Starting phenix.real_space_refine on Fri Nov 15 19:35:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6q_36011/11_2024/8j6q_36011.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6q_36011/11_2024/8j6q_36011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6q_36011/11_2024/8j6q_36011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6q_36011/11_2024/8j6q_36011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6q_36011/11_2024/8j6q_36011.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6q_36011/11_2024/8j6q_36011.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 69 5.16 5 C 5876 2.51 5 N 1554 2.21 5 O 1688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9187 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1795 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2420 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 284} Chain: "R" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 110 Unusual residues: {'3HR': 1, 'CLR': 2, 'IX8': 1, 'NAG': 1} Classifications: {'undetermined': 5, 'water': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.01, per 1000 atoms: 0.65 Number of scatterers: 9187 At special positions: 0 Unit cell: (106.02, 119.04, 113.46, 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 69 16.00 O 1688 8.00 N 1554 7.00 C 5876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R 405 " - " ASN R 17 " Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 1.4 seconds 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 38.3% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.616A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.335A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.034A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.607A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.526A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.098A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 220 through 224 Processing helix chain 'R' and resid 23 through 54 removed outlier: 3.877A pdb=" N VAL R 27 " --> pdb=" O ASP R 23 " (cutoff:3.500A) Proline residue: R 31 - end of helix Processing helix chain 'R' and resid 60 through 78 Processing helix chain 'R' and resid 79 through 89 removed outlier: 3.671A pdb=" N LEU R 83 " --> pdb=" O CYS R 79 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG R 89 " --> pdb=" O ASP R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 130 removed outlier: 3.728A pdb=" N CYS R 100 " --> pdb=" O GLY R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 139 removed outlier: 3.661A pdb=" N ILE R 139 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 160 Processing helix chain 'R' and resid 161 through 165 removed outlier: 3.672A pdb=" N LYS R 164 " --> pdb=" O HIS R 161 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS R 165 " --> pdb=" O LEU R 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 161 through 165' Processing helix chain 'R' and resid 170 through 174 removed outlier: 4.031A pdb=" N GLY R 173 " --> pdb=" O GLN R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 218 removed outlier: 3.523A pdb=" N ALA R 191 " --> pdb=" O GLN R 187 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 219 through 222 removed outlier: 3.644A pdb=" N ARG R 222 " --> pdb=" O GLN R 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 219 through 222' Processing helix chain 'R' and resid 223 through 261 Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 265 through 267 No H-bonds generated for 'chain 'R' and resid 265 through 267' Processing helix chain 'R' and resid 268 through 295 removed outlier: 4.461A pdb=" N VAL R 272 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR R 283 " --> pdb=" O THR R 279 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 5.945A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.455A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.787A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.836A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.518A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.657A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.672A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.547A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 5.958A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.860A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.525A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 10 through 12 448 hydrogen bonds defined for protein. 