Starting phenix.real_space_refine on Sat Dec 28 15:28:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7trk_26099/12_2024/7trk_26099.cif Found real_map, /net/cci-nas-00/data/ceres_data/7trk_26099/12_2024/7trk_26099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7trk_26099/12_2024/7trk_26099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7trk_26099/12_2024/7trk_26099.map" model { file = "/net/cci-nas-00/data/ceres_data/7trk_26099/12_2024/7trk_26099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7trk_26099/12_2024/7trk_26099.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 63 5.16 5 C 5523 2.51 5 N 1457 2.21 5 O 1616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8659 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2106 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2579 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 418 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1778 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1764 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'IXO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.51, per 1000 atoms: 0.64 Number of scatterers: 8659 At special positions: 0 Unit cell: (92.96, 118.69, 122.84, 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 63 16.00 O 1616 8.00 N 1457 7.00 C 5523 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 426 " - pdb=" SG CYS R 429 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 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: 2.26 Conformation dependent library (CDL) restraints added in 1.1 seconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 38.2% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'R' and resid 32 through 60 removed outlier: 3.689A pdb=" N ASN R 60 " --> pdb=" O SER R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 96 removed outlier: 4.148A pdb=" N PHE R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU R 71 " --> pdb=" O ASN R 67 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N MET R 86 " --> pdb=" O GLY R 82 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU R 88 " --> pdb=" O PHE R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 136 removed outlier: 3.540A pdb=" N CYS R 105 " --> pdb=" O GLY R 101 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP R 106 " --> pdb=" O ALA R 102 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU R 107 " --> pdb=" O VAL R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 144 removed outlier: 4.522A pdb=" N ALA R 142 " --> pdb=" O LEU R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 176 Proline residue: R 166 - end of helix removed outlier: 5.203A pdb=" N GLN R 172 " --> pdb=" O ILE R 168 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N PHE R 173 " --> pdb=" O LEU R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 191 removed outlier: 3.949A pdb=" N LEU R 190 " --> pdb=" O ILE R 187 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER R 191 " --> pdb=" O GLN R 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 187 through 191' Processing helix chain 'R' and resid 192 through 204 removed outlier: 3.544A pdb=" N THR R 196 " --> pdb=" O ASN R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 221 Processing helix chain 'R' and resid 393 through 424 removed outlier: 3.814A pdb=" N PHE R 409 " --> pdb=" O ILE R 405 " (cutoff:3.500A) Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 431 through 454 removed outlier: 4.280A pdb=" N SER R 446 " --> pdb=" O CYS R 442 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR R 447 " --> pdb=" O TYR R 443 " (cutoff:3.500A) Proline residue: R 450 - end of helix Processing helix chain 'R' and resid 457 through 466 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.588A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 removed outlier: 4.215A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.588A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.668A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.903A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.896A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 331 through 351 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.656A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.520A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.876A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.155A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.601A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.570A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.675A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.988A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.988A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.662A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.909A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.224A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) 451 hydrogen bonds defined for protein. 