Starting phenix.real_space_refine on Tue Feb 13 12:17:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g79_4358/02_2024/6g79_4358_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g79_4358/02_2024/6g79_4358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g79_4358/02_2024/6g79_4358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g79_4358/02_2024/6g79_4358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g79_4358/02_2024/6g79_4358_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g79_4358/02_2024/6g79_4358_updated.pdb" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.016 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 34 5.16 5 C 3922 2.51 5 N 1021 2.21 5 O 1076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "S ARG 308": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6053 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2270 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 359 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 7, 'ASP:plan': 23, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 226 Chain: "G" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 342 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1448 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 4, 'TRANS': 204} Chain breaks: 2 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 6, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 130 Chain: "S" Number of atoms: 1993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1993 Unusual residues: {'EP5': 1} Classifications: {'peptide': 262, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 251, None: 1} Not linked: pdbres="ARG S 385 " pdbres="EP5 S 401 " Chain breaks: 3 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 81 Time building chain proxies: 4.12, per 1000 atoms: 0.68 Number of scatterers: 6053 At special positions: 0 Unit cell: (94.34, 109.18, 97.52, 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 34 16.00 O 1076 8.00 N 1021 7.00 C 3922 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 122 " - pdb=" SG CYS S 199 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.4 seconds 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1634 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 8 sheets defined 43.6% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'B' and resid 4 through 25 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 8 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.600A pdb=" N SER A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 removed outlier: 3.548A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 216 removed outlier: 3.577A pdb=" N ILE A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N CYS A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE A 216 " --> pdb=" O TRP A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 209 through 216' Processing helix chain 'A' and resid 231 through 255 removed outlier: 3.593A pdb=" N LEU A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 281 removed outlier: 3.717A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 332 through 351 Processing helix chain 'S' and resid 46 through 76 Processing helix chain 'S' and resid 83 through 101 removed outlier: 3.846A pdb=" N LEU S 87 " --> pdb=" O PRO S 83 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE S 88 " --> pdb=" O ALA S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 112 removed outlier: 3.967A pdb=" N MET S 108 " --> pdb=" O PRO S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 118 through 152 removed outlier: 3.761A pdb=" N SER S 127 " --> pdb=" O ASP S 123 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU S 140 " --> pdb=" O SER S 136 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS S 141 " --> pdb=" O ILE S 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 155 through 160 removed outlier: 4.201A pdb=" N ALA S 159 " --> pdb=" O VAL S 155 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS S 160 " --> pdb=" O GLU S 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 155 through 160' Processing helix chain 'S' and resid 163 through 181 Processing helix chain 'S' and resid 206 through 215 Processing helix chain 'S' and resid 218 through 239 