Starting phenix.real_space_refine on Tue Sep 24 21:25:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gur_34277/09_2024/8gur_34277_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gur_34277/09_2024/8gur_34277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gur_34277/09_2024/8gur_34277.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gur_34277/09_2024/8gur_34277.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gur_34277/09_2024/8gur_34277_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gur_34277/09_2024/8gur_34277_neut.cif" } resolution = 2.84 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= 0.001 sd= 0.022 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 66 5.16 5 C 5656 2.51 5 N 1505 2.21 5 O 1661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8888 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1827 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 2, 'TRANS': 224} 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: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2188 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 11, 'TRANS': 270} Chain breaks: 1 Chain: "S" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1794 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'9GF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.35, per 1000 atoms: 0.60 Number of scatterers: 8888 At special positions: 0 Unit cell: (93.6, 115.44, 126.88, 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 66 16.00 O 1661 8.00 N 1505 7.00 C 5656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 179 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.1 seconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 38.8% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.916A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 205 removed outlier: 4.284A pdb=" N ARG A 205 " --> pdb=" O GLY A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.224A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.790A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.860A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.666A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.545A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.701A pdb=" N ARG C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'R' and resid 22 through 27 Processing helix chain 'R' and resid 31 through 62 removed outlier: 4.295A pdb=" N ALA R 35 " --> pdb=" O PRO R 31 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N HIS R 62 " --> pdb=" O ILE R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 66 Processing helix chain 'R' and resid 67 through 95 Processing helix chain 'R' and resid 102 through 137 removed outlier: 4.073A pdb=" N LEU R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 172 removed outlier: 3.840A pdb=" N LEU R 151 " --> pdb=" O ARG R 147 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL R 152 " --> pdb=" O GLY R 148 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 187 through 225 removed outlier: 3.502A pdb=" N LEU R 192 " --> pdb=" O ASN R 188 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR R 209 " --> pdb=" O ILE R 205 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY R 210 " --> pdb=" O ILE R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 258 Processing helix chain 'R' and resid 258 through 269 removed outlier: 3.700A pdb=" N LEU R 269 " --> pdb=" O MET R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 285 Processing helix chain 'R' and resid 285 through 300 removed outlier: 4.137A pdb=" N LEU R 289 " --> pdb=" O SER R 285 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 303 through 312 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.879A 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 sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.946A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.005A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.555A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.513A 