6.97 % Allowed : 24.55 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1127 helix: 0.85 (0.25), residues: 439 sheet: 0.01 (0.33), residues: 234 loop : -0.50 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS R 420 PHE 0.020 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.011 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 212 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 ASP cc_start: 0.6247 (p0) cc_final: 0.5951 (p0) REVERT: N 38 ARG cc_start: 0.7679 (ptm-80) cc_final: 0.7031 (ptm160) outliers start: 69 outliers final: 41 residues processed: 261 average time/residue: 1.1277 time to fit residues: 314.6315 Evaluate side-chains 236 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 195 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 214 ARG Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN N 74 ASN N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 1.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9407 Z= 0.282 Angle : 0.683 11.124 12732 Z= 0.359 Chirality : 0.044 0.205 1405 Planarity : 0.005 0.034 1621 Dihedral : 4.580 23.368 1259 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 6.46 % Allowed : 27.17 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1127 helix: 0.77 (0.25), residues: 434 sheet: 0.28 (0.33), residues: 226 loop : -0.54 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS R 420 PHE 0.020 0.002 PHE B 292 TYR 0.022 0.002 TYR R 191 ARG 0.011 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 209 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 ASP cc_start: 0.6503 (p0) cc_final: 0.6191 (p0) REVERT: B 22 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.5339 (mpt-90) outliers start: 64 outliers final: 33 residues processed: 255 average time/residue: 1.1449 time to fit residues: 311.7997 Evaluate side-chains 219 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 185 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 214 ARG Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 0.3980 chunk 91 optimal weight: 6.9990 chunk 60 optimal weight: 0.0470 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 348 ASN R 358 ASN R 402 GLN B 75 GLN N 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 1.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9407 Z= 0.189 Angle : 0.654 10.122 12732 Z= 0.344 Chirality : 0.042 0.180 1405 Planarity : 0.005 0.033 1621 Dihedral : 4.438 21.048 1259 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.05 % Allowed : 30.10 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1127 helix: 0.88 (0.25), residues: 435 sheet: 0.51 (0.34), residues: 219 loop : -0.52 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP P 23 HIS 0.004 0.001 HIS R 143 PHE 0.024 0.001 PHE R 314 TYR 0.022 0.001 TYR N 60 ARG 0.009 0.001 ARG P 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 205 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 37 GLN cc_start: 0.4871 (OUTLIER) cc_final: 0.4490 (tp40) REVERT: R 425 MET cc_start: 0.7009 (ppp) cc_final: 0.6474 (ptm) REVERT: A 310 ASP cc_start: 0.6485 (p0) cc_final: 0.6177 (p0) outliers start: 50 outliers final: 30 residues processed: 238 average time/residue: 1.1093 time to fit residues: 282.6880 Evaluate side-chains 213 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 182 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 0.0570 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 402 GLN P 16 ASN B 75 GLN N 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 1.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9407 Z= 0.245 Angle : 0.699 12.721 12732 Z= 0.366 Chirality : 0.043 0.178 1405 Planarity : 0.005 0.039 1621 Dihedral : 4.555 24.810 1259 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.34 % Allowed : 31.21 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1127 helix: 0.91 (0.25), residues: 437 sheet: 0.54 (0.35), residues: 218 loop : -0.53 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.011 0.001 HIS R 143 PHE 0.023 0.001 PHE R 335 TYR 0.020 0.001 TYR N 60 ARG 0.007 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 192 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 425 MET cc_start: 0.7074 (ppp) cc_final: 0.6576 (ptm) REVERT: A 299 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7896 (pm20) REVERT: A 310 ASP cc_start: 0.6706 (p0) cc_final: 0.6422 (p0) REVERT: G 24 ASN cc_start: 0.6299 (p0) cc_final: 0.6036 (p0) outliers start: 43 outliers final: 28 residues processed: 221 average time/residue: 1.1362 time to fit residues: 269.1393 Evaluate side-chains 207 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 9.9990 chunk 100 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 0.0470 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 402 GLN B 75 GLN N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 1.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9407 Z= 0.224 Angle : 0.694 11.126 12732 Z= 0.364 Chirality : 0.043 0.180 1405 Planarity : 0.005 0.036 1621 Dihedral : 4.544 25.616 1259 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.43 % Allowed : 32.83 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1127 helix: 0.93 (0.25), residues: 436 sheet: 0.39 (0.35), residues: 212 loop : -0.46 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 112 HIS 0.011 0.001 HIS R 114 PHE 0.025 0.001 PHE R 335 TYR 0.021 0.001 TYR R 191 ARG 0.009 0.001 ARG P 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 188 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 425 MET cc_start: 0.7022 (ppp) cc_final: 0.6572 (ptm) REVERT: A 310 ASP cc_start: 0.6727 (p0) cc_final: 0.6457 (p0) REVERT: G 24 ASN cc_start: 0.6499 (p0) cc_final: 0.6154 (p0) outliers start: 34 outliers final: 26 residues processed: 212 average time/residue: 1.1015 time to fit residues: 250.1253 Evaluate side-chains 205 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 179 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 402 GLN B 75 GLN N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 1.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9407 Z= 0.221 Angle : 0.697 11.274 12732 Z= 0.363 Chirality : 0.042 0.177 1405 Planarity : 0.004 0.034 1621 Dihedral : 4.481 24.633 1259 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.93 % Allowed : 33.03 % Favored : 64.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1127 helix: 0.97 (0.25), residues: 436 sheet: 0.47 (0.35), residues: 219 loop : -0.43 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 154 HIS 0.006 0.001 HIS R 143 PHE 0.026 0.001 PHE R 335 TYR 0.021 0.001 TYR R 191 ARG 0.008 0.001 ARG P 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 189 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 425 MET cc_start: 0.7101 (ppp) cc_final: 0.6624 (ptm) REVERT: A 310 ASP cc_start: 0.6800 (p0) cc_final: 0.6488 (p0) outliers start: 29 outliers final: 26 residues processed: 208 average time/residue: 1.1210 time to fit residues: 249.2624 Evaluate side-chains 202 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 176 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 214 ARG Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 449 SER Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 402 GLN B 75 GLN N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.137694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.103661 restraints weight = 14985.771| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.41 r_work: 0.3252 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 1.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9407 Z= 0.223 Angle : 0.704 11.254 12732 Z= 0.368 Chirality : 0.043 0.260 1405 Planarity : 0.005 0.036 1621 Dihedral : 4.574 24.410 1259 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.13 % Allowed : 33.03 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1127 helix: 0.91 (0.25), residues: 436 sheet: 0.53 (0.35), residues: 219 loop : -0.40 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP P 23 HIS 0.007 0.001 HIS R 143 PHE 0.026 0.001 PHE R 335 TYR 0.020 0.001 TYR R 191 ARG 0.008 0.001 ARG P 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4726.14 seconds wall clock time: 83 minutes 22.22 seconds (5002.22 seconds total)