Starting phenix.real_space_refine on Tue Feb 13 15:47:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7b_8997/02_2024/6e7b_8997_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7b_8997/02_2024/6e7b_8997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7b_8997/02_2024/6e7b_8997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7b_8997/02_2024/6e7b_8997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7b_8997/02_2024/6e7b_8997_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7b_8997/02_2024/6e7b_8997_updated.pdb" } resolution = 3.5 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 ------------------------------------------------------------------------------- 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= 0.204 sd= 1.216 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 4259 2.51 5 N 1155 2.21 5 O 1304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 62": "NH1" <-> "NH2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B ARG 276": "NH1" <-> "NH2" Residue "B ARG 309": "NH1" <-> "NH2" Residue "B ARG 320": "NH1" <-> "NH2" Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6774 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3350 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 19, 'TRANS': 406} Chain: "A" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3358 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 20, 'TRANS': 407} Chain breaks: 1 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.34, per 1000 atoms: 0.64 Number of scatterers: 6774 At special positions: 0 Unit cell: (72, 70, 108, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 6 15.00 Mg 2 11.99 O 1304 8.00 N 1155 7.00 C 4259 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.3 seconds 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 7 sheets defined 44.7% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'B' and resid 10 through 27 removed outlier: 3.533A pdb=" N VAL B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 24 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 No H-bonds generated for 'chain 'B' and resid 42 through 45' Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 71 through 78 removed outlier: 3.526A pdb=" N SER B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 107 through 126 removed outlier: 3.818A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU B 125 " --> pdb=" O ARG B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.852A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 192 removed outlier: 3.552A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 removed outlier: 3.651A pdb=" N TYR B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 241 removed outlier: 3.929A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 removed outlier: 4.109A pdb=" N ASN B 256 " --> pdb=" O LYS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 293 Processing helix chain 'B' and resid 323 through 336 removed outlier: 3.642A pdb=" N GLN B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 390 Processing helix chain 'B' and resid 395 through 401 removed outlier: 3.898A pdb=" N GLU B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 425 removed outlier: 3.879A pdb=" N GLU B 412 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL B 419 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN B 423 " --> pdb=" O SER B 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 27 Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 72 through 79 removed outlier: 3.932A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 115 through 128 removed outlier: 3.697A pdb=" N ASP A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 160 Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.963A pdb=" N ILE A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.114A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.752A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 283' Processing helix chain 'A' and resid 288 through 295 Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.772A pdb=" N ASP A 392 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP A 396 " --> pdb=" O HIS A 393 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 397 " --> pdb=" O LYS A 394 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 415 through 436 removed outlier: 4.009A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.513A pdb=" N