Starting phenix.real_space_refine on Sat Dec 28 21:05:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ykd_33891/12_2024/7ykd_33891.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ykd_33891/12_2024/7ykd_33891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ykd_33891/12_2024/7ykd_33891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ykd_33891/12_2024/7ykd_33891.map" model { file = "/net/cci-nas-00/data/ceres_data/7ykd_33891/12_2024/7ykd_33891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ykd_33891/12_2024/7ykd_33891.cif" } resolution = 2.81 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= 0.021 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 68 5.16 5 C 5778 2.51 5 N 1496 2.21 5 O 1623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8965 Number of models: 1 Model: "" Number of chains: 7 Chain: "L" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 76 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "A" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2250 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 10, 'TRANS': 271} Chain breaks: 1 Chain: "C" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1716 Classifications: {'peptide': 216} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2580 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.56, per 1000 atoms: 0.62 Number of scatterers: 8965 At special positions: 0 Unit cell: (87.98, 121.18, 121.18, 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 68 16.00 O 1623 8.00 N 1496 7.00 C 5778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 38.2% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 35 through 68 Processing helix chain 'A' and resid 72 through 101 removed outlier: 3.675A pdb=" N TRP A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 108 through 143 removed outlier: 3.987A pdb=" N LEU A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 151 Processing helix chain 'A' and resid 152 through 172 Processing helix chain 'A' and resid 172 through 177 removed outlier: 3.680A pdb=" N VAL A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 177' Processing helix chain 'A' and resid 211 through 250 removed outlier: 6.143A pdb=" N VAL A 231 " --> pdb=" O CYS A 227 " (cutoff:3.500A) Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 256 through 283 Proline residue: A 275 - end of helix Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 290 through 317 removed outlier: 4.018A pdb=" N PHE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Proline residue: A 299 - end of helix Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 319 through 328 removed outlier: 3.975A pdb=" N PHE A 323 " --> pdb=" O MET A 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.568A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 279 removed outlier: 4.200A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.610A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 removed outlier: 4.193A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 352 removed outlier: 3.651A pdb=" N GLN C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.656A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 183 removed outlier: 3.721A pdb=" N LEU A 183 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 185 through 191 removed outlier: 3.639A pdb=" N PHE C 189 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.141A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.511A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.968A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.752A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.651A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.635A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.010A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.654A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.340A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.577A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.661A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1308 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: 2.81 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: 1438 1.32 - 1.44: 2502 1.44 - 1.56: 5131 1.56 - 1.69: 0 1.69 - 1.81: 99 Bond restraints: 9170 Sorted by residual: bond pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 1.523 1.442 0.081 1.34e-02 5.57e+03 3.68e+01 bond pdb=" CA LYS B 337 " pdb=" C LYS B 337 " ideal model delta sigma weight residual 1.521 1.471 0.050 1.24e-02 6.50e+03 1.61e+01 bond pdb=" C LEU A 143 " pdb=" N PRO A 144 " ideal model delta sigma weight residual 1.336 1.381 -0.045 1.23e-02 6.61e+03 1.36e+01 bond pdb=" CA PHE B 335 " pdb=" C PHE B 335 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.20e-02 6.94e+03 1.30e+01 bond pdb=" C LYS B 337 " pdb=" O LYS B 337 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.22e-02 6.72e+03 1.02e+01 ... (remaining 9165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 11910 1.85 - 3.71: 438 3.71 - 5.56: 75 5.56 - 7.41: 19 7.41 - 9.27: 7 Bond angle restraints: 12449 Sorted by residual: angle pdb=" N VAL S 2 " pdb=" CA VAL S 2 " pdb=" C VAL S 2 " ideal model delta sigma weight residual 112.43 104.83 7.60 9.20e-01 1.18e+00 6.82e+01 angle pdb=" N LEU B 336 " pdb=" CA LEU B 336 " pdb=" C LEU B 336 " ideal model delta sigma weight residual 109.40 102.00 7.40 1.63e+00 3.76e-01 2.06e+01 angle pdb=" CA ASP B 291 " pdb=" C ASP B 291 " pdb=" O ASP B 291 " ideal model delta sigma weight residual 120.51 114.44 6.07 1.43e+00 4.89e-01 1.80e+01 angle pdb=" N VAL A 141 " pdb=" CA VAL A 141 " pdb=" C VAL A 141 " ideal model delta sigma weight residual 111.90 108.60 3.30 8.10e-01 1.52e+00 1.66e+01 angle pdb=" CA LEU A 143 " pdb=" C LEU A 143 " pdb=" N PRO A 144 " ideal model delta sigma weight residual 117.73 121.77 -4.04 1.04e+00 9.25e-01 1.51e+01 ... (remaining 12444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.97: 5384 23.97 - 47.94: 217 47.94 - 71.91: 31 71.91 - 95.88: 19 95.88 - 119.85: 1 Dihedral angle restraints: 5652 sinusoidal: 2373 harmonic: 3279 Sorted by residual: dihedral pdb=" CB CYS A 112 " pdb=" SG CYS A 112 " pdb=" SG CYS A 189 " pdb=" CB CYS A 189 " ideal model delta sinusoidal sigma weight residual 93.00 161.98 -68.98 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 152.46 27.54 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA PHE A 67 " pdb=" C PHE A 67 " pdb=" N LYS A 68 " pdb=" CA LYS A 68 " ideal model delta harmonic sigma weight residual -180.00 -158.32 -21.68 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 5649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1218 0.075 - 0.150: 204 0.150 - 0.226: 5 0.226 - 0.301: 3 0.301 - 0.376: 3 Chirality restraints: 1433 Sorted by residual: chirality pdb=" CA ASP B 312 " pdb=" N ASP B 312 " pdb=" C ASP B 312 " pdb=" CB ASP B 312 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" C20 CLR A 403 " pdb=" C17 CLR A 403 " pdb=" C21 CLR A 403 " pdb=" C22 CLR A 403 " both_signs ideal model delta sigma weight residual False 2.59 2.23 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C20 CLR A 405 " pdb=" C17 CLR A 405 " pdb=" C21 CLR A 405 " pdb=" C22 CLR A 405 " both_signs ideal model delta sigma weight residual False 2.59 2.24 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 1430 not shown) Planarity restraints: 1535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 23 " 0.033 2.00e-02 2.50e+03 2.02e-02 7.16e+00 pdb=" CG PHE L 23 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE L 23 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE L 23 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE L 23 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE L 23 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE L 23 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO S 75 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 226 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C LEU A 226 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU A 226 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS A 227 " -0.011 2.00e-02 2.50e+03 ... (remaining 1532 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 202 2.67 - 3.23: 8639 3.23 - 3.79: 14242 3.79 - 4.34: 19809 4.34 - 4.90: 33702 Nonbonded interactions: 76594 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.118 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.122 3.040 nonbonded pdb=" C25 CLR A 402 " pdb=" C21 CLR A 403 " model vdw 2.146 3.890 nonbonded pdb=" NZ LYS S 244 " pdb=" OE2 GLU S 246 " model vdw 2.160 3.120 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.175 3.120 ... (remaining 76589 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.380 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.009 0.081 9170 Z= 0.562 Angle : 0.860 9.265 12449 Z= 0.461 Chirality : 0.055 0.376 1433 Planarity : 0.004 0.057 1535 Dihedral : 14.190 119.850 3525 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.10 % Allowed : 0.83 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.18 (0.25), residues: 1111 helix: 0.91 (0.26), residues: 382 sheet: -0.04 (0.32), residues: 288 loop : -1.01 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 47 HIS 0.006 0.002 HIS A 217 PHE 0.033 0.003 PHE L 23 TYR 0.019 0.002 TYR B 105 ARG 0.009 0.001 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 1.110 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 33 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7468 (mm-30) REVERT: B 291 ASP cc_start: 0.7436 (m-30) cc_final: 0.7077 (m-30) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 1.5856 time to fit residues: 249.7171 Evaluate side-chains 118 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 chunk 87 optimal weight: 0.0070 chunk 33 