Starting phenix.real_space_refine on Wed Feb 14 07:52:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gur_34277/02_2024/8gur_34277_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gur_34277/02_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_34277/02_2024/8gur_34277.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gur_34277/02_2024/8gur_34277.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gur_34277/02_2024/8gur_34277_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gur_34277/02_2024/8gur_34277_neut.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.32, 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.80 Conformation dependent library (CDL) restraints added in 1.8 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: 1.01 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: 2.62 Time building geometry restraints manager: 4.09 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: 99.83 - 106.66: 205 106.66 - 113.49: 5028 113.49 - 120.33: 3179 120.33 - 127.16: 3774 127.16 - 133.99: 95 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 2.440 nonbonded pdb=" OH TYR R 70 " pdb=" OG SER R 303 " model vdw 2.139 2.440 nonbonded pdb=" NH1 ARG B 49 " pdb=" O TYR B 85 " model vdw 2.211 2.520 nonbonded pdb=" O CYS A 254 " pdb=" NZ LYS A 317 " model vdw 2.232 2.520 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.235 2.440 ... (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 ========== 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: 0.840 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: 3.970 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.330 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.770 ------------------------------------------------------------------------------- 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 : 1.100 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: 1.0112 time to fit residues: 218.1590 Evaluate side-chains 184 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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: 0.0870 chunk 84 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.2980 chunk 100 optimal weight: 3.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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: 0.7200 moved from start: 0.1067 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= 0.186 Angle : 0.537 9.207 12281 Z= 0.276 Chirality : 0.041 0.140 1400 Planarity : 0.003 0.033 1544 Dihedral : 10.390 151.629 1263 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.44 % Allowed : 10.41 % Favored : 88.14 % 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: 0.55 (0.25), residues: 1123 helix: 1.49 (0.26), residues: 401 sheet: -0.10 (0.29), residues: 296 loop : -0.26 (0.31), residues: 426 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 0.012 0.001 PHE R 117 TYR 0.027 0.001 TYR S 178 ARG 0.007 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 214 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 200 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 209 LYS cc_start: 0.7822 (pttm) cc_final: 0.7585 (pttm) REVERT: A 309 ASP cc_start: 0.7055 (t70) cc_final: 0.6668 (t0) REVERT: B 6 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7886 (tm-30) REVERT: B 13 GLN cc_start: 0.7700 (tm-30) cc_final: 0.7109 (tm-30) REVERT: B 14 LEU cc_start: 0.8264 (mt) cc_final: 0.7846 (mt) REVERT: B 17 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7749 (tm-30) REVERT: B 220 GLN cc_start: 0.8660 (pt0) cc_final: 0.8404 (pt0) REVERT: B 254 ASP cc_start: 0.7436 (p0) cc_final: 0.7149 (p0) REVERT: R 129 ILE cc_start: 0.8303 (pt) cc_final: 0.8096 (pt) REVERT: R 132 TYR cc_start: 0.7621 (t80) cc_final: 0.7264 (t80) REVERT: R 168 PRO cc_start: 0.7224 (Cg_endo) cc_final: 0.7018 (Cg_exo) REVERT: S 43 LYS cc_start: 0.8347 (mmpt) cc_final: 0.7989 (mmpt) REVERT: S 201 THR cc_start: 0.7935 (p) cc_final: 0.7692 (t) outliers start: 14 outliers final: 3 residues processed: 203 average time/residue: 1.1358 time to fit residues: 246.6913 Evaluate side-chains 197 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 194 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain R residue 306 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1416 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= 0.255 Angle : 0.549 9.878 12281 Z= 0.280 Chirality : 0.041 0.128 1400 Planarity : 0.003 0.042 1544 Dihedral : 10.291 152.356 1261 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.47 % Allowed : 12.99 % Favored : 84.54 % 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: 0.51 (0.25), residues: 1123 helix: 1.56 (0.26), residues: 399 sheet: -0.13 (0.29), residues: 290 loop : -0.38 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS A 213 PHE 0.012 0.001 PHE R 202 TYR 0.025 0.002 TYR S 178 ARG 0.009 0.000 ARG S 168 *********************** 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 224 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 200 time to evaluate : 1.033 Fit side-chains REVERT: A 209 LYS cc_start: 0.7893 (pttm) cc_final: 0.7659 (pttm) REVERT: A 309 ASP cc_start: 0.7068 (t70) cc_final: 0.6691 (t0) REVERT: B 6 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7886 (tm-30) REVERT: B 13 GLN cc_start: 0.7748 (tm-30) cc_final: 0.7126 (tm-30) REVERT: B 14 LEU cc_start: 0.8351 (mt) cc_final: 0.7921 (mt) REVERT: B 17 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7729 (tm-30) REVERT: B 147 SER cc_start: 0.7855 (p) cc_final: 0.7599 (p) REVERT: B 190 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8164 (pt) REVERT: B 220 GLN cc_start: 0.8705 (pt0) cc_final: 0.8476 (pt0) REVERT: B 254 ASP cc_start: 0.7419 (p0) cc_final: 0.7159 (p0) REVERT: R 132 TYR cc_start: 0.7702 (t80) cc_final: 0.7339 (t80) REVERT: R 157 MET cc_start: 0.7319 (tmm) cc_final: 0.6840 (tmm) REVERT: S 38 ARG cc_start: 0.8290 (mtp180) cc_final: 0.7691 (mtp180) REVERT: S 43 LYS cc_start: 0.8377 (mmpt) cc_final: 0.8009 (mmpt) REVERT: S 83 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7857 (mtm) outliers start: 24 outliers final: 11 residues processed: 206 average time/residue: 1.1117 time to fit residues: 245.2187 Evaluate side-chains 209 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 196 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 223 LEU 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 144 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 0.0170 chunk 67 optimal weight: 0.0770 chunk 101 optimal weight: 0.4980 chunk 107 optimal weight: 0.2980 chunk 96 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 340 ASN R 291 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1551 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= 0.166 Angle : 0.516 9.854 12281 Z= 0.261 Chirality : 0.040 0.130 1400 Planarity : 0.003 0.032 1544 Dihedral : 10.311 156.265 1261 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.78 % Allowed : 14.43 % Favored : 82.78 % 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: 0.62 (0.25), residues: 1123 helix: 1.66 (0.26), residues: 399 sheet: -0.08 (0.30), residues: 278 loop : -0.32 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS A 213 PHE 0.019 0.001 PHE R 94 TYR 0.025 0.001 TYR S 178 ARG 0.006 0.000 ARG S 168 *********************** 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 221 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 194 time to evaluate : 1.031 Fit side-chains REVERT: A 197 LYS cc_start: 0.7840 (mmmt) cc_final: 0.7514 (mmmt) REVERT: A 309 ASP cc_start: 0.7061 (t70) cc_final: 0.6671 (t0) REVERT: B 6 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 13 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7166 (tm-30) REVERT: B 14 LEU cc_start: 0.8338 (mt) cc_final: 0.7925 (mt) REVERT: B 17 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7703 (tm-30) REVERT: B 147 SER cc_start: 0.7850 (p) cc_final: 0.7599 (p) REVERT: B 254 ASP cc_start: 0.7397 (p0) cc_final: 0.7102 (p0) REVERT: R 132 TYR cc_start: 0.7670 (t80) cc_final: 0.7260 (t80) REVERT: R 157 MET cc_start: 0.7285 (tmm) cc_final: 0.6810 (tmm) REVERT: S 43 LYS cc_start: 0.8353 (mmpt) cc_final: 0.7972 (mmpt) REVERT: S 83 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7918 (mtm) outliers start: 27 outliers final: 14 residues processed: 204 average time/residue: 1.1091 time to fit residues: 242.5780 Evaluate side-chains 206 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 191 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 332 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP 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 Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 180 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 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 267 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 9071 Z= 0.323 Angle : 0.564 10.034 12281 Z= 0.290 Chirality : 0.042 0.130 1400 Planarity : 0.003 0.036 1544 Dihedral : 10.367 156.530 1261 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.78 % Allowed : 15.36 % Favored : 81.86 % 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: 0.39 (0.25), residues: 1123 helix: 1.44 (0.26), residues: 399 sheet: -0.11 (0.30), residues: 288 loop : -0.49 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.017 0.002 PHE R 94 TYR 0.025 0.002 TYR S 178 ARG 0.006 0.000 ARG S 168 *********************** 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 232 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 205 time to evaluate : 1.065 Fit side-chains REVERT: A 48 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8238 (t) REVERT: A 197 LYS cc_start: 0.7863 (mmmt) cc_final: 0.7591 (mtmt) REVERT: A 309 ASP cc_start: 0.7099 (t70) cc_final: 0.6715 (t0) REVERT: B 6 GLN cc_start: 0.8286 (tm-30) cc_final: 0.7890 (tm-30) REVERT: B 13 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7204 (tm-30) REVERT: B 14 LEU cc_start: 0.8385 (mt) cc_final: 0.7940 (mt) REVERT: B 17 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7748 (tm-30) REVERT: B 147 SER cc_start: 0.7800 (p) cc_final: 0.7563 (p) REVERT: B 227 SER cc_start: 0.8403 (t) cc_final: 0.8112 (m) REVERT: B 254 ASP cc_start: 0.7384 (p0) cc_final: 0.7170 (p0) REVERT: R 132 TYR cc_start: 0.7747 (t80) cc_final: 0.7350 (t80) REVERT: R 157 MET cc_start: 0.7325 (tmm) cc_final: 0.6885 (tmm) REVERT: S 38 ARG cc_start: 0.8276 (mtp180) cc_final: 0.8071 (mtp180) REVERT: S 43 LYS cc_start: 0.8385 (mmpt) cc_final: 0.8029 (mmpt) REVERT: S 83 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7931 (mtm) outliers start: 27 outliers final: 17 residues processed: 213 average time/residue: 1.1061 time to fit residues: 253.0868 Evaluate side-chains 225 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 206 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 114 CYS 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 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 285 SER 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 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1842 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= 0.261 Angle : 0.557 10.139 12281 Z= 0.281 Chirality : 0.041 0.129 1400 Planarity : 0.004 0.046 1544 Dihedral : 10.370 154.623 1261 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.89 % Allowed : 16.39 % Favored : 80.72 % 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: 1.48 (0.26), residues: 397 sheet: -0.20 (0.30), residues: 278 loop : -0.50 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS B 142 PHE 0.024 0.002 PHE R 281 TYR 0.026 0.001 TYR S 178 ARG 0.009 0.000 ARG S 168 *********************** 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 228 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 200 time to evaluate : 1.006 Fit side-chains REVERT: A 197 LYS cc_start: 0.7925 (mmmt) cc_final: 0.7626 (mtmt) REVERT: A 309 ASP cc_start: 0.7096 (t70) cc_final: 0.6715 (t0) REVERT: B 6 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7885 (tm-30) REVERT: B 13 GLN cc_start: 0.7763 (tm-30) cc_final: 0.7198 (tm-30) REVERT: B 14 LEU cc_start: 0.8385 (mt) cc_final: 0.7937 (mt) REVERT: B 17 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7774 (tm-30) REVERT: B 147 SER cc_start: 0.7812 (p) cc_final: 0.7563 (p) REVERT: B 227 SER cc_start: 0.8389 (t) cc_final: 0.8095 (m) REVERT: B 254 ASP cc_start: 0.7373 (p0) cc_final: 0.7163 (p0) REVERT: R 132 TYR cc_start: 0.7743 (t80) cc_final: 0.7354 (t80) REVERT: R 157 MET cc_start: 0.7326 (tmm) cc_final: 0.7009 (tmm) REVERT: S 38 ARG cc_start: 0.8250 (mtp180) cc_final: 0.8024 (mtp85) REVERT: S 43 LYS cc_start: 0.8389 (mmpt) cc_final: 0.8022 (mmpt) REVERT: S 83 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7897 (mtm) outliers start: 28 outliers final: 18 residues processed: 209 average time/residue: 1.1253 time to fit residues: 252.7925 Evaluate side-chains 215 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 196 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 114 CYS 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 317 CYS 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 160 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 59 optimal weight: 0.3980 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 42 optimal weight: 0.0980 chunk 63 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 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 : 0.003 0.025 9071 Z= 0.188 Angle : 0.528 9.978 12281 Z= 0.268 Chirality : 0.040 0.130 1400 Planarity : 0.003 0.043 1544 Dihedral : 10.328 153.839 1261 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.78 % Allowed : 17.73 % Favored : 79.48 % 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: 0.49 (0.25), residues: 1123 helix: 1.59 (0.26), residues: 399 sheet: -0.14 (0.30), residues: 274 