1284 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: 2.52 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1402 1.32 - 1.44: 2469 1.44 - 1.57: 4880 1.57 - 1.69: 1 1.69 - 1.81: 91 Bond restraints: 8843 Sorted by residual: bond pdb=" C10 IXO R 501 " pdb=" N11 IXO R 501 " ideal model delta sigma weight residual 1.270 1.469 -0.199 2.00e-02 2.50e+03 9.91e+01 bond pdb=" C10 IXO R 501 " pdb=" C14 IXO R 501 " ideal model delta sigma weight residual 1.492 1.345 0.147 2.00e-02 2.50e+03 5.41e+01 bond pdb=" C13 IXO R 501 " pdb=" O12 IXO R 501 " ideal model delta sigma weight residual 1.439 1.542 -0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C10 IXO R 501 " pdb=" O09 IXO R 501 " ideal model delta sigma weight residual 1.325 1.406 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C07 IXO R 501 " pdb=" C08 IXO R 501 " ideal model delta sigma weight residual 1.454 1.534 -0.080 2.00e-02 2.50e+03 1.61e+01 ... (remaining 8838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 11309 1.73 - 3.47: 598 3.47 - 5.20: 82 5.20 - 6.94: 22 6.94 - 8.67: 5 Bond angle restraints: 12016 Sorted by residual: angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 123.93 129.45 -5.52 1.54e+00 4.22e-01 1.28e+01 angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 121.54 128.34 -6.80 1.91e+00 2.74e-01 1.27e+01 angle pdb=" C TYR R 92 " pdb=" N ILE R 93 " pdb=" CA ILE R 93 " ideal model delta sigma weight residual 121.35 115.87 5.48 1.58e+00 4.01e-01 1.20e+01 angle pdb=" C ASP H 201 " pdb=" N ARG H 202 " pdb=" CA ARG H 202 " ideal model delta sigma weight residual 120.38 125.08 -4.70 1.46e+00 4.69e-01 1.04e+01 angle pdb=" N SER R 191 " pdb=" CA SER R 191 " pdb=" C SER R 191 " ideal model delta sigma weight residual 112.45 108.07 4.38 1.39e+00 5.18e-01 9.95e+00 ... (remaining 12011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.04: 4999 21.04 - 42.08: 182 42.08 - 63.12: 25 63.12 - 84.16: 5 84.16 - 105.21: 1 Dihedral angle restraints: 5212 sinusoidal: 1940 harmonic: 3272 Sorted by residual: dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA GLN B 259 " pdb=" C GLN B 259 " pdb=" N GLU B 260 " pdb=" CA GLU B 260 " ideal model delta harmonic sigma weight residual 180.00 161.34 18.66 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" C05 IXO R 501 " pdb=" C06 IXO R 501 " pdb=" C07 IXO R 501 " pdb=" C08 IXO R 501 " ideal model delta sinusoidal sigma weight residual -178.63 -73.42 -105.21 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 5209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1091 0.065 - 0.131: 245 0.131 - 0.196: 44 0.196 - 0.261: 5 0.261 - 0.327: 3 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CB VAL B 71 " pdb=" CA VAL B 71 " pdb=" CG1 VAL B 71 " pdb=" CG2 VAL B 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB ILE R 94 " pdb=" CA ILE R 94 " pdb=" CG1 ILE R 94 " pdb=" CG2 ILE R 94 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA PHE R 189 " pdb=" N PHE R 189 " pdb=" C PHE R 189 " pdb=" CB PHE R 189 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1385 not shown) Planarity restraints: 1511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 196 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C THR R 196 " -0.047 2.00e-02 2.50e+03 pdb=" O THR R 196 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE R 197 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO B 236 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 189 " 0.025 2.00e-02 2.50e+03 1.93e-02 6.54e+00 pdb=" CG PHE R 189 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE R 189 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE R 189 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 189 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 189 