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 0.4980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9170 Z= 0.198 Angle : 0.660 8.102 12449 Z= 0.330 Chirality : 0.046 0.300 1433 Planarity : 0.004 0.049 1535 Dihedral : 7.084 57.368 1539 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.56 % Allowed : 9.27 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.32 (0.25), residues: 1111 helix: 1.61 (0.26), residues: 385 sheet: 0.07 (0.32), residues: 263 loop : -0.87 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.009 0.001 HIS A 184 PHE 0.017 0.001 PHE A 190 TYR 0.016 0.001 TYR A 103 ARG 0.011 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 1.126 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 33 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7293 (mm-30) REVERT: C 248 LYS cc_start: 0.7982 (mmtt) cc_final: 0.7774 (mmtt) REVERT: B 13 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8472 (pp30) REVERT: B 19 ARG cc_start: 0.8034 (tmm160) cc_final: 0.7760 (ttp-110) REVERT: B 23 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8680 (ttmt) REVERT: S 202 ARG cc_start: 0.8399 (ptt-90) cc_final: 0.8106 (ptt-90) outliers start: 15 outliers final: 4 residues processed: 134 average time/residue: 1.3793 time to fit residues: 196.2806 Evaluate side-chains 119 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 83 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.0040 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 0.0170 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9170 Z= 0.193 Angle : 0.623 12.623 12449 Z= 0.308 Chirality : 0.045 0.259 1433 Planarity : 0.004 0.045 1535 Dihedral : 7.332 69.143 1539 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.77 % Allowed : 12.19 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.50 (0.26), residues: 1111 helix: 1.90 (0.26), residues: 385 sheet: -0.07 (0.30), residues: 282 loop : -0.74 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.010 0.001 HIS A 184 PHE 0.010 0.001 PHE B 151 TYR 0.013 0.001 TYR B 59 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 1.011 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 248 LYS cc_start: 0.7994 (mmtt) cc_final: 0.7773 (mmtt) REVERT: C 263 SER cc_start: 0.8842 (m) cc_final: 0.8618 (p) REVERT: B 19 ARG cc_start: 0.8073 (tmm160) cc_final: 0.7683 (ttp-110) REVERT: B 23 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8624 (ttmt) REVERT: B 160 SER cc_start: 0.8480 (t) cc_final: 0.7954 (p) REVERT: S 6 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7247 (mt-10) REVERT: S 202 ARG cc_start: 0.8386 (ptt-90) cc_final: 0.8089 (ptt-90) outliers start: 17 outliers final: 5 residues processed: 143 average time/residue: 1.3634 time to fit residues: 207.3914 Evaluate side-chains 131 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 197 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 0.3980 chunk 107 optimal weight: 0.9980 chunk 96 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN B 75 GLN S 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9170 Z= 0.203 Angle : 0.617 13.706 12449 Z= 0.305 Chirality : 0.045 0.264 1433 Planarity : 0.004 0.044 1535 Dihedral : 6.854 57.490 1539 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.08 % Allowed : 13.96 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.26), residues: 1111 helix: 2.07 (0.26), residues: 385 sheet: -0.05 (0.30), residues: 275 loop : -0.77 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.010 0.001 HIS A 184 PHE 0.015 0.001 PHE A 52 TYR 0.012 0.001 TYR B 264 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 1.065 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 263 SER cc_start: 0.8848 (m) cc_final: 0.8612 (p) REVERT: B 19 ARG cc_start: 0.8170 (tmm160) cc_final: 0.7854 (ttp-110) REVERT: B 44 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7841 (mm-40) REVERT: B 160 SER cc_start: 0.8546 (t) cc_final: 0.8196 (p) REVERT: B 217 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.6842 (pmm) REVERT: S 6 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7225 (mt-10) REVERT: S 109 ASP cc_start: 0.8350 (p0) cc_final: 0.8137 (p0) REVERT: S 186 GLN cc_start: 0.7988 (tt0) cc_final: 0.7784 (pt0) REVERT: S 202 ARG cc_start: 0.8357 (ptt-90) cc_final: 0.8009 (ptt-90) outliers start: 20 outliers final: 9 residues processed: 143 average time/residue: 1.3375 time to fit residues: 203.5533 Evaluate side-chains 130 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9170 Z= 0.302 Angle : 0.646 14.882 12449 Z= 0.325 Chirality : 0.045 0.269 1433 Planarity : 0.004 0.046 1535 Dihedral : 6.376 58.959 1539 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.29 % Allowed : 15.00 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.55 (0.25), residues: 1111 helix: 2.04 (0.26), residues: 385 sheet: -0.03 (0.30), residues: 267 loop : -0.82 