VAL B 60 " --> pdb=" O ASN B 52 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 134 through 138 removed outlier: 7.130A pdb=" N ASN B 165 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N HIS B 137 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N PHE B 167 " --> pdb=" O HIS B 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 349 through 352 removed outlier: 8.542A pdb=" N LYS B 350 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N THR B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASN B 370 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL B 313 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE B 368 " --> pdb=" O VAL B 313 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 6 through 9 removed outlier: 3.572A pdb=" N VAL A 66 " --> pdb=" O SER A 6 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 53 through 56 Processing sheet with id= F, first strand: chain 'A' and resid 134 through 137 removed outlier: 7.207A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 351 through 354 removed outlier: 6.172A pdb=" N CYS A 315 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLY A 354 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 317 " --> pdb=" O GLY A 354 " (cutoff:3.500A) 218 hydrogen bonds defined for protein. 558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.78 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2227 1.34 - 1.46: 1241 1.46 - 1.58: 3372 1.58 - 1.69: 10 1.69 - 1.81: 78 Bond restraints: 6928 Sorted by residual: bond pdb=" O3B G2P B 502 " pdb=" PG G2P B 502 " ideal model delta sigma weight residual 1.716 1.607 0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" O1B G2P B 502 " pdb=" PB G2P B 502 " ideal model delta sigma weight residual 1.510 1.609 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" O2A G2P B 502 " pdb=" PA G2P B 502 " ideal model delta sigma weight residual 1.513 1.608 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C5 GTP A 502 " pdb=" C6 GTP A 502 " ideal model delta sigma weight residual 1.390 1.473 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C4 G2P B 502 " pdb=" C5 G2P B 502 " ideal model delta sigma weight residual 1.384 1.465 -0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 6923 not shown) Histogram of bond angle deviations from ideal: 97.81 - 105.45: 156 105.45 - 113.10: 3684 113.10 - 120.74: 3210 120.74 - 128.38: 2281 128.38 - 136.02: 78 Bond angle restraints: 9409 Sorted by residual: angle pdb=" PA G2P B 502 " pdb=" C3A G2P B 502 " pdb=" PB G2P B 502 " ideal model delta sigma weight residual 120.83 108.09 12.74 3.00e+00 1.11e-01 1.80e+01 angle pdb=" N TYR B 222 " pdb=" CA TYR B 222 " pdb=" C TYR B 222 " ideal model delta sigma weight residual 111.28 107.15 4.13 1.09e+00 8.42e-01 1.44e+01 angle pdb=" C3A G2P B 502 " pdb=" PA G2P B 502 " pdb=" O5' G2P B 502 " ideal model delta sigma weight residual 99.14 109.87 -10.73 3.00e+00 1.11e-01 1.28e+01 angle pdb=" O1B GTP A 502 " pdb=" PB GTP A 502 " pdb=" O2B GTP A 502 " ideal model delta sigma weight residual 109.50 119.65 -10.15 3.00e+00 1.11e-01 1.14e+01 angle pdb=" O1A GTP A 502 " pdb=" PA GTP A 502 " pdb=" O2A GTP A 502 " ideal model delta sigma weight residual 109.50 119.32 -9.82 3.00e+00 1.11e-01 1.07e+01 ... (remaining 9404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.42: 4076 31.42 - 62.83: 53 62.83 - 94.24: 7 94.24 - 125.66: 1 125.66 - 157.07: 2 Dihedral angle restraints: 4139 sinusoidal: 1670 harmonic: 2469 Sorted by residual: dihedral pdb=" C5' GTP A 502 " pdb=" O5' GTP A 502 " pdb=" PA GTP A 502 " pdb=" O3A GTP A 502 " ideal model delta sinusoidal sigma weight residual 69.27 -133.66 -157.07 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" C8 GTP A 502 " pdb=" C1' GTP A 502 " pdb=" N9 GTP A 502 " pdb=" O4' GTP A 502 " ideal model delta sinusoidal sigma weight residual 104.59 -41.98 146.57 1 2.00e+01 2.50e-03 4.40e+01 dihedral pdb=" O3B GTP A 502 " pdb=" O3A GTP A 502 " pdb=" PB GTP A 502 " pdb=" PA GTP A 502 " ideal model delta sinusoidal sigma weight residual 291.08 171.08 120.00 1 2.00e+01 2.50e-03 3.60e+01 ... (remaining 4136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 572 0.030 - 0.061: 302 0.061 - 0.091: 101 0.091 - 0.122: 43 0.122 - 0.152: 10 Chirality restraints: 1028 Sorted by residual: chirality pdb=" CA VAL A 363 " pdb=" N VAL A 363 " pdb=" C VAL A 363 " pdb=" CB