1242 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: 3.21 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1985 1.33 - 1.46: 2469 1.46 - 1.58: 4837 1.58 - 1.71: 1 1.71 - 1.83: 100 Bond restraints: 9392 Sorted by residual: bond pdb=" C2 IX8 R 401 " pdb=" C25 IX8 R 401 " ideal model delta sigma weight residual 1.522 1.649 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C4 IX8 R 401 " pdb=" N3 IX8 R 401 " ideal model delta sigma weight residual 1.341 1.442 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C2 IX8 R 401 " pdb=" N3 IX8 R 401 " ideal model delta sigma weight residual 1.451 1.538 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C15 IX8 R 401 " pdb=" C16 IX8 R 401 " ideal model delta sigma weight residual 1.460 1.545 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C11 IX8 R 401 " pdb=" N10 IX8 R 401 " ideal model delta sigma weight residual 1.359 1.442 -0.083 2.00e-02 2.50e+03 1.74e+01 ... (remaining 9387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 12443 2.00 - 4.00: 207 4.00 - 6.00: 53 6.00 - 8.01: 12 8.01 - 10.01: 4 Bond angle restraints: 12719 Sorted by residual: angle pdb=" N CYS R 18 " pdb=" CA CYS R 18 " pdb=" C CYS R 18 " ideal model delta sigma weight residual 108.24 113.37 -5.13 1.32e+00 5.74e-01 1.51e+01 angle pdb=" N VAL S 64 " pdb=" CA VAL S 64 " pdb=" C VAL S 64 " ideal model delta sigma weight residual 113.20 109.70 3.50 9.60e-01 1.09e+00 1.33e+01 angle pdb=" C ASP S 73 " pdb=" N ASP S 74 " pdb=" CA ASP S 74 " ideal model delta sigma weight residual 120.06 124.17 -4.11 1.19e+00 7.06e-01 1.19e+01 angle pdb=" CA GLN R 170 " pdb=" CB GLN R 170 " pdb=" CG GLN R 170 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" N GLU A 25 " pdb=" CA GLU A 25 " pdb=" CB GLU A 25 " ideal model delta sigma weight residual 110.28 115.52 -5.24 1.55e+00 4.16e-01 1.14e+01 ... (remaining 12714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5174 17.82 - 35.64: 422 35.64 - 53.46: 55 53.46 - 71.28: 21 71.28 - 89.10: 6 Dihedral angle restraints: 5678 sinusoidal: 2343 harmonic: 3335 Sorted by residual: dihedral pdb=" CB CYS R 18 " pdb=" SG CYS R 18 " pdb=" SG CYS R 183 " pdb=" CB CYS R 183 " ideal model delta sinusoidal sigma weight residual 93.00 52.96 40.04 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.88 18.12 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 5675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1322 0.089 - 0.179: 101 0.179 - 0.268: 6 0.268 - 0.357: 0 0.357 - 0.446: 1 Chirality restraints: 1430 Sorted by residual: chirality pdb=" C2 IX8 R 401 " pdb=" C1 IX8 R 401 " pdb=" C25 IX8 R 401 " pdb=" N3 IX8 R 401 " both_signs ideal model delta sigma weight residual False 2.42 2.86 -0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" C3 3HR R 403 " pdb=" C2 3HR R 403 " pdb=" C4 3HR R 403 " pdb=" O2 3HR R 403 " both_signs ideal model delta sigma weight residual False -2.33 -2.58 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C13 CLR R 402 " pdb=" C12 CLR R 402 " pdb=" C14 CLR R 402 " pdb=" C17 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.93 -2.73 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1427 not shown) Planarity restraints: 1596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.049 5.00e-02 4.00e+02 7.45e-02 8.87e+00 pdb=" N PRO S 75 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO B 236 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 38 " 0.006 2.00e-02 2.50e+03 1.36e-02 3.23e+00 pdb=" CG PHE R 38 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE R 38 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE R 38 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE R 38 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 38 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE R 38 " 0.001 2.00e-02 2.50e+03 ... (remaining 1593 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 534 2.73 - 3.27: 8950 3.27 - 3.82: 16278 3.82 - 4.36: 20262 4.36 - 4.90: 34023 Nonbonded interactions: 80047 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 175 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.206 3.040 nonbonded pdb=" OD1 ASN A 269 " pdb=" OG1 THR A 324 " model vdw 2.230 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.230 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.266 3.040 ... (remaining 80042 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.820 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 9392 Z= 0.281 Angle : 0.695 10.008 12719 Z= 0.355 Chirality : 0.048 0.446 1430 Planarity : 0.004 0.074 1595 Dihedral : 13.239 89.104 3507 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 (0.25), residues: 1137 helix: 1.12 (0.26), residues: 384 sheet: 0.12 (0.30), residues: 283 loop : -0.23 