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE R 189 " 0.006 2.00e-02 2.50e+03 ... (remaining 1508 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1839 2.78 - 3.31: 7711 3.31 - 3.84: 14682 3.84 - 4.37: 17795 4.37 - 4.90: 30654 Nonbonded interactions: 72681 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.253 3.040 nonbonded pdb=" OD2 ASP R 112 " pdb=" OH TYR R 443 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR H 175 " pdb=" OE2 GLU A 8 " model vdw 2.289 3.040 nonbonded pdb=" O GLU R 395 " pdb=" OG1 THR R 399 " model vdw 2.303 3.040 nonbonded pdb=" OG SER H 161 " pdb=" O LYS H 163 " model vdw 2.306 3.040 ... (remaining 72676 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.500 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:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.199 8843 Z= 0.366 Angle : 0.888 8.674 12016 Z= 0.511 Chirality : 0.058 0.327 1388 Planarity : 0.007 0.067 1511 Dihedral : 11.327 105.205 3088 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.11 % Allowed : 1.52 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.23), residues: 1110 helix: -0.71 (0.24), residues: 395 sheet: 0.33 (0.30), residues: 278 loop : -1.13 (0.26), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 82 HIS 0.004 0.001 HIS H 35 PHE 0.044 0.003 PHE R 189 TYR 0.019 0.002 TYR R 416 ARG 0.004 0.001 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 64 GLN cc_start: 0.8344 (mt0) cc_final: 0.7735 (mt0) REVERT: R 107 LEU cc_start: 0.8106 (mt) cc_final: 0.7737 (tm) REVERT: R 143 ARG cc_start: 0.7998 (ptm160) cc_final: 0.7517 (mtm110) REVERT: R 223 ARG cc_start: 0.8449 (ptp-170) cc_final: 0.8089 (ptm160) REVERT: R 465 ARG cc_start: 0.7863 (ttt90) cc_final: 0.6987 (tpt170) REVERT: B 10 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8477 (tp30) REVERT: B 61 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8609 (ppp) REVERT: B 254 ASP cc_start: 0.8202 (t70) cc_final: 0.7950 (t0) REVERT: G 20 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8602 (mtmp) REVERT: G 24 ASN cc_start: 0.9040 (m-40) cc_final: 0.8769 (m-40) REVERT: H 148 PRO cc_start: 0.9326 (Cg_exo) cc_final: 0.9053 (Cg_endo) REVERT: H 192 MET cc_start: 0.8923 (ttp) cc_final: 0.8720 (ttm) REVERT: H 223 ASP cc_start: 0.8921 (m-30) cc_final: 0.8696 (m-30) REVERT: H 234 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7731 (mt-10) REVERT: H 244 LYS cc_start: 0.9176 (tttt) cc_final: 0.8835 (ttmm) REVERT: A 9 ASP cc_start: 0.8497 (m-30) cc_final: 0.8085 (m-30) REVERT: A 24 ARG cc_start: 0.7956 (ttm110) cc_final: 0.7738 (ttm110) REVERT: A 188 HIS cc_start: 0.8046 (m-70) cc_final: 0.7654 (m-70) REVERT: A 329 THR cc_start: 0.8189 (m) cc_final: 0.7962 (t) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 1.6381 time to fit residues: 340.8305 Evaluate side-chains 142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 0.0970 chunk 99 optimal weight: 5.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 60 ASN R 117 ASN R 192 ASN B 13 GLN B 75 GLN B 340 ASN G 18 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8843 Z= 0.234 Angle : 0.566 8.163 12016 Z= 0.307 Chirality : 0.043 0.138 1388 Planarity : 0.004 0.048 1511 Dihedral : 4.840 35.163 1223 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.95 % Allowed : 8.98 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1110 helix: 0.89 (0.26), residues: 398 sheet: 0.44 (0.30), residues: 280 loop : -0.65 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.018 0.001 PHE R 189 TYR 0.017 0.001 TYR H 190 ARG 0.004 0.000 ARG R 144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: R 64 GLN cc_start: 0.8303 (mt0) cc_final: 0.7703 (mt0) REVERT: R 107 LEU cc_start: 0.8152 (mt) cc_final: 0.7856 (tm) REVERT: R 143 ARG cc_start: 0.7624 (ptm160) cc_final: 0.7316 (mtm110) REVERT: R 223 ARG cc_start: 0.8437 (ptp-170) cc_final: 0.8195 (ptp-170) REVERT: R 439 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.7459 (t80) REVERT: R 465 ARG cc_start: 0.7840 (ttt90) cc_final: 0.6980 (tpt170) REVERT: B 13 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7987 (tm-30) REVERT: B 215 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8299 (mp0) REVERT: B 217 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7285 (pmt) REVERT: B 254 ASP cc_start: 0.8118 (t70) cc_final: 0.7843 (t0) REVERT: G 20 LYS cc_start: 0.8856 (mtmm) cc_final: 0.8484 (mtmp) REVERT: G 24 ASN cc_start: 0.9079 (m-40) cc_final: 0.8848 (m-40) REVERT: H 140 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8710 (mmm) REVERT: H 223 ASP cc_start: 0.8953 (m-30) cc_final: 0.7867 (m-30) REVERT: H 234 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 242 ARG cc_start: 0.8909 (mmm-85) cc_final: 0.8569 (mmm-85) REVERT: A 302 TYR cc_start: 0.9191 (t80) cc_final: 0.8977 (t80) outliers start: 18 outliers final: 3 residues processed: 159 average time/residue: 1.5664 time to fit residues: 261.7964 Evaluate side-chains 141 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 439 TYR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 0.0170 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8843 Z= 0.235 Angle : 0.567 8.163 12016 Z= 0.308 Chirality : 0.043 0.138 1388 Planarity : 0.004 0.048 1511 Dihedral : 4.763 35.162 1220 Min Nonbonded Distance : 1.585 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.76 % Allowed : 13.10 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1110 helix: 0.89 (0.26), residues: 398 sheet: 0.44 (0.30), residues: 280 loop : -0.65 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.018 0.001 PHE R 189 TYR 0.017 0.001 TYR H 190 ARG 0.004 0.000 ARG R 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: R 64 GLN cc_start: 0.8299 (mt0) cc_final: 0.7703 (mt0) REVERT: R 107 LEU cc_start: 0.8152 (mt) cc_final: 0.7856 (tm) REVERT: R 143 ARG cc_start: 0.7624 (ptm160) cc_final: 0.7316 (mtm110) REVERT: R 223 ARG cc_start: 0.8509 (ptp-170) cc_final: 0.8195 (ptp-170) REVERT: R 439 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.7459 (t80) REVERT: R 465 ARG cc_start: 0.7840 (ttt90) cc_final: 0.6980 (tpt170) REVERT: B 215 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8299 (mp0) REVERT: B 217 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7285 (pmt) REVERT: B 254 ASP cc_start: 0.8119 (t70) cc_final: 0.7843 (t0) REVERT: G 20 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8484 (mtmp) REVERT: G 24 ASN cc_start: 0.9078 (m-40) cc_final: 0.8848 (m-40) REVERT: H 140 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8710 (mmm) REVERT: H 223 ASP cc_start: 0.8286 (m-30) cc_final: 0.7867 (m-30) REVERT: H 234 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 242 ARG cc_start: 0.8909 (mmm-85) cc_final: 0.8569 (mmm-85) outliers start: 7 outliers final: 3 residues processed: 138 average time/residue: 1.7294 time to fit residues: 249.9009 Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 439 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 10.0000 chunk 75 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.0470 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 18 GLN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8843 Z= 0.235 Angle : 0.567 8.163 12016 Z= 0.308 Chirality : 0.043 0.138 1388 Planarity : 0.004 0.048 1511 Dihedral : 4.763 35.162 1220 Min Nonbonded Distance : 1.585 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.65 % Allowed : 13.42 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1110 helix: 0.89 (0.26), residues: 398 sheet: 0.44 (0.30), residues: 280 loop : -0.65 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.018 0.001 PHE R 189 TYR 0.017 0.001 TYR H 190 ARG 0.004 0.000 ARG R 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: R 64 GLN cc_start: 0.8299 (mt0) cc_final: 0.7703 (mt0) REVERT: R 107 LEU cc_start: 0.8152 (mt) cc_final: 0.7856 (tm) REVERT: R 143 ARG cc_start: 0.7624 (ptm160) cc_final: 0.7316 (mtm110) REVERT: R 223 ARG cc_start: 0.8509 (ptp-170) cc_final: 0.8195 (ptp-170) REVERT: R 439 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.7459 (t80) REVERT: R 465 ARG cc_start: 0.7840 (ttt90) cc_final: 0.6980 (tpt170) REVERT: B 215 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8299 (mp0) REVERT: B 217 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7285 (pmt) REVERT: B 254 ASP cc_start: 0.8119 (t70) cc_final: 0.7843 (t0) REVERT: G 20 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8484 (mtmp) REVERT: G 24 ASN cc_start: 0.9078 (m-40) cc_final: 0.8848 (m-40) REVERT: H 140 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8710 (mmm) REVERT: H 223 ASP cc_start: 0.8286 (m-30) cc_final: 0.7867 (m-30) REVERT: H 234 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 242 ARG cc_start: 0.8909 (mmm-85) cc_final: 0.8569 (mmm-85) outliers start: 6 outliers final: 3 residues processed: 137 average time/residue: 1.7121 time to fit residues: 245.7704 Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 439 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 43 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 18 GLN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8843 Z= 0.235 Angle : 0.567 8.163 12016 Z= 0.308 Chirality : 0.043 0.138 1388 Planarity : 0.004 0.048 1511 Dihedral : 4.763 35.162 1220 Min Nonbonded Distance : 1.585 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.65 % Allowed : 13.42 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1110 helix: 0.89 (0.26), residues: 398 sheet: 0.44 (0.30), residues: 280 loop : -0.65 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.018 0.001 PHE R 189 TYR 0.017 0.001 TYR H 190 ARG 0.004 0.000 ARG R 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: R 64 GLN cc_start: 0.8299 (mt0) cc_final: 0.7703 (mt0) REVERT: R 107 LEU cc_start: 0.8152 (mt) cc_final: 0.7856 (tm) REVERT: R 143 ARG cc_start: 0.7624 (ptm160) cc_final: 0.7316 (mtm110) REVERT: R 223 ARG cc_start: 0.8509 (ptp-170) cc_final: 0.8195 (ptp-170) REVERT: R 439 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.7459 (t80) REVERT: R 465 ARG cc_start: 0.7840 (ttt90) cc_final: 0.6980 (tpt170) REVERT: B 215 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8299 (mp0) REVERT: B 217 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7285 (pmt) REVERT: B 254 ASP cc_start: 0.8119 (t70) cc_final: 0.7843 (t0) REVERT: G 20 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8484 (mtmp) REVERT: G 24 ASN cc_start: 0.9078 (m-40) cc_final: 0.8848 (m-40) REVERT: H 140 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8710 (mmm) REVERT: H 223 ASP cc_start: 0.8286 (m-30) cc_final: 0.7867 (m-30) REVERT: H 234 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 242 ARG cc_start: 0.8909 (mmm-85) cc_final: 0.8569 (mmm-85) outliers start: 6 outliers final: 3 residues processed: 137 average time/residue: 1.7059 time to fit residues: 244.9276 Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 439 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.8980 chunk 95 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 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 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 18 GLN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8843 Z= 0.235 Angle : 0.567 8.163 12016 Z= 0.308 Chirality : 0.043 0.138 1388 Planarity : 0.004 0.048 1511 Dihedral : 4.763 35.162 1220 Min Nonbonded Distance : 1.585 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.65 % Allowed : 13.42 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1110 helix: 0.89 (0.26), residues: 398 sheet: 0.44 (0.30), residues: 280 loop : -0.65 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.018 0.001 PHE R 189 TYR 0.017 0.001 TYR H 190 ARG 0.004 0.000 ARG R 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: R 64 GLN cc_start: 0.8299 (mt0) cc_final: 0.7703 (mt0) REVERT: R 107 LEU cc_start: 0.8152 (mt) cc_final: 0.7856 (tm) REVERT: R 143 ARG cc_start: 0.7624 (ptm160) cc_final: 0.7316 (mtm110) REVERT: R 223 ARG cc_start: 0.8509 (ptp-170) cc_final: 0.8195 (ptp-170) REVERT: R 439 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.7459 (t80) REVERT: R 465 ARG cc_start: 0.7840 (ttt90) cc_final: 0.6980 (tpt170) REVERT: B 215 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8299 (mp0) REVERT: B 217 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7285 (pmt) REVERT: B 254 ASP cc_start: 0.8119 (t70) cc_final: 0.7843 (t0) REVERT: G 20 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8484 (mtmp) REVERT: G 24 ASN cc_start: 0.9078 (m-40) cc_final: 0.8848 (m-40) REVERT: H 140 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8710 (mmm) REVERT: H 223 ASP cc_start: 0.8286 (m-30) cc_final: 0.7867 (m-30) REVERT: H 234 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 242 ARG cc_start: 0.8909 (mmm-85) cc_final: 0.8569 (mmm-85) outliers start: 6 outliers final: 3 residues processed: 137 average time/residue: 1.7668 time to fit residues: 253.8424 Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 439 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 0.0980 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 