VAL A 363 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CB ILE A 115 " pdb=" CA ILE A 115 " pdb=" CG1 ILE A 115 " pdb=" CG2 ILE A 115 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA ILE B 368 " pdb=" N ILE B 368 " pdb=" C ILE B 368 " pdb=" CB ILE B 368 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 1025 not shown) Planarity restraints: 1221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 79 " -0.172 9.50e-02 1.11e+02 7.73e-02 3.68e+00 pdb=" NE ARG A 79 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 79 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 79 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 79 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 267 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.38e+00 pdb=" N PRO B 268 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 268 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 268 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 356 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO B 357 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 357 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 357 " 0.024 5.00e-02 4.00e+02 ... (remaining 1218 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 105 2.59 - 3.17: 6344 3.17 - 3.74: 10724 3.74 - 4.32: 15832 4.32 - 4.90: 25118 Nonbonded interactions: 58123 Sorted by model distance: nonbonded pdb="MG MG B 501 " pdb=" O1G G2P B 502 " model vdw 2.009 2.170 nonbonded pdb="MG MG A 501 " pdb=" O3G GTP A 502 " model vdw 2.012 2.170 nonbonded pdb="MG MG B 501 " pdb=" O1B G2P B 502 " model vdw 2.049 2.170 nonbonded pdb="MG MG B 501 " pdb=" O3B G2P B 502 " model vdw 2.069 2.170 nonbonded pdb=" OE1 GLU A 71 " pdb="MG MG A 501 " model vdw 2.099 2.170 ... (remaining 58118 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 group one per residue 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: 6.020 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: 27.090 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.750 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 : 0.006 0.109 6928 Z= 0.388 Angle : 0.828 12.742 9409 Z= 0.401 Chirality : 0.043 0.152 1028 Planarity : 0.004 0.077 1221 Dihedral : 11.890 157.073 2555 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.14 % Allowed : 3.84 % Favored : 96.02 % 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: -4.13 (0.25), residues: 848 helix: -2.97 (0.19), residues: 352 sheet: -3.95 (0.43), residues: 93 loop : -2.06 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 21 HIS 0.008 0.001 HIS B 6 PHE 0.019 0.002 PHE B 212 TYR 0.013 0.002 TYR B 208 ARG 0.008 0.001 ARG B 241 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 ASN cc_start: 0.7481 (t0) cc_final: 0.7193 (t0) REVERT: B 289 LEU cc_start: 0.8010 (mp) cc_final: 0.7745 (mp) REVERT: B 403 MET cc_start: 0.7705 (tpt) cc_final: 0.6434 (mmm) REVERT: A 50 ASN cc_start: 0.7276 (t0) cc_final: 0.7027 (t0) REVERT: A 203 MET cc_start: 0.7696 (mmm) cc_final: 0.7317 (mmm) outliers start: 1 outliers final: 1 residues processed: 224 average time/residue: 0.2414 time to fit residues: 67.6138 Evaluate side-chains 135 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN B 291 GLN B 329 GLN A 11 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6928 Z= 0.320 Angle : 0.676 6.964 9409 Z= 0.342 Chirality : 0.047 0.163 1028 Planarity : 0.005 0.038 1221 Dihedral : 10.910 164.106 976 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.61 % Allowed : 11.66 % Favored : 85.73 % 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: -2.87 (0.26), residues: 848 helix: -1.69 (0.22), residues: 363 sheet: -3.19 (0.47), residues: 87 loop : -1.67 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 21 HIS 0.005 0.001 HIS A 197 PHE 0.027 0.002 PHE B 20 TYR 0.018 0.002 TYR B 208 ARG 0.008 0.001 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.7105 (tm-30) REVERT: B 86 ARG cc_start: 0.7143 (mmp-170) cc_final: 0.6463 (tpm170) REVERT: B 118 ASP cc_start: 0.7310 (m-30) cc_final: 0.7101 (m-30) REVERT: B 300 MET cc_start: 0.8550 (ptp) cc_final: 0.8327 (ptp) REVERT: A 108 TYR cc_start: 0.6150 (OUTLIER) cc_final: 0.5861 (t80) REVERT: A 380 ASN cc_start: 0.8128 (t0) cc_final: 0.7771 (t0) outliers start: 19 outliers final: 9 residues processed: 162 average time/residue: 0.2140 time to fit residues: 44.7179 Evaluate side-chains 129 