Processing helix chain 'S' and resid 306 through 336 removed outlier: 3.808A pdb=" N PHE S 323 " --> pdb=" O ILE S 319 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS S 326 " --> pdb=" O ALA S 322 " (cutoff:3.500A) Proline residue: S 329 - end of helix removed outlier: 3.807A pdb=" N LEU S 335 " --> pdb=" O PHE S 331 " (cutoff:3.500A) Processing helix chain 'S' and resid 349 through 372 removed outlier: 3.628A pdb=" N TRP S 356 " --> pdb=" O ASP S 352 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER S 362 " --> pdb=" O GLY S 358 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU S 363 " --> pdb=" O TYR S 359 " (cutoff:3.500A) Proline residue: S 366 - end of helix Processing helix chain 'S' and resid 374 through 383 removed outlier: 3.607A pdb=" N HIS S 381 " --> pdb=" O LYS S 377 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.060A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.500A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.842A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 240 through 243 removed outlier: 3.627A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.722A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 318 through 320 removed outlier: 3.587A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.697A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 197 through 200 removed outlier: 6.742A pdb=" N VAL A 34 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA A 221 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU A 39 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE A 223 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER A 264 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N PHE A 224 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE A 266 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL A 226 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N PHE A 268 " --> pdb=" O VAL A 226 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 936 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: 1.99 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 943 1.29 - 1.42: 1667 1.42 - 1.55: 3482 1.55 - 1.68: 53 1.68 - 1.81: 42 Bond restraints: 6187 Sorted by residual: bond pdb=" C10 EP5 S 401 " pdb=" C7 EP5 S 401 " ideal model delta sigma weight residual 1.421 1.284 0.137 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C15 EP5 S 401 " pdb=" C16 EP5 S 401 " ideal model delta sigma weight residual 1.412 1.476 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" N TYR A 231 " pdb=" CA TYR A 231 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.64e+00 bond pdb=" CA PRO S 183 " pdb=" C PRO S 183 " ideal model delta sigma weight residual 1.517 1.542 -0.025 9.30e-03 1.16e+04 7.21e+00 bond pdb=" C15 EP5 S 401 " pdb=" C20 EP5 S 401 " ideal model delta sigma weight residual 1.432 1.480 -0.048 2.00e-02 2.50e+03 5.74e+00 ... (remaining 6182 not shown) Histogram of bond angle deviations from ideal: 99.88 - 115.10: 3887 115.10 - 130.33: 4562 130.33 - 145.56: 41 145.56 - 160.79: 0 160.79 - 176.02: 1 Bond angle restraints: 8491 Sorted by residual: angle pdb=" N TYR A 231 " pdb=" CA TYR A 231 " pdb=" C TYR A 231 " ideal model delta sigma weight residual 112.90 119.49 -6.59 1.31e+00 5.83e-01 2.53e+01 angle pdb=" N PRO S 183 " pdb=" CA PRO S 183 " pdb=" C PRO S 183 " ideal model delta sigma weight residual 110.70 116.78 -6.08 1.22e+00 6.72e-01 2.48e+01 angle pdb=" CA TYR A 231 " pdb=" CB TYR A 231 " pdb=" CG TYR A 231 " ideal model delta sigma weight residual 113.90 105.57 8.33 1.80e+00 3.09e-01 2.14e+01 angle pdb=" N ILE A 213 " pdb=" CA ILE A 213 " pdb=" C ILE A 213 " ideal model delta sigma weight residual 110.72 115.01 -4.29 1.01e+00 9.80e-01 1.81e+01 angle pdb=" N ASN A 242 " pdb=" CA ASN A 242 " pdb=" C ASN A 242 " ideal model delta sigma weight residual 111.28 106.88 4.40 1.09e+00 8.42e-01 1.63e+01 ... (remaining 8486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 3292 16.39 - 32.77: 191 32.77 - 49.15: 50 49.15 - 65.54: 8 65.54 - 81.92: 2 Dihedral angle restraints: 3543 sinusoidal: 1035 harmonic: 2508 Sorted by residual: dihedral pdb=" C TYR A 231 " pdb=" N TYR A 231 " pdb=" CA TYR A 231 " pdb=" CB TYR A 231 " ideal model