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 77 HIS 0.010 0.001 HIS A 184 PHE 0.015 0.001 PHE A 124 TYR 0.014 0.001 TYR B 264 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.090 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 53 MET cc_start: 0.7308 (mpp) cc_final: 0.6814 (mtt) REVERT: B 19 ARG cc_start: 0.8205 (tmm160) cc_final: 0.7730 (ttp-110) REVERT: B 44 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7855 (mm-40) REVERT: B 217 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7006 (pmm) REVERT: B 301 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8607 (mtpp) REVERT: G 42 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: S 6 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7193 (mt-10) REVERT: S 109 ASP cc_start: 0.8395 (p0) cc_final: 0.8188 (p0) REVERT: S 202 ARG cc_start: 0.8358 (ptt-90) cc_final: 0.7994 (ptt-90) outliers start: 22 outliers final: 9 residues processed: 138 average time/residue: 1.4527 time to fit residues: 213.1643 Evaluate side-chains 131 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.0270 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9170 Z= 0.208 Angle : 0.612 15.756 12449 Z= 0.307 Chirality : 0.044 0.269 1433 Planarity : 0.004 0.044 1535 Dihedral : 6.206 59.290 1539 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.92 % Allowed : 15.73 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.66 (0.26), residues: 1111 helix: 2.13 (0.26), residues: 385 sheet: -0.01 (0.30), residues: 267 loop : -0.73 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 77 HIS 0.009 0.001 HIS A 184 PHE 0.016 0.001 PHE A 52 TYR 0.013 0.001 TYR B 59 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 1.046 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 53 MET cc_start: 0.7296 (mpp) cc_final: 0.6949 (mtt) REVERT: C 263 SER cc_start: 0.8838 (m) cc_final: 0.8604 (p) REVERT: B 19 ARG cc_start: 0.8200 (tmm160) cc_final: 0.7724 (ttp-110) REVERT: B 44 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7869 (mm-40) REVERT: B 217 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7015 (pmm) REVERT: B 301 LYS cc_start: 0.8841 (mtpt) cc_final: 0.8620 (mtpp) REVERT: G 21 MET cc_start: 0.8432 (tpp) cc_final: 0.8143 (tpp) REVERT: G 42 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: S 6 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7197 (mt-10) REVERT: S 186 GLN cc_start: 0.8005 (tt0) cc_final: 0.7783 (pt0) REVERT: S 202 ARG cc_start: 0.8359 (ptt-90) cc_final: 0.7968 (ptt-90) outliers start: 28 outliers final: 12 residues processed: 138 average time/residue: 1.3771 time to fit residues: 201.9983 Evaluate side-chains 130 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 0.0770 chunk 66 optimal weight: 0.0060 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 overall best weight: 0.4554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9170 Z= 0.173 Angle : 0.604 16.724 12449 Z= 0.300 Chirality : 0.043 0.265 1433 Planarity : 0.003 0.043 1535 Dihedral : 5.988 57.598 1539 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.29 % Allowed : 17.40 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1111 helix: 2.22 (0.26), residues: 385 sheet: 0.14 (0.30), residues: 276 loop : -0.70 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.010 0.001 HIS A 184 PHE 0.010 0.001 PHE B 151 TYR 0.012 0.001 TYR B 59 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.070 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 53 MET cc_start: 0.7261 (mpp) cc_final: 0.6767 (mtt) REVERT: C 263 SER cc_start: 0.8845 (m) cc_final: 0.8634 (p) REVERT: B 19 ARG cc_start: 0.8188 (tmm160) cc_final: 0.7709 (ttp-110) REVERT: B 44 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7919 (mm-40) REVERT: B 217 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7086 (pmm) REVERT: B 301 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8604 (mtpp) REVERT: G 21 MET cc_start: 0.8453 (tpp) cc_final: 0.8171 (tpp) REVERT: G 42 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: S 186 GLN cc_start: 0.8011 (tt0) cc_final: 0.7694 (pt0) outliers start: 22 outliers final: 10 residues processed: 140 average time/residue: 1.3188 time to fit residues: 196.9466 Evaluate side-chains 127 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 197 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9170 Z= 0.300 Angle : 0.665 16.418 12449 Z= 0.334 Chirality : 0.046 0.263 1433 Planarity : 0.004 0.044 1535 Dihedral : 6.184 59.648 1539 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.81 % Allowed : 17.71 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.67 (0.26), residues: 1111 helix: 2.09 (0.26), residues: 385 sheet: -0.05 (0.30), residues: 287 loop : -0.66 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 77 HIS 0.009 0.001 HIS A 184 PHE 0.033 0.002 PHE C 274 TYR 0.011 0.001 TYR B 59 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 