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 367 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 chunk 76 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6928 Z= 0.192 Angle : 0.579 8.348 9409 Z= 0.289 Chirality : 0.043 0.128 1028 Planarity : 0.004 0.035 1221 Dihedral : 10.589 166.398 974 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.19 % Allowed : 13.44 % Favored : 84.36 % 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: -2.17 (0.27), residues: 848 helix: -0.98 (0.25), residues: 355 sheet: -2.87 (0.49), residues: 95 loop : -1.37 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 21 HIS 0.004 0.001 HIS B 105 PHE 0.024 0.002 PHE A 395 TYR 0.008 0.001 TYR B 310 ARG 0.009 0.001 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 146 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.8535 (mpp) cc_final: 0.7931 (mpp) REVERT: B 77 ARG cc_start: 0.8163 (mtt90) cc_final: 0.7922 (mtt-85) REVERT: B 86 ARG cc_start: 0.6959 (mmp-170) cc_final: 0.5158 (tpt170) REVERT: B 300 MET cc_start: 0.8581 (ptp) cc_final: 0.8370 (ptp) REVERT: B 323 MET cc_start: 0.8433 (mmm) cc_final: 0.8195 (mmm) REVERT: A 103 TYR cc_start: 0.7155 (t80) cc_final: 0.6724 (t80) REVERT: A 108 TYR cc_start: 0.6137 (OUTLIER) cc_final: 0.5835 (t80) REVERT: A 269 LEU cc_start: 0.8508 (pp) cc_final: 0.8265 (pt) REVERT: A 313 MET cc_start: 0.9035 (mtm) cc_final: 0.8800 (mtm) outliers start: 16 outliers final: 8 residues processed: 156 average time/residue: 0.2124 time to fit residues: 43.3016 Evaluate side-chains 129 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 367 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.0970 chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 8 optimal weight: 0.0370 chunk 36 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 overall best weight: 0.4860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 ASN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6928 Z= 0.152 Angle : 0.558 6.840 9409 Z= 0.278 Chirality : 0.042 0.170 1028 Planarity : 0.004 0.037 1221 Dihedral : 10.347 167.748 974 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.16 % Allowed : 14.68 % Favored : 82.17 % 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: -1.88 (0.28), residues: 848 helix: -0.66 (0.26), residues: 362 sheet: -2.48 (0.49), residues: 95 loop : -1.38 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 21 HIS 0.004 0.001 HIS A 8 PHE 0.026 0.001 PHE B 20 TYR 0.012 0.001 TYR A 185 ARG 0.005 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.8580 (mpp) cc_final: 0.7936 (mpp) REVERT: B 86 ARG cc_start: 0.6933 (mmp-170) cc_final: 0.5145 (tpt170) REVERT: B 267 MET cc_start: 0.8550 (mtm) cc_final: 0.8337 (mtm) REVERT: B 276 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6907 (mmm160) REVERT: B 403 MET cc_start: 0.8477 (mmm) cc_final: 0.7740 (mmm) REVERT: A 56 THR cc_start: 0.8228 (m) cc_final: 0.7720 (p) REVERT: A 103 TYR cc_start: 0.7112 (t80) cc_final: 0.6726 (t80) REVERT: A 108 TYR cc_start: 0.6146 (OUTLIER) cc_final: 0.5536 (t80) REVERT: A 306 ASP cc_start: 0.6598 (OUTLIER) cc_final: 0.6138 (p0) outliers start: 23 outliers final: 14 residues processed: 155 average time/residue: 0.2177 time to fit residues: 43.6751 Evaluate side-chains 137 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 367 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6928 Z= 0.181 Angle : 0.572 11.314 9409 Z= 0.281 Chirality : 0.042 0.136 1028 Planarity : 0.004 0.034 1221 Dihedral : 10.349 175.106 974 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.84 % Allowed : 16.05 % Favored : 80.11 % 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: -1.67 (0.27), residues: 848 helix: -0.53 (0.26), residues: 367 sheet: -2.39 (0.50), residues: 95 loop : -1.21 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.004 0.001 HIS B 6 PHE 0.023 0.002 PHE A 395 TYR 0.008 0.001 TYR B 310 ARG 0.005 0.000 ARG A 422 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: B 73 MET cc_start: 0.8474 (mpp) cc_final: 0.7698 (mpp) REVERT: B 86 ARG cc_start: 0.6952 (mmp-170) cc_final: 0.5431 (tpt170) REVERT: B 267 MET cc_start: 0.8539 (mtm) cc_final: 0.8290 (mtm) REVERT: B 276 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6873 (mmm160) REVERT: A 56 THR cc_start: 0.8193 (m) cc_final: 0.7790 (p) REVERT: A 103 TYR cc_start: 0.7175 (t80) cc_final: 0.6653 (t80) REVERT: A 108 TYR