delta harmonic sigma weight residual -122.60 -130.65 8.05 0 2.50e+00 1.60e-01 1.04e+01 dihedral pdb=" CA HIS S 347 " pdb=" C HIS S 347 " pdb=" N LEU S 348 " pdb=" CA LEU S 348 " ideal model delta harmonic sigma weight residual -180.00 -164.47 -15.53 0 5.00e+00 4.00e-02 9.64e+00 dihedral pdb=" CA ARG S 308 " pdb=" CB ARG S 308 " pdb=" CG ARG S 308 " pdb=" CD ARG S 308 " ideal model delta sinusoidal sigma weight residual -180.00 -124.25 -55.75 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 3540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 859 0.075 - 0.150: 162 0.150 - 0.225: 30 0.225 - 0.300: 1 0.300 - 0.375: 1 Chirality restraints: 1053 Sorted by residual: chirality pdb=" CA TYR A 231 " pdb=" N TYR A 231 " pdb=" C TYR A 231 " pdb=" CB TYR A 231 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1050 not shown) Planarity restraints: 1051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N EP5 S 401 " 0.004 2.00e-02 2.50e+03 9.37e-02 1.32e+02 pdb=" O EP5 S 401 " -0.120 2.00e-02 2.50e+03 pdb=" C1 EP5 S 401 " 0.117 2.00e-02 2.50e+03 pdb=" C11 EP5 S 401 " -0.007 2.00e-02 2.50e+03 pdb=" C12 EP5 S 401 " 0.114 2.00e-02 2.50e+03 pdb=" C2 EP5 S 401 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 231 " 0.029 2.00e-02 2.50e+03 1.96e-02 7.68e+00 pdb=" CG TYR A 231 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A 231 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 231 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 231 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 231 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 231 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 231 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE S 219 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO S 220 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO S 220 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO S 220 " 0.035 5.00e-02 4.00e+02 ... (remaining 1048 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 2414 2.93 - 3.43: 6113 3.43 - 3.92: 10005 3.92 - 4.41: 11099 4.41 - 4.90: 19058 Nonbonded interactions: 48689 Sorted by model distance: nonbonded pdb=" O ARG A 243 " pdb=" OG SER A 247 " model vdw 2.442 2.440 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.553 2.440 nonbonded pdb=" O PRO S 366 " pdb=" OG1 THR S 370 " model vdw 2.559 2.440 nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.561 2.440 nonbonded pdb=" O ILE S 130 " pdb=" OG1 THR S 134 " model vdw 2.564 2.440 ... (remaining 48684 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: 0.330 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: 1.180 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.250 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 : 0.008 0.137 6187 Z= 0.502 Angle : 1.153 8.494 8491 Z= 0.779 Chirality : 0.060 0.375 1053 Planarity : 0.005 0.094 1051 Dihedral : 12.120 81.922 1906 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.88 % Favored : 94.64 % Rotamer: Outliers : 0.56 % Allowed : 6.15 % Favored : 93.30 % 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: -2.95 (0.24), residues: 840 helix: -0.61 (0.22), residues: 360 sheet: -3.35 (0.27), residues: 164 loop : -2.61 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 149 HIS 0.006 0.001 HIS A 214 PHE 0.015 0.002 PHE A 190 TYR 0.046 0.002 TYR A 231 ARG 0.003 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 189 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 188 MET cc_start: 0.7993 (mmm) cc_final: 0.7060 (mmm) REVERT: B 323 ASP cc_start: 0.8728 (p0) cc_final: 0.8515 (p0) REVERT: B 339 TRP cc_start: 0.8405 (m100) cc_final: 0.8087 (m100) REVERT: G 18 GLN cc_start: 0.9014 (tp40) cc_final: 0.8552 (tp-100) REVERT: A 244 MET cc_start: 0.8375 (tpp) cc_final: 0.7516 (mmt) REVERT: A 305 GLN cc_start: 0.8798 (tt0) cc_final: 0.7820 (tm-30) REVERT: A 312 ASN cc_start: 0.8860 (t0) cc_final: 0.8527 (t0) REVERT: S 169 MET cc_start: 0.8507 (mmm) cc_final: 0.8016 (mmp) REVERT: S 205 HIS cc_start: 0.7891 (m170) cc_final: 0.7681 (m-70) REVERT: S 313 THR cc_start: 0.9124 (m) cc_final: 0.8916 (p) outliers start: 3 outliers final: 1 residues processed: 191 average time/residue: 0.1478 time to fit residues: 38.3452 Evaluate side-chains 115 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 333 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 overall best weight: 2.