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: 6.693A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.293A 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: 4.297A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.207A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.612A 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: 6.409A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.080A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.569A 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: 6.848A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.014A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 137 removed outlier: 5.800A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN S 182 " --> pdb=" O TYR S 178 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2858 1.34 - 1.46: 2129 1.46 - 1.58: 3988 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 9071 Sorted by residual: bond pdb=" CAV 9GF R 401 " pdb=" CAW 9GF R 401 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.00e-02 2.50e+03 1.09e+00 bond pdb=" CAD 9GF R 401 " pdb=" CAE 9GF R 401 " ideal model delta sigma weight residual 1.531 1.510 0.021 2.00e-02 2.50e+03 1.06e+00 bond pdb=" CAB 9GF R 401 " pdb=" CAC 9GF R 401 " ideal model delta sigma weight residual 1.527 1.507 0.020 2.00e-02 2.50e+03 9.82e-01 bond pdb=" CAC 9GF R 401 " pdb=" CAD 9GF R 401 " ideal model delta sigma weight residual 1.528 1.509 0.019 2.00e-02 2.50e+03 9.07e-01 bond pdb=" CAA 9GF R 401 " pdb=" CAB 9GF R 401 " ideal model delta sigma weight residual 1.526 1.508 0.018 2.00e-02 2.50e+03 8.10e-01 ... (remaining 9066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 12035 1.45 - 2.91: 195 2.91 - 4.36: 34 4.36 - 5.82: 11 5.82 - 7.27: 6 Bond angle restraints: 12281 Sorted by residual: angle pdb=" C CYS A 3 " pdb=" N THR A 4 " pdb=" CA THR A 4 " ideal model delta sigma weight residual 121.54 126.07 -4.53 1.91e+00 2.74e-01 5.63e+00 angle pdb=" CA TYR S 178 " pdb=" CB TYR S 178 " pdb=" CG TYR S 178 " ideal model delta sigma weight residual 113.90 117.82 -3.92 1.80e+00 3.09e-01 4.73e+00 angle pdb=" CA LEU R 46 " pdb=" CB LEU R 46 " pdb=" CG LEU R 46 " ideal model delta sigma weight residual 116.30 123.57 -7.27 3.50e+00 8.16e-02 4.31e+00 angle pdb=" C MET S 180 " pdb=" N SER S 181 " pdb=" CA SER S 181 " ideal model delta sigma weight residual 123.47 126.58 -3.11 1.53e+00 4.27e-01 4.13e+00 angle pdb=" CA LEU R 71 " pdb=" CB LEU R 71 " pdb=" CG LEU R 71 " ideal model delta sigma weight residual 116.30 123.38 -7.08 3.50e+00 8.16e-02 4.09e+00 ... (remaining 12276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.23: 5282 30.23 - 60.46: 115 60.46 - 90.69: 11 90.69 - 120.92: 3 120.92 - 151.15: 3 Dihedral angle restraints: 5414 sinusoidal: 2117 harmonic: 3297 Sorted by residual: dihedral pdb=" CB CYS R 174 " pdb=" SG CYS R 174 " pdb=" SG CYS R 179 " pdb=" CB CYS R 179 " ideal model delta sinusoidal sigma weight residual -86.00 -144.62 58.62 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CA ARG S 179 " pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta harmonic sigma weight residual -180.00 -147.40 -32.60 0 5.00e+00 4.00e-02 4.25e+01 dihedral pdb=" CAD 9GF R 401 " pdb=" CAE 9GF R 401 " pdb=" CAF 9GF R 401 " pdb=" CAG 9GF R 401 " ideal model delta sinusoidal sigma weight residual -62.05 89.10 -151.15 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 5411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 929 0.033 - 0.066: 330 0.066 - 0.100: 88 0.100 - 0.133: 50 0.133 - 0.166: 3 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CG LEU R 43 " pdb=" CB LEU R 43 " pdb=" CD1 LEU R 43 " pdb=" CD2 LEU R 43 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CB THR S 160 " pdb=" CA THR S 160 " pdb=" OG1 THR S 160 " pdb=" CG2 THR S 160 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 1397 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR S 178 " -0.011 2.00e-02 2.50e+03 9.22e-03 1.70e+00 pdb=" CG TYR S 178 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR S 178 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR S 178 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR S 178 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR S 178 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR S 178 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR S 178 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 137 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.64e+00 pdb=" N PRO R 138 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO R 138 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 138 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 295 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO R 296 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO R 296 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 296 " 0.017 5.00e-02 4.00e+02 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 168 2.69 - 3.24: 8522 3.24 - 3.79: 14083 3.79 - 4.35: 19070 4.35 - 4.90: 31751 Nonbonded interactions: 73594 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.131 3.040 nonbonded pdb=" OH TYR R 70 " pdb=" OG SER R 303 " model vdw 2.139 3.040 nonbonded pdb=" NH1 ARG B 49 " pdb=" O TYR B 85 " model vdw 2.211 3.120 nonbonded pdb=" O CYS A 254 " pdb=" NZ LYS A 317 " model vdw 2.232 3.120 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.235 3.040 ... (remaining 73589 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: 1.520 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.210 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 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 : 0.002 0.027 9071 Z= 0.160 Angle : 0.502 7.270 12281 Z= 0.253 Chirality : 0.040 0.166 1400 Planarity : 0.003 0.038 1544 Dihedral : 13.745 151.154 3279 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.31 (0.25), residues: 1123 helix: 1.29 (0.26), residues: 391 sheet: -0.19 (0.30), residues: 296 loop : -0.37 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 211 HIS 0.003 0.001 HIS A 195 PHE 0.014 0.001 PHE R 117 TYR 0.023 0.001 TYR S 178 ARG 0.013 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.321 Fit side-chains REVERT: A 209 LYS cc_start: 0.7656 (pttm) cc_final: 0.7435 (pttm) REVERT: A 309 ASP cc_start: 0.7071 (t70) cc_final: 0.6684 (t0) REVERT: B 6 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7847 (tm-30) REVERT: B 13 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7155 (tm-30) REVERT: B 14 LEU cc_start: 0.8239 (mt) cc_final: 0.7867 (mt) REVERT: B 254 ASP cc_start: 0.7318 (p0) cc_final: 0.7051 (p0) REVERT: R 132 TYR cc_start: 0.7584 (t80) cc_final: 0.7239 (t80) REVERT: R 157 MET cc_start: 0.7218 (tmm) cc_final: 0.6792 (tmm) REVERT: R 237 MET cc_start: 0.4133 (ppp) cc_final: 0.3902 (ppp) REVERT: S 43 LYS cc_start: 0.8370 (mmpt) cc_final: 0.8017 (mmpt) outliers start: 0 outliers final: 1 residues processed: 200 average time/residue: 1.0480 time to fit residues: 225.8441 Evaluate side-chains 184 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 75 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9071 Z= 0.321 Angle : 0.604 9.409 12281 Z= 0.312 Chirality : 0.043 0.164 1400 Planarity : 0.004 0.034 1544 Dihedral : 10.409 150.648 1263 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.96 % Allowed : 10.31 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.36 (0.25), residues: 1123 helix: 1.26 (0.25), residues: 400 sheet: -0.16 (0.30), residues: 282 loop : -0.30 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.005 0.001 HIS A 213 PHE 0.014 0.002 PHE R 202 TYR 0.029 0.002 TYR S 178 ARG 0.009 0.000 ARG R 149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 