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.028 0.002 PHE R 38 TYR 0.025 0.002 TYR S 190 ARG 0.005 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.073 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 1.3693 time to fit residues: 231.2661 Evaluate side-chains 142 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 269 ASN A 331 ASN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9392 Z= 0.218 Angle : 0.544 8.350 12719 Z= 0.294 Chirality : 0.042 0.190 1430 Planarity : 0.004 0.066 1595 Dihedral : 7.049 89.157 1415 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.31 % Allowed : 8.74 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.70 (0.25), residues: 1137 helix: 1.71 (0.27), residues: 381 sheet: 0.04 (0.30), residues: 279 loop : -0.20 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.003 0.001 HIS R 189 PHE 0.013 0.001 PHE R 38 TYR 0.025 0.002 TYR S 190 ARG 0.004 0.000 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.012 Fit side-chains REVERT: B 96 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7475 (mtt-85) REVERT: B 217 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.6866 (pp-130) REVERT: G 36 ASP cc_start: 0.8168 (m-30) cc_final: 0.7916 (m-30) REVERT: R 102 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7253 (mm) REVERT: R 110 ASN cc_start: 0.8466 (m110) cc_final: 0.8261 (m110) outliers start: 13 outliers final: 2 residues processed: 148 average time/residue: 1.4724 time to fit residues: 230.9681 Evaluate side-chains 139 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain R residue 102 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 268 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9392 Z= 0.198 Angle : 0.514 7.173 12719 Z= 0.279 Chirality : 0.042 0.183 1430 Planarity : 0.004 0.064 1595 Dihedral : 6.460 82.203 1415 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.11 % Allowed : 12.26 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.77 (0.26), residues: 1137 helix: 1.92 (0.27), residues: 381 sheet: -0.07 (0.29), residues: 290 loop : -0.20 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.003 0.001 HIS R 189 PHE 0.010 0.001 PHE A 189 TYR 0.025 0.001 TYR S 190 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 1.125 Fit side-chains REVERT: G 36 ASP cc_start: 0.8172 (m-30) cc_final: 0.7891 (m-30) REVERT: R 102 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7309 (mm) REVERT: R 253 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.6947 (tpm170) outliers start: 11 outliers final: 3 residues processed: 147 average time/residue: 1.3574 time to fit residues: 212.6518 Evaluate side-chains 134 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 253 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 0.1980 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 0.0980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 268 ASN B 340 ASN S 186 GLN R 219 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9392 Z= 0.178 Angle : 0.500 7.140 12719 Z= 0.271 Chirality : 0.041 0.177 1430 Planarity : 0.004 0.061 1595 Dihedral : 6.172 76.461 1415 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.51 % Allowed : 13.57 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.82 (0.26), residues: 1137 helix: 2.01 (0.27), residues: 381 sheet: -0.18 (0.29), residues: 281 loop : -0.11 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS R 189 PHE 0.021 0.001 PHE R 38 TYR 0.024 0.001 TYR S 190 ARG 0.005 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 1.080 Fit side-chains REVERT: G 36 ASP cc_start: 0.8176 (m-30) cc_final: 0.7912 (m-30) REVERT: R 42 LEU cc_start: 0.8212 (tp) cc_final: 0.7975 (tp) REVERT: R 253 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.6878 (tpm170) outliers start: 15 outliers final: 6 residues processed: 144 average time/residue: 1.4052 time to fit residues: 215.2426 Evaluate side-chains 137 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain R residue 253 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 268 ASN B 340 ASN S 186 GLN R 189 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9392 Z= 0.405 Angle : 0.638 8.560 12719 Z= 0.340 Chirality : 0.047 0.223 1430 Planarity : 0.005 0.064 1595 Dihedral : 6.677 72.736 1415 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.91 % Allowed : 13.87 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1137 helix: 1.73 (0.27), residues: 378 sheet: -0.15 (0.29), residues: 291 loop : -0.24 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.008 0.001 HIS R 189 PHE 0.018 0.002 PHE R 38 TYR 0.026 0.002 TYR S 190 ARG 0.017 0.001 