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 230 ASN B 295 ASN G 18 GLN A 307 GLN S 202 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6187 Z= 0.300 Angle : 0.656 16.672 8491 Z= 0.331 Chirality : 0.042 0.183 1053 Planarity : 0.006 0.077 1051 Dihedral : 6.173 77.697 906 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.55 % Favored : 98.21 % Rotamer: Outliers : 4.28 % Allowed : 15.46 % Favored : 80.26 % 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: -1.04 (0.28), residues: 840 helix: 1.49 (0.25), residues: 378 sheet: -3.03 (0.29), residues: 185 loop : -1.99 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 82 HIS 0.005 0.001 HIS A 214 PHE 0.015 0.002 PHE A 216 TYR 0.013 0.002 TYR B 264 ARG 0.005 0.001 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 0.689 Fit side-chains REVERT: B 219 ARG cc_start: 0.8431 (tpp-160) cc_final: 0.8228 (tpp80) REVERT: B 253 PHE cc_start: 0.8471 (m-80) cc_final: 0.8138 (m-80) REVERT: B 323 ASP cc_start: 0.8804 (p0) cc_final: 0.8596 (p0) REVERT: B 339 TRP cc_start: 0.8706 (m100) cc_final: 0.8158 (m100) REVERT: G 18 GLN cc_start: 0.8783 (tp-100) cc_final: 0.8565 (tp-100) REVERT: A 305 GLN cc_start: 0.8771 (tt0) cc_final: 0.8049 (tm-30) REVERT: A 312 ASN cc_start: 0.8916 (t0) cc_final: 0.8655 (t0) REVERT: A 320 TYR cc_start: 0.8173 (m-80) cc_final: 0.7946 (m-10) REVERT: A 341 ASP cc_start: 0.8235 (t70) cc_final: 0.7980 (t0) REVERT: S 141 CYS cc_start: 0.7691 (p) cc_final: 0.7318 (m) REVERT: S 148 TYR cc_start: 0.8541 (t80) cc_final: 0.8276 (t80) REVERT: S 353 PHE cc_start: 0.8269 (t80) cc_final: 0.8026 (t80) REVERT: S 367 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8449 (pt) outliers start: 23 outliers final: 15 residues processed: 149 average time/residue: 0.1536 time to fit residues: 30.9242 Evaluate side-chains 130 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 231 ILE Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 320 LEU Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 367 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 205 HIS S 365 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6187 Z= 0.184 Angle : 0.565 16.131 8491 Z= 0.276 Chirality : 0.040 0.165 1053 Planarity : 0.005 0.080 1051 Dihedral : 5.607 74.070 906 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.38 % Favored : 97.38 % Rotamer: Outliers : 4.10 % Allowed : 17.88 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.29), residues: 840 helix: 2.01 (0.26), residues: 379 sheet: -2.29 (0.31), residues: 182 loop : -1.67 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.006 0.001 HIS A 214 PHE 0.007 0.001 PHE A 275 TYR 0.012 0.001 TYR B 264 ARG 0.004 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 0.738 Fit side-chains REVERT: B 120 ILE cc_start: 0.8925 (mt) cc_final: 0.8657 (tt) REVERT: B 150 ARG cc_start: 0.8724 (mmt90) cc_final: 0.8197 (mmt-90) REVERT: B 253 PHE cc_start: 0.8399 (m-80) cc_final: 0.8047 (m-80) REVERT: G 18 GLN cc_start: 0.8915 (tp-100) cc_final: 0.8665 (tp-100) REVERT: A 305 GLN cc_start: 0.8775 (tt0) cc_final: 0.8029 (tm-30) REVERT: S 148 TYR cc_start: 0.8498 (t80) cc_final: 0.8208 (t80) REVERT: S 157 TYR cc_start: 0.8600 (t80) cc_final: 0.8119 (t80) outliers start: 22 outliers final: 14 residues processed: 143 average time/residue: 0.1489 time to fit residues: 29.1102 Evaluate side-chains 121 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 320 LEU Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 367 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6187 Z= 0.226 Angle : 0.575 16.186 8491 Z= 0.281 Chirality : 0.040 0.169 1053 Planarity : 0.005 0.087 1051 Dihedral : 5.449 73.727 906 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.38 % Favored : 97.38 % Rotamer: Outliers : 4.28 % Allowed : 21.04 % Favored : 74.67 % 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: 0.08 (0.29), residues: 840 helix: 2.12 (0.26), residues: 381 sheet: -1.78 (0.33), residues: 181 loop : -1.57 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.006 0.001 HIS A 214 PHE 0.010 0.001 