1.357 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 53 MET cc_start: 0.7296 (mpp) cc_final: 0.6864 (mtt) REVERT: B 19 ARG cc_start: 0.8207 (tmm160) cc_final: 0.7738 (ttp-110) REVERT: B 44 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7841 (mm-40) REVERT: B 217 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7103 (pmm) REVERT: B 301 LYS cc_start: 0.8876 (mtpt) cc_final: 0.8650 (mtpp) REVERT: G 21 MET cc_start: 0.8457 (tpp) cc_final: 0.8167 (tpp) REVERT: G 42 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6780 (mp0) REVERT: S 186 GLN cc_start: 0.8020 (tt0) cc_final: 0.7758 (pt0) outliers start: 27 outliers final: 11 residues processed: 135 average time/residue: 1.5029 time to fit residues: 215.7216 Evaluate side-chains 126 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9170 Z= 0.211 Angle : 0.644 17.204 12449 Z= 0.324 Chirality : 0.044 0.256 1433 Planarity : 0.004 0.043 1535 Dihedral : 6.066 59.977 1539 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.46 % Allowed : 19.27 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.72 (0.26), residues: 1111 helix: 2.13 (0.26), residues: 385 sheet: 0.04 (0.30), residues: 276 loop : -0.66 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 77 HIS 0.009 0.001 HIS A 184 PHE 0.028 0.001 PHE C 274 TYR 0.012 0.001 TYR B 59 ARG 0.013 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 1.152 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 53 MET cc_start: 0.7288 (mpp) cc_final: 0.6901 (mtt) REVERT: C 263 SER cc_start: 0.8846 (m) cc_final: 0.8626 (p) REVERT: B 19 ARG cc_start: 0.8177 (tmm160) cc_final: 0.7685 (ttp-110) REVERT: B 44 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7811 (mm-40) REVERT: B 217 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7113 (pmm) REVERT: B 259 GLN cc_start: 0.8376 (pm20) cc_final: 0.8019 (pm20) REVERT: B 301 LYS cc_start: 0.8856 (mtpt) cc_final: 0.8587 (mtpp) REVERT: G 21 MET cc_start: 0.8457 (tpp) cc_final: 0.8155 (tpp) REVERT: G 42 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: S 186 GLN cc_start: 0.7987 (tt0) cc_final: 0.7751 (pt0) outliers start: 14 outliers final: 9 residues processed: 131 average time/residue: 1.4139 time to fit residues: 196.5388 Evaluate side-chains 125 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 197 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 101 optimal weight: 0.4980 chunk 88 optimal weight: 0.0770 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9170 Z= 0.194 Angle : 0.645 17.753 12449 Z= 0.324 Chirality : 0.044 0.243 1433 Planarity : 0.004 0.046 1535 Dihedral : 5.933 59.886 1539 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.98 % Allowed : 18.75 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.74 (0.26), residues: 1111 helix: 2.09 (0.26), residues: 386 sheet: 0.06 (0.30), residues: 276 loop : -0.60 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 77 HIS 0.009 0.001 HIS A 184 PHE 0.028 0.001 PHE C 274 TYR 0.012 0.001 TYR B 59 ARG 0.013 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.144 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 53 MET cc_start: 0.7283 (mpp) cc_final: 0.6910 (mtt) REVERT: C 263 SER cc_start: 0.8853 (m) cc_final: 0.8641 (p) REVERT: B 19 ARG cc_start: 0.8151 (tmm160) cc_final: 0.7666 (ttp-110) REVERT: B 44 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7863 (mt0) REVERT: B 217 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7132 (pmm) REVERT: B 259 GLN cc_start: 0.8383 (pm20) cc_final: 0.8069 (pm20) REVERT: B 301 LYS cc_start: 0.8854 (mtpt) cc_final: 0.8588 (mtpp) REVERT: G 21 MET cc_start: 0.8457 (tpp) cc_final: 0.8158 (tpp) REVERT: G 42 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: S 186 GLN cc_start: 0.7979 (tt0) cc_final: 0.7757 (pt0) outliers start: 19 outliers final: 11 residues processed: 129 average time/residue: 1.4122 time to fit residues: 193.9584 Evaluate side-chains 124 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.148260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102562 restraints weight = 11436.240| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.61 r_work: 0.3143 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9170 Z= 0.210 Angle : 0.653 18.255 12449 Z= 0.328 Chirality : 0.044 0.233 1433 Planarity : 0.004 0.046 1535 Dihedral : 5.912 58.684 1539 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.98 % Allowed : 19.06 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.69 (0.26), residues: 1111 helix: 1.99 (0.27), residues: 392 sheet: 0.11 (0.31), residues: 270 loop : -0.66 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 77 HIS 0.009 0.001 HIS A 184 PHE 0.028 0.001 PHE C 274 TYR 0.012 0.001 TYR B 59 ARG 0.012 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3919.61 seconds wall clock time: 71 minutes 5.56 seconds (4265.56 seconds total)