18 GLN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8843 Z= 0.235 Angle : 0.567 8.163 12016 Z= 0.308 Chirality : 0.043 0.138 1388 Planarity : 0.004 0.048 1511 Dihedral : 4.763 35.162 1220 Min Nonbonded Distance : 1.585 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.65 % Allowed : 13.42 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1110 helix: 0.89 (0.26), residues: 398 sheet: 0.44 (0.30), residues: 280 loop : -0.65 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.018 0.001 PHE R 189 TYR 0.017 0.001 TYR H 190 ARG 0.004 0.000 ARG R 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: R 64 GLN cc_start: 0.8299 (mt0) cc_final: 0.7703 (mt0) REVERT: R 107 LEU cc_start: 0.8152 (mt) cc_final: 0.7856 (tm) REVERT: R 143 ARG cc_start: 0.7624 (ptm160) cc_final: 0.7316 (mtm110) REVERT: R 223 ARG cc_start: 0.8509 (ptp-170) cc_final: 0.8195 (ptp-170) REVERT: R 439 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.7459 (t80) REVERT: R 465 ARG cc_start: 0.7840 (ttt90) cc_final: 0.6980 (tpt170) REVERT: B 215 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8299 (mp0) REVERT: B 217 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7285 (pmt) REVERT: B 254 ASP cc_start: 0.8119 (t70) cc_final: 0.7843 (t0) REVERT: G 20 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8484 (mtmp) REVERT: G 24 ASN cc_start: 0.9078 (m-40) cc_final: 0.8848 (m-40) REVERT: H 140 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8710 (mmm) REVERT: H 223 ASP cc_start: 0.8286 (m-30) cc_final: 0.7867 (m-30) REVERT: H 234 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 242 ARG cc_start: 0.8909 (mmm-85) cc_final: 0.8569 (mmm-85) outliers start: 6 outliers final: 3 residues processed: 137 average time/residue: 1.7539 time to fit residues: 251.5130 Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 439 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 18 GLN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8843 Z= 0.235 Angle : 0.567 8.163 12016 Z= 0.308 Chirality : 0.043 0.138 1388 Planarity : 0.004 0.048 1511 Dihedral : 4.763 35.162 1220 Min Nonbonded Distance : 1.585 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.65 % Allowed : 13.42 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1110 helix: 0.89 (0.26), residues: 398 sheet: 0.44 (0.30), residues: 280 loop : -0.65 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.018 0.001 PHE R 189 TYR 0.017 0.001 TYR H 190 ARG 0.004 0.000 ARG R 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: R 64 GLN cc_start: 0.8299 (mt0) cc_final: 0.7703 (mt0) REVERT: R 107 LEU cc_start: 0.8152 (mt) cc_final: 0.7856 (tm) REVERT: R 143 ARG cc_start: 0.7624 (ptm160) cc_final: 0.7316 (mtm110) REVERT: R 223 ARG cc_start: 0.8509 (ptp-170) cc_final: 0.8195 (ptp-170) REVERT: R 439 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.7459 (t80) REVERT: R 465 ARG cc_start: 0.7840 (ttt90) cc_final: 0.6980 (tpt170) REVERT: B 215 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8299 (mp0) REVERT: B 217 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7285 (pmt) REVERT: B 254 ASP cc_start: 0.8119 (t70) cc_final: 0.7843 (t0) REVERT: G 20 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8484 (mtmp) REVERT: G 24 ASN cc_start: 0.9078 (m-40) cc_final: 0.8848 (m-40) REVERT: H 140 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8710 (mmm) REVERT: H 223 ASP cc_start: 0.8286 (m-30) cc_final: 0.7867 (m-30) REVERT: H 234 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 242 ARG cc_start: 0.8909 (mmm-85) cc_final: 0.8569 (mmm-85) outliers start: 6 outliers final: 3 residues processed: 137 average time/residue: 1.7555 time to fit residues: 251.7157 Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 439 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 18 GLN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8843 Z= 0.235 Angle : 0.567 8.163 12016 Z= 0.308 Chirality : 0.043 0.138 1388 Planarity : 0.004 0.048 1511 Dihedral : 4.763 35.162 1220 Min Nonbonded Distance : 1.585 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.65 % Allowed : 13.42 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1110 helix: 0.89 (0.26), residues: 398 sheet: 0.44 (0.30), residues: 280 loop : -0.65 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.018 0.001 PHE R 189 TYR 0.017 0.001 TYR H 190 ARG 