cc_start: 0.6208 (OUTLIER) cc_final: 0.5421 (t80) REVERT: A 124 LYS cc_start: 0.8079 (mptt) cc_final: 0.7853 (tmtt) REVERT: A 212 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8121 (mt) REVERT: A 284 GLU cc_start: 0.7779 (tp30) cc_final: 0.7480 (tp30) REVERT: A 390 ARG cc_start: 0.7875 (mtt180) cc_final: 0.7504 (mtt180) outliers start: 28 outliers final: 20 residues processed: 145 average time/residue: 0.1924 time to fit residues: 37.1370 Evaluate side-chains 138 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 367 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN A 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6928 Z= 0.283 Angle : 0.630 11.417 9409 Z= 0.310 Chirality : 0.045 0.180 1028 Planarity : 0.004 0.033 1221 Dihedral : 10.640 176.657 974 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.80 % Allowed : 15.64 % Favored : 79.56 % 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: -1.71 (0.28), residues: 848 helix: -0.59 (0.26), residues: 366 sheet: -2.40 (0.46), residues: 111 loop : -1.12 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 388 HIS 0.004 0.001 HIS B 6 PHE 0.036 0.002 PHE B 20 TYR 0.017 0.001 TYR A 357 ARG 0.006 0.001 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 HIS cc_start: 0.5386 (t-90) cc_final: 0.5124 (t-90) REVERT: B 73 MET cc_start: 0.8829 (mpp) cc_final: 0.7899 (mpp) REVERT: B 86 ARG cc_start: 0.7133 (mmp-170) cc_final: 0.5472 (tpt170) REVERT: B 207 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8066 (mm) REVERT: A 103 TYR cc_start: 0.7175 (t80) cc_final: 0.6704 (t80) REVERT: A 108 TYR cc_start: 0.6039 (OUTLIER) cc_final: 0.5148 (t80) REVERT: A 212 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8254 (mt) outliers start: 35 outliers final: 25 residues processed: 148 average time/residue: 0.2032 time to fit residues: 39.6624 Evaluate side-chains 139 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 367 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 80 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6928 Z= 0.169 Angle : 0.576 6.976 9409 Z= 0.283 Chirality : 0.042 0.178 1028 Planarity : 0.004 0.054 1221 Dihedral : 10.688 179.516 974 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.25 % Allowed : 17.42 % Favored : 78.33 % 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: -1.52 (0.28), residues: 848 helix: -0.42 (0.26), residues: 365 sheet: -2.15 (0.48), residues: 111 loop : -1.07 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 388 HIS 0.004 0.001 HIS A 8 PHE 0.037 0.002 PHE B 20 TYR 0.017 0.001 TYR A 185 ARG 0.012 0.001 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.8756 (mpp) cc_final: 0.7871 (mpp) REVERT: B 86 ARG cc_start: 0.7003 (mmp-170) cc_final: 0.5371 (tpt170) REVERT: B 233 MET cc_start: 0.6771 (OUTLIER) cc_final: 0.6414 (ptp) REVERT: A 56 THR cc_start: 0.8231 (m) cc_final: 0.7932 (p) REVERT: A 103 TYR cc_start: 0.7141 (t80) cc_final: 0.6678 (t80) REVERT: A 108 TYR cc_start: 0.6169 (OUTLIER) cc_final: 0.5603 (t80) REVERT: A 121 ARG cc_start: 0.7140 (tpp-160) cc_final: 0.6873 (tpp-160) REVERT: A 212 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8198 (mt) outliers start: 31 outliers final: 19 residues processed: 149 average time/residue: 0.1979 time to fit residues: 39.2199 Evaluate side-chains 134 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 275 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.5755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6928 Z= 0.227 Angle : 0.606 10.162 9409 Z= 0.296 Chirality : 0.044 0.174 1028 Planarity : 0.004 0.053 1221 Dihedral : 10.644 177.266 974 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.53 % Allowed : 19.20 % Favored : 76.27 % 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: -1.52 (0.28), residues: 848 helix: -0.40 (0.26), residues: 365 sheet: -2.19 (0.48), residues: 111 loop : -1.10 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 21 HIS 0.005 0.001 HIS B 6 PHE 0.022 0.002 PHE B 385 TYR 0.011 0.001 TYR A 185 ARG 0.012 0.001 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.8810 (mpp) cc_final: 0.7811 (mpp) REVERT: B 276 ARG cc_start: 0.7311 (mmm160) cc_final: 0.7017 (mmm160) REVERT: A 56 THR cc_start: 0.8244 (m) cc_final: 0.7941 (p) REVERT: A 103 TYR cc_start: 0.7096 (t80) cc_final: 0.6690 (t80) REVERT: A 108 TYR cc_start: 0.6058 (OUTLIER) cc_final: 0.5449 (t80) REVERT: A 