0.989 Fit side-chains REVERT: A 309 ASP cc_start: 0.7078 (t70) cc_final: 0.6701 (t0) REVERT: B 4 LEU cc_start: 0.8427 (tt) cc_final: 0.8197 (tm) REVERT: B 6 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7863 (tm-30) REVERT: B 13 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7113 (tm-30) REVERT: B 14 LEU cc_start: 0.8292 (mt) cc_final: 0.7852 (mt) REVERT: B 17 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7766 (tm-30) REVERT: B 118 ASP cc_start: 0.7374 (p0) cc_final: 0.7164 (p0) REVERT: B 146 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7935 (mt) REVERT: B 160 SER cc_start: 0.7958 (p) cc_final: 0.7543 (t) REVERT: B 220 GLN cc_start: 0.8694 (pt0) cc_final: 0.8486 (pt0) REVERT: B 227 SER cc_start: 0.8435 (t) cc_final: 0.8127 (m) REVERT: B 254 ASP cc_start: 0.7323 (p0) cc_final: 0.7085 (p0) REVERT: R 132 TYR cc_start: 0.7668 (t80) cc_final: 0.7263 (t80) REVERT: R 157 MET cc_start: 0.7283 (tmm) cc_final: 0.6979 (tmm) REVERT: S 43 LYS cc_start: 0.8395 (mmpt) cc_final: 0.8041 (mmpt) REVERT: S 168 ARG cc_start: 0.8309 (mtt90) cc_final: 0.8098 (mtt90) REVERT: S 201 THR cc_start: 0.7969 (p) cc_final: 0.7728 (t) outliers start: 19 outliers final: 7 residues processed: 210 average time/residue: 1.0681 time to fit residues: 240.4897 Evaluate side-chains 204 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 196 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 86 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 75 GLN R 267 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9071 Z= 0.288 Angle : 0.569 9.819 12281 Z= 0.295 Chirality : 0.042 0.132 1400 Planarity : 0.003 0.031 1544 Dihedral : 10.397 153.121 1261 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.78 % Allowed : 12.58 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.30 (0.25), residues: 1123 helix: 1.34 (0.26), residues: 399 sheet: -0.22 (0.29), residues: 286 loop : -0.45 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.005 0.001 HIS B 142 PHE 0.018 0.002 PHE R 94 TYR 0.025 0.002 TYR S 178 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 207 time to evaluate : 0.985 Fit side-chains REVERT: A 9 ASP cc_start: 0.6986 (m-30) cc_final: 0.6648 (m-30) REVERT: A 309 ASP cc_start: 0.7091 (t70) cc_final: 0.6709 (t0) REVERT: B 6 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7870 (tm-30) REVERT: B 13 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7162 (tm-30) REVERT: B 14 LEU cc_start: 0.8361 (mt) cc_final: 0.7922 (mt) REVERT: B 17 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7748 (tm-30) REVERT: B 160 SER cc_start: 0.7929 (p) cc_final: 0.7718 (t) REVERT: B 190 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8153 (pt) REVERT: B 227 SER cc_start: 0.8426 (t) cc_final: 0.8108 (m) REVERT: B 254 ASP cc_start: 0.7307 (p0) cc_final: 0.7055 (p0) REVERT: R 132 TYR cc_start: 0.7698 (t80) cc_final: 0.7298 (t80) REVERT: R 157 MET cc_start: 0.7288 (tmm) cc_final: 0.6999 (tmm) REVERT: R 285 SER cc_start: 0.7898 (m) cc_final: 0.7686 (p) REVERT: R 306 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7747 (mp) REVERT: S 43 LYS cc_start: 0.8417 (mmpt) cc_final: 0.8050 (mmpt) REVERT: S 83 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7864 (mtm) REVERT: S 168 ARG cc_start: 0.8316 (mtt90) cc_final: 0.8116 (mtt90) outliers start: 27 outliers final: 10 residues processed: 215 average time/residue: 1.0750 time to fit residues: 247.9849 Evaluate side-chains 211 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 198 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 75 GLN B 220 GLN B 340 ASN ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 9071 Z= 0.331 Angle : 0.596 10.766 12281 Z= 0.303 Chirality : 0.043 0.204 1400 Planarity : 0.003 0.032 1544 Dihedral : 10.382 152.612 1261 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.78 % Allowed : 14.95 