PHE B 199 TYR 0.009 0.001 TYR S 369 ARG 0.005 0.001 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 0.700 Fit side-chains REVERT: B 120 ILE cc_start: 0.8902 (mt) cc_final: 0.8650 (tt) REVERT: B 150 ARG cc_start: 0.8738 (mmt90) cc_final: 0.8316 (mmt-90) REVERT: B 253 PHE cc_start: 0.8557 (m-80) cc_final: 0.8126 (m-80) REVERT: G 18 GLN cc_start: 0.8938 (tp-100) cc_final: 0.8688 (tp-100) REVERT: A 305 GLN cc_start: 0.8724 (tt0) cc_final: 0.8149 (tm-30) REVERT: S 148 TYR cc_start: 0.8538 (t80) cc_final: 0.8144 (t80) REVERT: S 157 TYR cc_start: 0.8705 (t80) cc_final: 0.8136 (t80) REVERT: S 210 VAL cc_start: 0.8429 (t) cc_final: 0.8200 (p) REVERT: S 218 TYR cc_start: 0.7791 (m-80) cc_final: 0.7431 (m-80) REVERT: S 238 ARG cc_start: 0.9062 (tpp80) cc_final: 0.8739 (tpp-160) outliers start: 23 outliers final: 15 residues processed: 127 average time/residue: 0.1481 time to fit residues: 25.9918 Evaluate side-chains 119 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 178 ILE Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 320 LEU Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 367 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 50.0000 chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 56 optimal weight: 0.0030 chunk 0 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 72 optimal weight: 0.0770 chunk 20 optimal weight: 6.9990 overall best weight: 0.5750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 205 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6187 Z= 0.135 Angle : 0.525 15.964 8491 Z= 0.254 Chirality : 0.038 0.163 1053 Planarity : 0.005 0.087 1051 Dihedral : 5.209 72.343 906 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.90 % Favored : 97.86 % Rotamer: Outliers : 3.54 % Allowed : 21.60 % Favored : 74.86 % 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: 0.40 (0.29), residues: 840 helix: 2.27 (0.26), residues: 384 sheet: -1.39 (0.35), residues: 182 loop : -1.45 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS A 214 PHE 0.008 0.001 PHE A 200 TYR 0.016 0.001 TYR G 40 ARG 0.006 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 0.757 Fit side-chains REVERT: B 253 PHE cc_start: 0.8470 (m-80) cc_final: 0.8155 (m-80) REVERT: G 18 GLN cc_start: 0.8925 (tp-100) cc_final: 0.8662 (tp-100) REVERT: A 305 GLN cc_start: 0.8655 (tt0) cc_final: 0.8070 (tm-30) REVERT: S 148 TYR cc_start: 0.8477 (t80) cc_final: 0.8108 (t80) REVERT: S 157 TYR cc_start: 0.8628 (t80) cc_final: 0.8089 (t80) REVERT: S 210 VAL cc_start: 0.8370 (t) cc_final: 0.8152 (p) outliers start: 19 outliers final: 12 residues processed: 129 average time/residue: 0.1553 time to fit residues: 27.2994 Evaluate side-chains 124 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain S residue 142 VAL Chi-restraints excluded: chain S residue 178 ILE Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 320 LEU Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 367 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 47 optimal weight: 0.0670 chunk 20 optimal weight: 0.2980 chunk 81 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.0370 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 overall best weight: 1.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6187 Z= 0.173 Angle : 0.538 15.904 8491 Z= 0.259 Chirality : 0.038 0.142 1053 Planarity : 0.005 0.089 1051 Dihedral : 5.238 76.800 906 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.90 % Favored : 97.86 % Rotamer: Outliers : 4.10 % Allowed : 22.91 % Favored : 73.00 % 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: 0.59 (0.29), residues: 840 helix: 2.34 (0.26), residues: 384 sheet: -1.12 (0.36), residues: 179 loop : -1.35 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.008 0.001 HIS S 205 PHE 0.009 0.001 PHE B 199 TYR 0.010 0.001 TYR B 85 ARG 0.004 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 0.650 Fit side-chains REVERT: B 253 PHE cc_start: 0.8572 (m-80) cc_final: 0.8157 (m-80) REVERT: G 18 GLN cc_start: 0.8922 (tp-100) cc_final: 0.8665 (tp-100) REVERT: A 305 GLN cc_start: 0.8651 (tt0) cc_final: 0.8049 (tm-30) REVERT: S 148 TYR cc_start: 0.8485 (t80) cc_final: 0.8104 (t80) REVERT: S 157 TYR cc_start: 0.8687 (t80) cc_final: 