121 ARG cc_start: 0.7231 (tpp-160) cc_final: 0.6929 (tpp-160) REVERT: A 212 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8248 (mt) outliers start: 33 outliers final: 24 residues processed: 138 average time/residue: 0.1923 time to fit residues: 35.4871 Evaluate side-chains 136 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 110 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 275 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 6.9990 chunk 77 optimal weight: 0.2980 chunk 45 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 0.0060 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN A 11 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6928 Z= 0.187 Angle : 0.607 9.992 9409 Z= 0.295 Chirality : 0.043 0.187 1028 Planarity : 0.004 0.055 1221 Dihedral : 10.522 172.555 974 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.12 % Allowed : 20.16 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.28), residues: 848 helix: -0.29 (0.26), residues: 365 sheet: -2.07 (0.50), residues: 111 loop : -1.08 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 21 HIS 0.004 0.001 HIS A 8 PHE 0.022 0.002 PHE B 385 TYR 0.012 0.001 TYR A 185 ARG 0.012 0.001 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.8802 (mpp) cc_final: 0.8015 (mpp) REVERT: B 276 ARG cc_start: 0.7331 (mmm160) cc_final: 0.7081 (mmm160) REVERT: B 298 ASN cc_start: 0.7860 (t0) cc_final: 0.7639 (t0) REVERT: A 56 THR cc_start: 0.8234 (m) cc_final: 0.7971 (p) REVERT: A 103 TYR cc_start: 0.7097 (t80) cc_final: 0.6686 (t80) REVERT: A 108 TYR cc_start: 0.6140 (OUTLIER) cc_final: 0.5563 (t80) REVERT: A 121 ARG cc_start: 0.7207 (tpp-160) cc_final: 0.6938 (tpp-160) REVERT: A 212 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8262 (mt) outliers start: 30 outliers final: 24 residues processed: 140 average time/residue: 0.1907 time to fit residues: 35.7908 Evaluate side-chains 135 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 109 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 367 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 6928 Z= 0.382 Angle : 0.727 14.153 9409 Z= 0.357 Chirality : 0.047 0.174 1028 Planarity : 0.005 0.054 1221 Dihedral : 10.776 170.050 974 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.25 % Allowed : 19.75 % Favored : 75.99 % 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: -1.76 (0.28), residues: 848 helix: -0.61 (0.25), residues: 373 sheet: -2.23 (0.49), residues: 110 loop : -1.25 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 388 HIS 0.006 0.001 HIS B 6 PHE 0.024 0.002 PHE B 385 TYR 0.021 0.002 TYR B 106 ARG 0.012 0.001 ARG B 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.8848 (mpp) cc_final: 0.7835 (mpp) REVERT: A 103 TYR cc_start: 0.7185 (t80) cc_final: 0.6730 (t80) REVERT: A 108 TYR cc_start: 0.6358 (OUTLIER) cc_final: 0.5600 (t80) REVERT: A 212 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8356 (mt) outliers start: 31 outliers final: 23 residues processed: 143 average time/residue: 0.2055 time to fit residues: 38.9923 Evaluate side-chains 138 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 367 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 0.0270 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.130406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.113815 restraints weight = 9379.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.117630 restraints weight = 4992.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.120156 restraints weight = 3205.379| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.6205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6928 Z= 0.192 Angle : 0.649 12.634 9409 Z= 0.316 Chirality : 0.044 0.194 1028 Planarity : 0.004 0.065 1221 Dihedral : 10.487 160.233 974 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.25 % Allowed : 19.89 % Favored : 75.86 % 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: -1.50 (0.28), residues: 848 helix: -0.33 (0.26), residues: 364 sheet: -2.17 (0.50), residues: 111 loop : -1.16 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 346 HIS 0.005 0.001 HIS B 6 PHE 0.023 0.002 PHE B 385 TYR 0.014 0.001 TYR B 106 ARG 0.015 0.001 ARG B 213 =============================================================================== Job complete usr+sys time: 2055.55 seconds wall clock time: 38 minutes 11.86 seconds (2291.86 seconds total)