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.18 (0.25), residues: 1123 helix: 1.25 (0.25), residues: 399 sheet: -0.31 (0.29), residues: 289 loop : -0.51 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 211 HIS 0.005 0.001 HIS B 142 PHE 0.014 0.002 PHE B 151 TYR 0.026 0.002 TYR S 178 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 205 time to evaluate : 1.066 Fit side-chains REVERT: A 9 ASP cc_start: 0.7002 (m-30) cc_final: 0.6690 (m-30) REVERT: A 197 LYS cc_start: 0.7867 (mmmt) cc_final: 0.7567 (mmmt) REVERT: A 309 ASP cc_start: 0.7099 (t70) cc_final: 0.6722 (t0) REVERT: B 6 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7869 (tm-30) REVERT: B 13 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7173 (tm-30) REVERT: B 14 LEU cc_start: 0.8388 (mt) cc_final: 0.7926 (mt) REVERT: B 17 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7744 (tm-30) REVERT: B 160 SER cc_start: 0.7929 (p) cc_final: 0.7711 (t) REVERT: B 227 SER cc_start: 0.8428 (t) cc_final: 0.8110 (m) REVERT: B 254 ASP cc_start: 0.7292 (p0) cc_final: 0.7040 (p0) REVERT: R 132 TYR cc_start: 0.7742 (t80) cc_final: 0.7336 (t80) REVERT: R 157 MET cc_start: 0.7306 (tmm) cc_final: 0.7000 (tmm) REVERT: R 285 SER cc_start: 0.8089 (m) cc_final: 0.7878 (p) REVERT: R 306 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7898 (mt) REVERT: S 43 LYS cc_start: 0.8420 (mmpt) cc_final: 0.8061 (mmpt) REVERT: S 83 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7922 (mtm) REVERT: S 109 ASP cc_start: 0.7829 (p0) cc_final: 0.7614 (p0) REVERT: S 168 ARG cc_start: 0.8318 (mtt90) cc_final: 0.8108 (mtt90) outliers start: 27 outliers final: 14 residues processed: 215 average time/residue: 1.0638 time to fit residues: 245.4059 Evaluate side-chains 216 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 200 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 86 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 75 GLN B 220 GLN ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9071 Z= 0.296 Angle : 0.581 12.354 12281 Z= 0.296 Chirality : 0.043 0.147 1400 Planarity : 0.004 0.037 1544 Dihedral : 10.359 151.644 1261 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.40 % Allowed : 15.77 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.19 (0.25), residues: 1123 helix: 1.24 (0.26), residues: 398 sheet: -0.24 (0.29), residues: 285 loop : -0.54 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.015 0.001 PHE R 94 TYR 0.024 0.002 TYR S 178 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 203 time to evaluate : 0.933 Fit side-chains REVERT: A 8 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7247 (mt-10) REVERT: A 9 ASP cc_start: 0.6997 (m-30) cc_final: 0.6672 (m-30) REVERT: A 48 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8204 (t) REVERT: A 197 LYS cc_start: 0.7902 (mmmt) cc_final: 0.7603 (mtmt) REVERT: A 309 ASP cc_start: 0.7101 (t70) cc_final: 0.6723 (t0) REVERT: B 6 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7864 (tm-30) REVERT: B 13 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7190 (tm-30) REVERT: B 14 LEU cc_start: 0.8385 (mt) cc_final: 0.7929 (mt) REVERT: B 17 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7762 (tm-30) REVERT: B 160 SER cc_start: 0.7897 (p) cc_final: 0.7656 (t) REVERT: B 227 SER cc_start: 0.8412 (t) cc_final: 0.8090 (m) REVERT: B 254 ASP cc_start: 0.7282 (p0) cc_final: 0.7034 (p0) REVERT: R 132 TYR cc_start: 0.7765 (t80) cc_final: 0.7366 (t80) REVERT: R 157 MET cc_start: 0.7302 (tmm) cc_final: 0.7007 (tmm) REVERT: R 285 SER cc_start: 0.8110 (m) cc_final: 0.7902 (p) REVERT: R 306 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7907 (mt) REVERT: S 43 LYS cc_start: 0.8399 (mmpt) cc_final: 0.8044 (mmpt) REVERT: S 83 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7910 (mtm) REVERT: S 109 ASP cc_start: 0.7829 (p0) cc_final: 0.7625 (p0) REVERT: S 168 ARG cc_start: 0.8314 (mtt90) cc_final: 0.8093 (mtt90) outliers start: 33 outliers final: 17 residues processed: 215 average time/residue: 1.0859 time to fit residues: 250.5416 Evaluate side-chains 219 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 198 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 75 GLN B 220 GLN ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9071 Z= 0.295 Angle : 0.591 13.706 12281 Z= 0.297 Chirality : 0.043 0.140 1400 Planarity : 0.003 0.032 1544 Dihedral : 10.317 150.930 1261 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.40 % Allowed : 16.19 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.16 (0.25), residues: 1123 helix: 1.22 (0.25), residues: 398 sheet: -0.23 (0.29), residues: 284 loop : -0.58 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS A 213 PHE 0.013 0.001 PHE R 94 TYR 0.025 0.002 TYR S 178 ARG 0.006 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 207 time to evaluate : 1.037 Fit side-chains REVERT: A 9 ASP cc_start: 0.6998 (m-30) cc_final: 0.6664 (m-30) REVERT: A 197 LYS cc_start: 0.7921 (mmmt) cc_final: 0.7614 (mtmt) REVERT: A 309 ASP cc_start: 0.7103 (t70) cc_final: 0.6725 (t0) REVERT: B 6 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7863 (tm-30) REVERT: B 13 GLN cc_start: 0.7767 (tm-30) cc_final: 0.7198 (tm-30) REVERT: B 14 LEU cc_start: 0.8391 (mt) cc_final: 0.7937 (mt) REVERT: B 17 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7752 (tm-30) REVERT: B 227 SER cc_start: 0.8405 (t) cc_final: 0.8081 (m) REVERT: B 239 ASN cc_start: 0.8107 (m110) cc_final: 0.7727 (m110) REVERT: B 254 ASP cc_start: 0.7275 (p0) cc_final: 0.7022 (p0) REVERT: R 132 TYR cc_start: 0.7771 (t80) cc_final: 0.7320 (t80) REVERT: R 157 MET cc_start: 0.7303 (tmm) cc_final: 0.6995 (tmm) REVERT: R 285 SER cc_start: 0.8110 (m) cc_final: 0.7908 (p) REVERT: S 43 LYS cc_start: 0.8398 (mmpt) cc_final: 0.8037 (mmpt) REVERT: S 83 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7937 (mtm) REVERT: S 109 ASP cc_start: 0.7835 (p0) cc_final: 0.7626 (p0) REVERT: S 168 ARG cc_start: 0.8315 (mtt90) cc_final: 0.8105 (mtt90) outliers start: 33 outliers final: 19 residues processed: 218 average time/residue: 1.1024 time to fit residues: 258.5652 Evaluate side-chains 216 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 196 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 160 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 220 GLN B 230 ASN B 293 ASN R 291 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9071 Z= 0.248 Angle : 0.577 15.007 12281 Z= 0.291 Chirality : 0.042 0.132 1400 Planarity : 0.003 0.031 1544 Dihedral : 10.276 150.009 1261 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.40 % Allowed : 17.32 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.21 (0.25), residues: 1123 helix: 1.27 (0.26), residues: 398 sheet: -0.23 (0.30), residues: 282 loop : -0.54 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS A 213 PHE 0.013 0.001 PHE R 94 TYR 0.026 0.002 TYR S 178 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 209 time to evaluate : 1.041 Fit side-chains REVERT: A 9 ASP cc_start: 0.6990 (m-30) cc_final: 0.6636 (m-30) REVERT: A 48 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8205 (t) REVERT: A 197 LYS cc_start: 0.7926 (mmmt) cc_final: 0.7628 (mtmt) REVERT: A 309 ASP cc_start: 0.7096 (t70) cc_final: 0.6718 (t0) REVERT: B 6 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7860 (tm-30) REVERT: B 13 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7184 (tm-30) REVERT: B 14 LEU cc_start: 0.8390 (mt) cc_final: 0.7927 (mt) REVERT: B 17 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7739 (tm-30) REVERT: B 227 SER cc_start: 0.8394 (t) cc_final: 0.8073 (m) REVERT: B 254 ASP cc_start: 0.7270 (p0) cc_final: 0.7030 (p0) REVERT: R 132 TYR cc_start: 0.7747 (t80) cc_final: 0.7312 (t80) REVERT: R 157 MET cc_start: 0.7300 (tmm) cc_final: 