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.101 Fit side-chains REVERT: A 306 GLN cc_start: 0.8218 (mm110) cc_final: 0.7908 (mm-40) REVERT: B 259 GLN cc_start: 0.8151 (tt0) cc_final: 0.7832 (tt0) REVERT: B 325 MET cc_start: 0.8630 (tpp) cc_final: 0.8285 (tpt) REVERT: G 36 ASP cc_start: 0.8264 (m-30) cc_final: 0.7923 (m-30) REVERT: S 89 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6567 (pp20) REVERT: R 102 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7363 (mm) REVERT: R 126 TYR cc_start: 0.8833 (t80) cc_final: 0.8624 (t80) REVERT: R 232 PHE cc_start: 0.8108 (m-80) cc_final: 0.7868 (m-80) REVERT: R 253 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.6732 (tpm170) outliers start: 19 outliers final: 7 residues processed: 145 average time/residue: 1.5499 time to fit residues: 237.6491 Evaluate side-chains 143 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 287 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 268 ASN B 340 ASN ** S 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9392 Z= 0.182 Angle : 0.508 7.118 12719 Z= 0.275 Chirality : 0.041 0.175 1430 Planarity : 0.004 0.062 1595 Dihedral : 6.036 66.704 1415 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.71 % Allowed : 14.67 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.80 (0.26), residues: 1137 helix: 1.97 (0.27), residues: 379 sheet: -0.18 (0.29), residues: 281 loop : -0.09 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.002 0.001 HIS B 91 PHE 0.025 0.001 PHE R 38 TYR 0.024 0.001 TYR S 190 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 1.094 Fit side-chains REVERT: B 226 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7244 (mt-10) REVERT: B 325 MET cc_start: 0.8549 (tpp) cc_final: 0.8205 (tpt) REVERT: G 36 ASP cc_start: 0.8211 (m-30) cc_final: 0.7869 (m-30) REVERT: R 42 LEU cc_start: 0.8138 (tp) cc_final: 0.7931 (tp) REVERT: R 102 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7341 (mm) REVERT: R 253 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.6873 (tpm170) outliers start: 17 outliers final: 6 residues processed: 145 average time/residue: 1.4630 time to fit residues: 224.8727 Evaluate side-chains 140 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 222 ARG Chi-restraints excluded: chain R residue 253 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 6.9990 chunk 61 optimal weight: 0.0060 chunk 79 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.0370 overall best weight: 0.4274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 75 GLN B 268 ASN B 340 ASN ** S 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9392 Z= 0.159 Angle : 0.496 7.074 12719 Z= 0.270 Chirality : 0.041 0.170 1430 Planarity : 0.004 0.061 1595 Dihedral : 5.794 62.114 1415 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.11 % Allowed : 15.28 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.89 (0.26), residues: 1137 helix: 2.08 (0.27), residues: 380 sheet: -0.17 (0.29), residues: 278 loop : -0.05 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS S 35 PHE 0.018 0.001 PHE R 38 TYR 0.024 0.001 TYR S 190 ARG 0.007 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 1.029 Fit side-chains REVERT: A 318 GLU cc_start: 0.6140 (tm-30) cc_final: 0.5821 (tt0) REVERT: B 259 GLN cc_start: 0.7728 (tt0) cc_final: 0.7406 (tt0) REVERT: G 21 MET cc_start: 0.5990 (ttt) cc_final: 0.5218 (ttt) REVERT: G 36 ASP cc_start: 0.8072 (m-30) cc_final: 0.7829 (m-30) REVERT: R 42 LEU cc_start: 0.8162 (tp) cc_final: 0.7937 (tp) REVERT: R 253 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.6860 (tpm170) outliers start: 11 outliers final: 4 residues processed: 147 average time/residue: 1.4337 time to fit residues: 223.9059 Evaluate side-chains 135 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 253 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN B 340 ASN S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9392 Z= 0.234 Angle : 0.543 7.119 12719 Z= 0.293 Chirality : 0.042 0.187 1430 Planarity : 0.004 0.062 1595 Dihedral : 5.937 60.440 1415 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.51 % Allowed : 15.68 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.79 (0.26), residues: 1137 helix: 1.97 (0.27), residues: 380 sheet: -0.30 (0.29), residues: 285 loop : -0.03 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.029 0.001 PHE R 38 TYR 0.025 0.001 TYR S 190 ARG 0.006 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 1.096 Fit side-chains REVERT: A 4 THR cc_start: 0.7088 (OUTLIER) cc_final: 0.6730 (m) REVERT: A 318 GLU cc_start: 0.6390 (tm-30) cc_final: 