0.004 0.000 ARG R 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: R 64 GLN cc_start: 0.8299 (mt0) cc_final: 0.7703 (mt0) REVERT: R 107 LEU cc_start: 0.8152 (mt) cc_final: 0.7856 (tm) REVERT: R 143 ARG cc_start: 0.7624 (ptm160) cc_final: 0.7316 (mtm110) REVERT: R 223 ARG cc_start: 0.8509 (ptp-170) cc_final: 0.8195 (ptp-170) REVERT: R 439 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.7459 (t80) REVERT: R 465 ARG cc_start: 0.7840 (ttt90) cc_final: 0.6980 (tpt170) REVERT: B 215 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8299 (mp0) REVERT: B 217 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7285 (pmt) REVERT: B 254 ASP cc_start: 0.8119 (t70) cc_final: 0.7843 (t0) REVERT: G 20 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8484 (mtmp) REVERT: G 24 ASN cc_start: 0.9078 (m-40) cc_final: 0.8848 (m-40) REVERT: H 140 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8710 (mmm) REVERT: H 223 ASP cc_start: 0.8286 (m-30) cc_final: 0.7867 (m-30) REVERT: H 234 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 242 ARG cc_start: 0.8909 (mmm-85) cc_final: 0.8569 (mmm-85) outliers start: 6 outliers final: 3 residues processed: 137 average time/residue: 1.7228 time to fit residues: 247.3327 Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 439 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 0.0980 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 18 GLN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8843 Z= 0.235 Angle : 0.567 8.163 12016 Z= 0.308 Chirality : 0.043 0.138 1388 Planarity : 0.004 0.048 1511 Dihedral : 4.763 35.162 1220 Min Nonbonded Distance : 1.585 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.65 % Allowed : 13.42 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1110 helix: 0.89 (0.26), residues: 398 sheet: 0.44 (0.30), residues: 280 loop : -0.65 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.018 0.001 PHE R 189 TYR 0.017 0.001 TYR H 190 ARG 0.004 0.000 ARG R 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: R 64 GLN cc_start: 0.8299 (mt0) cc_final: 0.7703 (mt0) REVERT: R 107 LEU cc_start: 0.8152 (mt) cc_final: 0.7856 (tm) REVERT: R 143 ARG cc_start: 0.7624 (ptm160) cc_final: 0.7316 (mtm110) REVERT: R 223 ARG cc_start: 0.8509 (ptp-170) cc_final: 0.8195 (ptp-170) REVERT: R 439 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.7459 (t80) REVERT: R 465 ARG cc_start: 0.7840 (ttt90) cc_final: 0.6980 (tpt170) REVERT: B 215 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8299 (mp0) REVERT: B 217 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7285 (pmt) REVERT: B 254 ASP cc_start: 0.8119 (t70) cc_final: 0.7843 (t0) REVERT: G 20 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8484 (mtmp) REVERT: G 24 ASN cc_start: 0.9078 (m-40) cc_final: 0.8848 (m-40) REVERT: H 140 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8710 (mmm) REVERT: H 223 ASP cc_start: 0.8286 (m-30) cc_final: 0.7867 (m-30) REVERT: H 234 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 242 ARG cc_start: 0.8909 (mmm-85) cc_final: 0.8569 (mmm-85) outliers start: 6 outliers final: 3 residues processed: 137 average time/residue: 1.7218 time to fit residues: 247.1424 Evaluate side-chains 139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 439 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 87 optimal weight: 0.0370 chunk 36 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 18 GLN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.090600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.062208 restraints weight = 16560.899| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.86 r_work: 0.2644 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8843 Z= 0.235 Angle : 0.567 8.163 12016 Z= 0.308 Chirality : 0.043 0.138 1388 Planarity : 0.004 0.048 1511 Dihedral : 4.763 35.162 1220 Min Nonbonded Distance : 1.585 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.65 % Allowed : 13.42 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1110 helix: 0.89 (0.26), residues: 398 sheet: 0.44 (0.30), residues: 280 loop : -0.65 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.018 0.001 PHE R 189 TYR 0.017 0.001 TYR H 190 ARG 0.004 0.000 ARG R 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4133.93 seconds wall clock time: 74 minutes 40.17 seconds (4480.17 seconds total)