loop : -0.45 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS S 35 PHE 0.022 0.001 PHE R 281 TYR 0.023 0.001 TYR S 178 ARG 0.009 0.000 ARG S 168 *********************** 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 222 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 195 time to evaluate : 0.873 Fit side-chains REVERT: A 197 LYS cc_start: 0.7927 (mmmt) cc_final: 0.7626 (mtmt) REVERT: A 207 GLU cc_start: 0.6294 (tt0) cc_final: 0.6050 (tt0) REVERT: A 309 ASP cc_start: 0.7081 (t70) cc_final: 0.6698 (t0) REVERT: B 6 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7880 (tm-30) REVERT: B 13 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7195 (tm-30) REVERT: B 14 LEU cc_start: 0.8370 (mt) cc_final: 0.7925 (mt) REVERT: B 17 GLN cc_start: 0.8068 (tm-30) cc_final: 0.7736 (tm-30) REVERT: B 147 SER cc_start: 0.7828 (p) cc_final: 0.7573 (p) REVERT: B 254 ASP cc_start: 0.7365 (p0) cc_final: 0.7134 (p0) REVERT: R 132 TYR cc_start: 0.7730 (t80) cc_final: 0.7345 (t80) REVERT: R 157 MET cc_start: 0.7336 (tmm) cc_final: 0.7106 (tmm) REVERT: S 38 ARG cc_start: 0.8237 (mtp180) cc_final: 0.7989 (mtp85) REVERT: S 43 LYS cc_start: 0.8373 (mmpt) cc_final: 0.7986 (mmpt) REVERT: S 83 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7941 (mtm) REVERT: S 178 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.7011 (p90) outliers start: 27 outliers final: 15 residues processed: 203 average time/residue: 1.0848 time to fit residues: 236.0562 Evaluate side-chains 209 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 192 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER 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 178 TYR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 0.0870 chunk 97 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9071 Z= 0.215 Angle : 0.540 9.986 12281 Z= 0.273 Chirality : 0.041 0.140 1400 Planarity : 0.003 0.040 1544 Dihedral : 10.318 154.695 1261 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.47 % Allowed : 18.25 % 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: 0.47 (0.25), residues: 1123 helix: 1.58 (0.26), residues: 399 sheet: -0.14 (0.30), residues: 275 loop : -0.45 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS A 213 PHE 0.019 0.001 PHE R 281 TYR 0.025 0.001 TYR S 178 ARG 0.008 0.000 ARG S 168 *********************** 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 221 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 197 time to evaluate : 0.933 Fit side-chains REVERT: A 207 GLU cc_start: 0.6277 (tt0) cc_final: 0.6065 (tt0) REVERT: A 309 ASP cc_start: 0.7089 (t70) cc_final: 0.6708 (t0) REVERT: B 6 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7882 (tm-30) REVERT: B 13 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7195 (tm-30) REVERT: B 14 LEU cc_start: 0.8377 (mt) cc_final: 0.7928 (mt) REVERT: B 17 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7741 (tm-30) REVERT: B 147 SER cc_start: 0.7844 (p) cc_final: 0.7616 (p) REVERT: B 254 ASP cc_start: 0.7367 (p0) cc_final: 0.7147 (p0) REVERT: R 132 TYR cc_start: 0.7733 (t80) cc_final: 0.7341 (t80) REVERT: R 157 MET cc_start: 0.7360 (tmm) cc_final: 0.7050 (tmm) REVERT: S 38 ARG cc_start: 0.8257 (mtp180) cc_final: 0.8014 (mtp85) REVERT: S 43 LYS cc_start: 0.8372 (mmpt) cc_final: 0.7992 (mmpt) REVERT: S 83 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7939 (ptp) REVERT: S 178 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.7011 (p90) outliers start: 24 outliers final: 17 residues processed: 206 average time/residue: 1.1746 time to fit residues: 261.2266 Evaluate side-chains 212 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 193 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 114 CYS 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 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 178 TYR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 43 optimal weight: 0.1980 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9071 Z= 0.197 Angle : 0.542 9.882 12281 Z= 0.271 Chirality : 0.041 0.167 1400 Planarity : 0.003 0.048 1544 Dihedral : 10.354 153.670 1261 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.37 % Allowed : 18.76 % Favored : 78.87 % 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: 0.51 (0.25), residues: 1123 helix: 1.62 (0.26), residues: 399 sheet: -0.08 (0.30), residues: 286 loop : -0.48 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS A 213 PHE 0.020 0.001 PHE A 259 TYR 0.023 0.001 TYR S 178 ARG 0.011 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 215 