0.8195 (t80) REVERT: S 316 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8583 (mp) outliers start: 22 outliers final: 17 residues processed: 124 average time/residue: 0.1503 time to fit residues: 25.4276 Evaluate side-chains 129 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 142 VAL Chi-restraints excluded: chain S residue 178 ILE Chi-restraints excluded: chain S residue 316 LEU Chi-restraints excluded: chain S residue 320 LEU Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 364 ILE Chi-restraints excluded: chain S residue 367 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 37 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6187 Z= 0.148 Angle : 0.520 15.555 8491 Z= 0.253 Chirality : 0.038 0.186 1053 Planarity : 0.005 0.091 1051 Dihedral : 5.143 75.138 906 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.79 % Favored : 97.98 % Rotamer: Outliers : 3.91 % Allowed : 24.02 % Favored : 72.07 % 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: 0.76 (0.29), residues: 840 helix: 2.48 (0.26), residues: 385 sheet: -0.97 (0.37), residues: 177 loop : -1.34 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS S 205 PHE 0.008 0.001 PHE B 199 TYR 0.008 0.001 TYR B 85 ARG 0.006 0.001 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.668 Fit side-chains REVERT: B 105 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.8192 (t80) REVERT: B 230 ASN cc_start: 0.8786 (m-40) cc_final: 0.8498 (t0) REVERT: B 253 PHE cc_start: 0.8550 (m-80) cc_final: 0.8157 (m-80) REVERT: G 18 GLN cc_start: 0.8914 (tp-100) cc_final: 0.8659 (tp-100) REVERT: A 305 GLN cc_start: 0.8618 (tt0) cc_final: 0.8044 (tm-30) REVERT: S 157 TYR cc_start: 0.8611 (t80) cc_final: 0.8181 (t80) REVERT: S 238 ARG cc_start: 0.8604 (tpp-160) cc_final: 0.8388 (tpp-160) REVERT: S 316 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8548 (mp) REVERT: S 359 TYR cc_start: 0.8911 (m-10) cc_final: 0.8642 (m-10) outliers start: 21 outliers final: 17 residues processed: 130 average time/residue: 0.1430 time to fit residues: 25.7042 Evaluate side-chains 129 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 142 VAL Chi-restraints excluded: chain S residue 178 ILE Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 316 LEU Chi-restraints excluded: chain S residue 320 LEU Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 367 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6187 Z= 0.343 Angle : 0.631 15.807 8491 Z= 0.316 Chirality : 0.041 0.198 1053 Planarity : 0.005 0.091 1051 Dihedral : 5.470 76.840 904 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.62 % Favored : 97.14 % Rotamer: Outliers : 4.66 % Allowed : 23.46 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.30), residues: 840 helix: 2.15 (0.26), residues: 390 sheet: -1.09 (0.38), residues: 179 loop : -1.39 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.008 0.002 HIS B 311 PHE 0.014 0.002 PHE A 197 TYR 0.012 0.002 TYR B 111 ARG 0.004 0.001 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 0.780 Fit side-chains REVERT: B 58 ILE cc_start: 0.8917 (mt) cc_final: 0.8417 (tt) REVERT: B 105 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.8281 (t80) REVERT: B 120 ILE cc_start: 0.8922 (mt) cc_final: 0.8717 (tt) REVERT: G 18 GLN cc_start: 0.8993 (tp-100) cc_final: 0.8725 (tp-100) REVERT: A 305 GLN cc_start: 0.8630 (tt0) cc_final: 0.8047 (tm-30) REVERT: S 141 CYS cc_start: 0.7870 (p) cc_final: 0.7661 (m) REVERT: S 157 TYR cc_start: 0.8746 (t80) cc_final: 0.8319 (t80) REVERT: S 316 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8662 (mp) outliers start: 25 outliers final: 20 residues processed: 127 average time/residue: 0.1635 time to fit residues: 28.3025 Evaluate side-chains 134 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 142 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 178 ILE Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain S residue 205 HIS Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 316 LEU Chi-restraints excluded: chain S residue 320 LEU Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 355 THR Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 367 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 0.0670 