0.6994 (tmm) REVERT: R 285 SER cc_start: 0.8108 (m) cc_final: 0.7903 (p) REVERT: S 43 LYS cc_start: 0.8400 (mmpt) cc_final: 0.8032 (mmpt) REVERT: S 83 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7931 (mtm) REVERT: S 109 ASP cc_start: 0.7854 (p0) cc_final: 0.7647 (p0) REVERT: S 168 ARG cc_start: 0.8312 (mtt90) cc_final: 0.8084 (mtt90) outliers start: 33 outliers final: 18 residues processed: 223 average time/residue: 1.0934 time to fit residues: 261.5395 Evaluate side-chains 220 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 200 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 180 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 97 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 75 GLN B 119 ASN B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9071 Z= 0.199 Angle : 0.567 15.342 12281 Z= 0.283 Chirality : 0.041 0.132 1400 Planarity : 0.003 0.030 1544 Dihedral : 10.242 148.502 1261 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.89 % Allowed : 18.56 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.31 (0.25), residues: 1123 helix: 1.41 (0.26), residues: 398 sheet: -0.27 (0.30), residues: 271 loop : -0.47 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS B 142 PHE 0.017 0.001 PHE A 259 TYR 0.025 0.001 TYR S 178 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 208 time to evaluate : 0.907 Fit side-chains REVERT: A 48 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8203 (t) REVERT: A 197 LYS cc_start: 0.7949 (mmmt) cc_final: 0.7639 (mtmt) REVERT: A 309 ASP cc_start: 0.7082 (t70) cc_final: 0.6697 (t0) REVERT: B 6 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7866 (tm-30) REVERT: B 13 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7190 (tm-30) REVERT: B 14 LEU cc_start: 0.8379 (mt) cc_final: 0.7939 (mt) REVERT: B 17 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7727 (tm-30) REVERT: B 239 ASN cc_start: 0.8105 (m110) cc_final: 0.7693 (m110) REVERT: B 254 ASP cc_start: 0.7253 (p0) cc_final: 0.7008 (p0) REVERT: R 132 TYR cc_start: 0.7730 (t80) cc_final: 0.7296 (t80) REVERT: R 157 MET cc_start: 0.7308 (tmm) cc_final: 0.7020 (tmm) REVERT: R 285 SER cc_start: 0.8100 (m) cc_final: 0.7897 (p) REVERT: S 43 LYS cc_start: 0.8366 (mmpt) cc_final: 0.8005 (mmpt) REVERT: S 83 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7868 (mtm) outliers start: 28 outliers final: 18 residues processed: 217 average time/residue: 1.0554 time to fit residues: 245.8194 Evaluate side-chains 219 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 199 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 180 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 0.0070 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 75 GLN B 110 ASN B 119 ASN B 125 ASN B 155 ASN B 220 GLN B 230 ASN S 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9071 Z= 0.249 Angle : 0.590 15.631 12281 Z= 0.295 Chirality : 0.042 0.149 1400 Planarity : 0.004 0.044 1544 Dihedral : 10.252 148.977 1261 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.47 % Allowed : 19.48 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.27 (0.25), residues: 1123 helix: 1.38 (0.26), residues: 398 sheet: -0.27 (0.30), residues: 271 loop : -0.53 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.017 0.001 PHE A 259 TYR 0.026 0.002 TYR S 178 ARG 0.009 0.000 ARG S 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 206 time to evaluate : 1.035 Fit side-chains REVERT: A 197 LYS cc_start: 0.7945 (mmmt) cc_final: 0.7649 (mtmt) REVERT: A 309 ASP cc_start: 0.7087 (t70) cc_final: 0.6703 (t0) REVERT: B 6 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7870 (tm-30) REVERT: B 13 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7184 (tm-30) REVERT: B 14 LEU cc_start: 0.8390 (mt) cc_final: 0.7927 (mt) REVERT: B 17 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7730 (tm-30) REVERT: B 147 SER cc_start: 0.7902 (p) cc_final: 0.7622 (p) REVERT: B 227 SER cc_start: 0.8397 (t) cc_final: 0.8128 (m) REVERT: B 239 ASN cc_start: 0.8091 (m110) cc_final: 0.7701 (m110) REVERT: B 254 ASP cc_start: 0.7267 (p0) cc_final: 0.7018 (p0) REVERT: R 132 TYR cc_start: 0.7733 (t80) cc_final: 0.7299 (t80) REVERT: R 157 MET cc_start: 0.7336 (tmm) cc_final: 0.7037 (tmm) REVERT: S 38 ARG cc_start: 0.8354 (mtp85) cc_final: 0.8006 (ptp-170) REVERT: S 43 LYS cc_start: 0.8378 (mmpt) cc_final: 0.8009 (mmpt) REVERT: S 83 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7939 (mtm) outliers start: 24 outliers final: 17 residues processed: 213 average time/residue: 1.0545 time to fit residues: 241.2578 Evaluate side-chains 212 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 293 MET Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 180 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 75 GLN B 125 ASN B 155 ASN B 220 GLN B 230 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9071 Z= 0.269 Angle : 0.604 15.870 12281 Z= 0.301 Chirality : 0.042 0.180 1400 Planarity : 0.004 0.063 1544 Dihedral : 10.275 148.123 1261 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.37 % Allowed : 19.69 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.22 (0.25), residues: 1123 helix: 1.36 (0.26), residues: 398 sheet: -0.31 (0.29), residues: 271 loop : -0.55 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.015 0.001 PHE A 259 TYR 0.027 0.002 TYR S 178 ARG 0.013 0.001 ARG S 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 205 time to evaluate : 0.917 Fit side-chains REVERT: A 197 LYS cc_start: 0.7944 (mmmt) cc_final: 0.7653 (mtmt) REVERT: A 309 ASP cc_start: 0.7088 (t70) cc_final: 0.6705 (t0) REVERT: B 6 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7874 (tm-30) REVERT: B 13 GLN cc_start: 0.7770 (tm-30) cc_final: 0.7188 (tm-30) REVERT: B 14 LEU cc_start: 0.8398 (mt) cc_final: 0.7933 (mt) REVERT: B 17 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7735 (tm-30) REVERT: B 239 ASN cc_start: 0.8101 (m110) cc_final: 0.7712 (m110) REVERT: B 254 ASP cc_start: 0.7266 (p0) cc_final: 0.7007 (p0) REVERT: R 132 TYR cc_start: 0.7734 (t80) cc_final: 0.7362 (t80) REVERT: R 157 MET cc_start: 0.7337 (tmm) cc_final: 0.7028 (tmm) REVERT: S 38 ARG cc_start: 0.8376 (mtp85) cc_final: 0.8014 (ptp-170) REVERT: S 43 LYS cc_start: 0.8385 (mmpt) cc_final: 0.8014 (mmpt) REVERT: S 83 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7942 (mtm) REVERT: S 154 LEU cc_start: 0.8685 (tt) cc_final: 0.8474 (tp) outliers start: 23 outliers final: 17 residues processed: 213 average time/residue: 1.0924 time to fit residues: 251.5491 Evaluate side-chains 214 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 196 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 180 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 63 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 36 ASN B 75 GLN B 110 ASN B 155 ASN B 220 GLN B 230 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.141352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.123715 restraints weight = 12614.105| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.12 r_work: 0.3517 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9071 Z= 0.234 Angle : 0.598 16.020 12281 Z= 0.296 Chirality : 0.042 0.147 1400 Planarity : 0.004 0.065 1544 Dihedral : 10.245 148.334 1261 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.16 % Allowed : 19.79 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.30 (0.25), residues: 1123 helix: 1.42 (0.26), residues: 403 sheet: -0.31 (0.29), residues: 271 loop : -0.50 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.015 0.001 PHE A 259 TYR 0.025 0.002 TYR S 178 ARG 0.015 0.000 ARG S 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4287.01 seconds wall clock time: 76 minutes 3.25 seconds (4563.25 seconds total)