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 192 time to evaluate : 1.044 Fit side-chains REVERT: A 207 GLU cc_start: 0.6268 (tt0) cc_final: 0.6046 (tt0) REVERT: A 309 ASP cc_start: 0.7089 (t70) cc_final: 0.6710 (t0) REVERT: B 6 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7893 (tm-30) REVERT: B 13 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7196 (tm-30) REVERT: B 14 LEU cc_start: 0.8377 (mt) cc_final: 0.7927 (mt) REVERT: B 17 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7722 (tm-30) REVERT: B 147 SER cc_start: 0.7832 (p) cc_final: 0.7611 (p) REVERT: B 254 ASP cc_start: 0.7361 (p0) cc_final: 0.7128 (p0) REVERT: R 132 TYR cc_start: 0.7714 (t80) cc_final: 0.7331 (t80) REVERT: R 157 MET cc_start: 0.7355 (tmm) cc_final: 0.7111 (tmm) REVERT: S 38 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7996 (mtp85) REVERT: S 43 LYS cc_start: 0.8372 (mmpt) cc_final: 0.7974 (mmpt) REVERT: S 83 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7887 (ptp) REVERT: S 178 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.7029 (p90) outliers start: 23 outliers final: 14 residues processed: 201 average time/residue: 1.1037 time to fit residues: 237.9697 Evaluate side-chains 210 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER 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 38 ARG Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 178 TYR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 9 optimal weight: 0.0970 chunk 68 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9071 Z= 0.208 Angle : 0.544 9.896 12281 Z= 0.273 Chirality : 0.041 0.146 1400 Planarity : 0.003 0.052 1544 Dihedral : 10.364 153.889 1261 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.16 % Allowed : 19.07 % Favored : 78.76 % 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: 0.50 (0.25), residues: 1123 helix: 1.62 (0.26), residues: 399 sheet: -0.09 (0.30), residues: 287 loop : -0.49 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS S 35 PHE 0.018 0.001 PHE R 281 TYR 0.025 0.001 TYR S 178 ARG 0.011 0.000 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 210 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 1.008 Fit side-chains REVERT: A 207 GLU cc_start: 0.6271 (tt0) cc_final: 0.6053 (tt0) REVERT: A 309 ASP cc_start: 0.7091 (t70) cc_final: 0.6714 (t0) REVERT: B 6 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7888 (tm-30) REVERT: B 13 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7200 (tm-30) REVERT: B 14 LEU cc_start: 0.8378 (mt) cc_final: 0.7929 (mt) REVERT: B 17 GLN cc_start: 0.8077 (tm-30) cc_final: 0.7724 (tm-30) REVERT: B 147 SER cc_start: 0.7857 (p) cc_final: 0.7617 (p) REVERT: B 254 ASP cc_start: 0.7361 (p0) cc_final: 0.7142 (p0) REVERT: R 132 TYR cc_start: 0.7715 (t80) cc_final: 0.7327 (t80) REVERT: R 157 MET cc_start: 0.7362 (tmm) cc_final: 0.7059 (tmm) REVERT: S 38 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.8003 (mtp180) REVERT: S 43 LYS cc_start: 0.8363 (mmpt) cc_final: 0.7970 (mmpt) REVERT: S 83 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7886 (ptp) REVERT: S 178 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.7011 (p90) outliers start: 21 outliers final: 15 residues processed: 196 average time/residue: 1.1119 time to fit residues: 233.4069 Evaluate side-chains 208 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER 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 38 ARG Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 178 TYR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.0570 chunk 88 optimal weight: 0.0040 chunk 36 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.3710 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.141578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.124326 restraints weight = 12863.343| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.14 r_work: 0.3537 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9071 Z= 0.169 Angle : 0.529 10.335 12281 Z= 0.265 Chirality : 0.040 0.133 1400 Planarity : 0.003 0.044 1544 Dihedral : 10.357 154.605 1261 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.27 % Allowed : 18.87 % Favored : 78.87 % 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: 0.58 (0.25), residues: 1123 helix: 1.68 (0.26), residues: 409 sheet: -0.05 (0.30), residues: 286 loop : -0.50 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.003 0.001 HIS A 213 PHE 0.019 0.001 PHE R 281 TYR 0.022 0.001 TYR S 178 ARG 0.010 0.000 ARG S 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4222.27 seconds wall clock time: 75 minutes 37.94 seconds (4537.94 seconds total)