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6187 Z= 0.156 Angle : 0.532 14.889 8491 Z= 0.261 Chirality : 0.038 0.206 1053 Planarity : 0.005 0.092 1051 Dihedral : 5.227 73.907 904 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.67 % Favored : 98.10 % Rotamer: Outliers : 4.28 % Allowed : 24.58 % Favored : 71.14 % 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: 0.76 (0.30), residues: 840 helix: 2.39 (0.26), residues: 389 sheet: -0.92 (0.37), residues: 176 loop : -1.28 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.007 0.001 HIS A 214 PHE 0.014 0.001 PHE S 176 TYR 0.007 0.001 TYR B 85 ARG 0.006 0.001 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 0.712 Fit side-chains REVERT: B 105 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.8074 (t80) REVERT: B 230 ASN cc_start: 0.8815 (m-40) cc_final: 0.8543 (t0) REVERT: B 296 VAL cc_start: 0.8890 (t) cc_final: 0.8686 (m) REVERT: G 18 GLN cc_start: 0.8907 (tp-100) cc_final: 0.8650 (tp-100) REVERT: A 305 GLN cc_start: 0.8624 (tt0) cc_final: 0.8030 (tm-30) REVERT: S 157 TYR cc_start: 0.8701 (t80) cc_final: 0.8264 (t80) REVERT: S 238 ARG cc_start: 0.8826 (tpp-160) cc_final: 0.8591 (tpp-160) outliers start: 23 outliers final: 21 residues processed: 134 average time/residue: 0.1512 time to fit residues: 27.7529 Evaluate side-chains 140 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 142 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 178 ILE Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 320 LEU Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 367 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6187 Z= 0.290 Angle : 0.594 14.875 8491 Z= 0.296 Chirality : 0.040 0.188 1053 Planarity : 0.005 0.090 1051 Dihedral : 5.474 75.927 904 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.98 % Favored : 96.79 % Rotamer: Outliers : 4.28 % Allowed : 25.88 % Favored : 69.83 % 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: 0.65 (0.30), residues: 840 helix: 2.33 (0.26), residues: 383 sheet: -0.97 (0.38), residues: 176 loop : -1.32 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.007 0.001 HIS A 214 PHE 0.025 0.002 PHE B 253 TYR 0.010 0.002 TYR B 59 ARG 0.006 0.001 ARG A 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 0.713 Fit side-chains REVERT: B 58 ILE cc_start: 0.8870 (mt) cc_final: 0.8322 (tt) REVERT: B 105 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.8225 (t80) REVERT: G 18 GLN cc_start: 0.8961 (tp-100) cc_final: 0.8698 (tp-100) REVERT: A 305 GLN cc_start: 0.8633 (tt0) cc_final: 0.8070 (tm-30) REVERT: S 141 CYS cc_start: 0.7881 (p) cc_final: 0.7649 (m) REVERT: S 157 TYR cc_start: 0.8765 (t80) cc_final: 0.8323 (t80) outliers start: 23 outliers final: 20 residues processed: 130 average time/residue: 0.1608 time to fit residues: 28.5812 Evaluate side-chains 132 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 142 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 178 ILE Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 320 LEU Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 367 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.0970 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.129810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110321 restraints weight = 11050.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.113215 restraints weight = 6504.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.115187 restraints weight = 4604.147| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6187 Z= 0.151 Angle : 0.535 13.899 8491 Z= 0.265 Chirality : 0.038 0.169 1053 Planarity : 0.005 0.092 1051 Dihedral : 5.244 74.179 904 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.67 % Favored : 98.10 % Rotamer: Outliers : 3.72 % Allowed : 26.63 % Favored : 69.65 % 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: 0.83 (0.30), residues: 840 helix: 2.49 (0.26), residues: 384 sheet: -0.78 (0.39), residues: 165 loop : -1.35 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 214 PHE 0.023 0.001 PHE A 308 TYR 0.007 0.001 TYR B 289 ARG 0.006 0.001 ARG A 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1457.40 seconds wall clock time: 27 minutes 25.35 seconds (1645.35 seconds total)