0.6060 (tt0) REVERT: B 226 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7239 (mt-10) REVERT: B 259 GLN cc_start: 0.7922 (tt0) cc_final: 0.7619 (tt0) REVERT: G 21 MET cc_start: 0.6206 (ttt) cc_final: 0.5513 (ttt) REVERT: G 36 ASP cc_start: 0.8216 (m-30) cc_final: 0.7940 (m-30) REVERT: R 102 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7404 (mm) REVERT: R 253 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.6933 (tpm170) outliers start: 15 outliers final: 5 residues processed: 144 average time/residue: 1.4844 time to fit residues: 226.3232 Evaluate side-chains 141 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 253 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN B 340 ASN S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9392 Z= 0.212 Angle : 0.540 10.747 12719 Z= 0.289 Chirality : 0.042 0.173 1430 Planarity : 0.004 0.062 1595 Dihedral : 6.147 59.555 1415 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.51 % Allowed : 16.18 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.82 (0.26), residues: 1137 helix: 2.01 (0.26), residues: 380 sheet: -0.29 (0.29), residues: 283 loop : -0.03 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS S 35 PHE 0.027 0.001 PHE R 38 TYR 0.023 0.001 TYR S 190 ARG 0.007 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 1.136 Fit side-chains REVERT: A 4 THR cc_start: 0.6968 (OUTLIER) cc_final: 0.6702 (m) REVERT: A 318 GLU cc_start: 0.6315 (tm-30) cc_final: 0.5979 (tt0) REVERT: B 226 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7274 (mt-10) REVERT: B 259 GLN cc_start: 0.7976 (tt0) cc_final: 0.7646 (tt0) REVERT: B 325 MET cc_start: 0.8566 (tpp) cc_final: 0.8219 (tpt) REVERT: G 36 ASP cc_start: 0.8127 (m-30) cc_final: 0.7834 (m-30) REVERT: R 102 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7400 (mm) REVERT: R 253 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.6927 (tpm170) outliers start: 15 outliers final: 7 residues processed: 143 average time/residue: 1.4902 time to fit residues: 227.9977 Evaluate side-chains 142 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 287 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN B 340 ASN ** S 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9392 Z= 0.219 Angle : 0.540 9.118 12719 Z= 0.290 Chirality : 0.042 0.177 1430 Planarity : 0.004 0.061 1595 Dihedral : 5.983 59.704 1415 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.21 % Allowed : 16.58 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.82 (0.26), residues: 1137 helix: 2.01 (0.27), residues: 380 sheet: -0.31 (0.30), residues: 287 loop : 0.00 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 PHE 0.024 0.001 PHE R 38 TYR 0.024 0.001 TYR S 190 ARG 0.007 0.000 ARG G 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 1.067 Fit side-chains REVERT: A 4 THR cc_start: 0.6947 (t) cc_final: 0.6687 (m) REVERT: A 318 GLU cc_start: 0.6355 (tm-30) cc_final: 0.6022 (tt0) REVERT: B 226 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7267 (mt-10) REVERT: B 259 GLN cc_start: 0.7947 (tt0) cc_final: 0.7606 (tt0) REVERT: G 36 ASP cc_start: 0.8216 (m-30) cc_final: 0.7866 (m-30) REVERT: R 102 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7389 (mm) REVERT: R 253 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.6925 (tpm170) outliers start: 12 outliers final: 8 residues processed: 144 average time/residue: 1.3955 time to fit residues: 213.7264 Evaluate side-chains 144 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 253 ARG Chi-restraints excluded: chain R residue 287 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.1980 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN B 340 ASN S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.160339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.121676 restraints weight = 9133.940| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.88 r_work: 0.3054 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9392 Z= 0.202 Angle : 0.532 8.542 12719 Z= 0.286 Chirality : 0.042 0.177 1430 Planarity : 0.004 0.061 1595 Dihedral : 5.868 59.479 1415 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.31 % Allowed : 16.68 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.87 (0.26), residues: 1137 helix: 2.06 (0.27), residues: 379 sheet: -0.26 (0.30), residues: 285 loop : 0.00 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS S 35 PHE 0.024 0.001 PHE R 38 TYR 0.024 0.001 TYR S 190 ARG 0.005 0.000 ARG B 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4107.11 seconds wall clock time: 74 minutes 16.20 seconds (4456.20 seconds total)