Starting phenix.real_space_refine on Thu Feb 13 15:49:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ykd_33891/02_2025/7ykd_33891.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ykd_33891/02_2025/7ykd_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_33891/02_2025/7ykd_33891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ykd_33891/02_2025/7ykd_33891.map" model { file = "/net/cci-nas-00/data/ceres_data/7ykd_33891/02_2025/7ykd_33891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ykd_33891/02_2025/7ykd_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.36, per 1000 atoms: 0.60 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: 2.40 Conformation dependent library (CDL) restraints added in 1.0 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: 1.15 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: 2.66 Time building geometry restraints manager: 2.74 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: 1.720 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.670 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.070 ------------------------------------------------------------------------------- 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 : 0.970 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: 1.5744 time to fit residues: 247.5067 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 : 1.164 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.148088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.103659 restraints weight = 11461.094| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.39 r_work: 0.3151 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 : 0.988 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 33 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7458 (mm-30) REVERT: C 248 LYS cc_start: 0.7885 (mmtt) cc_final: 0.7632 (mmtt) REVERT: B 13 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8471 (pp30) REVERT: B 19 ARG cc_start: 0.7669 (tmm160) cc_final: 0.7416 (ttp-110) REVERT: B 198 LEU cc_start: 0.8331 (pp) cc_final: 0.8108 (pt) REVERT: S 202 ARG cc_start: 0.8113 (ptt-90) cc_final: 0.7823 (ptt-90) outliers start: 15 outliers final: 4 residues processed: 134 average time/residue: 1.3966 time to fit residues: 198.4603 Evaluate side-chains 119 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 LEU 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 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN S 82 GLN S 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.146062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.100457 restraints weight = 11712.804| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.62 r_work: 0.3120 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9170 Z= 0.214 Angle : 0.631 12.970 12449 Z= 0.313 Chirality : 0.045 0.257 1433 Planarity : 0.004 0.046 1535 Dihedral : 7.424 71.508 1539 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.98 % Allowed : 11.98 % 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: 0.48 (0.26), residues: 1111 helix: 1.88 (0.26), residues: 385 sheet: -0.09 (0.30), residues: 282 loop : -0.76 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 77 HIS 0.010 0.001 HIS A 184 PHE 0.011 0.001 PHE A 124 TYR 0.013 0.001 TYR B 59 ARG 0.005 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: 19 poor density : 133 time to evaluate : 1.070 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 25 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6542 (tt0) REVERT: C 248 LYS cc_start: 0.7636 (mmtt) cc_final: 0.7365 (mptt) REVERT: C 263 SER cc_start: 0.9017 (m) cc_final: 0.8725 (p) REVERT: B 19 ARG cc_start: 0.7462 (tmm160) cc_final: 0.7101 (ttp-110) REVERT: B 44 GLN cc_start: 0.8409 (mt0) cc_final: 0.7997 (mm-40) REVERT: B 160 SER cc_start: 0.8523 (t) cc_final: 0.7748 (p) REVERT: B 198 LEU cc_start: 0.8009 (pp) cc_final: 0.7728 (pt) REVERT: S 6 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.6970 (mt-10) REVERT: S 202 ARG cc_start: 0.7761 (ptt-90) cc_final: 0.7489 (ptt-90) REVERT: S 246 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8012 (mp0) outliers start: 19 outliers final: 7 residues processed: 144 average time/residue: 1.3746 time to fit residues: 210.2693 Evaluate side-chains 133 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 339 VAL 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 Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 246 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.144378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.098861 restraints weight = 11598.593| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.59 r_work: 0.3094 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1767 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= 0.299 Angle : 0.654 13.934 12449 Z= 0.326 Chirality : 0.046 0.266 1433 Planarity : 0.004 0.046 1535 Dihedral : 7.129 57.998 1539 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.40 % Allowed : 13.96 % Favored : 83.65 % 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: 0.44 (0.25), residues: 1111 helix: 1.94 (0.26), residues: 385 sheet: -0.16 (0.30), residues: 274 loop : -0.83 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 77 HIS 0.010 0.001 HIS A 184 PHE 0.015 0.002 PHE A 124 TYR 0.014 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 147 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.994 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 188 SER cc_start: 0.6097 (OUTLIER) cc_final: 0.5662 (p) REVERT: C 25 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6613 (tt0) REVERT: C 33 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7290 (mt-10) REVERT: C 248 LYS cc_start: 0.7702 (mmtt) cc_final: 0.7433 (mmtt) REVERT: B 19 ARG cc_start: 0.7520 (tmm160) cc_final: 0.7223 (ttp-110) REVERT: B 44 GLN cc_start: 0.8417 (mt0) cc_final: 0.8040 (mm-40) REVERT: B 100 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8714 (m) REVERT: B 217 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.6723 (pmm) REVERT: G 42 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: S 6 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.6978 (mt-10) REVERT: S 202 ARG cc_start: 0.7770 (ptt-90) cc_final: 0.7450 (ptt-90) REVERT: S 246 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8081 (mt-10) outliers start: 23 outliers final: 9 residues processed: 140 average time/residue: 1.4376 time to fit residues: 213.9237 Evaluate side-chains 132 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 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 158 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 246 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.144052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098091 restraints weight = 11572.573| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.61 r_work: 0.3078 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9170 Z= 0.306 Angle : 0.643 14.718 12449 Z= 0.324 Chirality : 0.045 0.270 1433 Planarity : 0.004 0.046 1535 Dihedral : 6.517 58.750 1539 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.12 % Allowed : 13.96 % Favored : 82.92 % 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: 0.41 (0.25), residues: 1111 helix: 1.93 (0.26), residues: 385 sheet: -0.18 (0.30), residues: 274 loop : -0.85 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 77 HIS 0.010 0.001 HIS A 184 PHE 0.017 0.002 PHE A 190 TYR 0.014 0.001 TYR B 264 ARG 0.009 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 154 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 1.061 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 289 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8420 (mtp) REVERT: C 25 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6606 (tt0) REVERT: C 33 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7329 (mt-10) REVERT: C 248 LYS cc_start: 0.7708 (mmtt) cc_final: 0.7453 (mmtt) REVERT: B 19 ARG cc_start: 0.7647 (tmm160) cc_final: 0.7194 (ttp-110) REVERT: B 44 GLN cc_start: 0.8447 (mt0) cc_final: 0.8094 (mm-40) REVERT: B 100 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8727 (m) REVERT: B 217 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7199 (pmm) REVERT: B 301 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7905 (mtpp) REVERT: G 42 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: S 6 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: S 186 GLN cc_start: 0.8225 (tt0) cc_final: 0.7912 (pt0) REVERT: S 202 ARG cc_start: 0.7748 (ptt-90) cc_final: 0.7400 (ptt-90) REVERT: S 246 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8146 (mt-10) outliers start: 30 outliers final: 14 residues processed: 143 average time/residue: 1.3466 time to fit residues: 205.8401 Evaluate side-chains 139 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 33 GLU 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 305 CYS Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 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 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 Chi-restraints excluded: chain S residue 246 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 84 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.144794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.099007 restraints weight = 11523.997| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.60 r_work: 0.3092 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9170 Z= 0.260 Angle : 0.635 16.035 12449 Z= 0.319 Chirality : 0.045 0.272 1433 Planarity : 0.004 0.045 1535 Dihedral : 6.407 59.488 1539 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.33 % Allowed : 15.42 % Favored : 81.25 % 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: 0.47 (0.25), residues: 1111 helix: 2.00 (0.26), residues: 385 sheet: -0.16 (0.30), residues: 274 loop : -0.83 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 77 HIS 0.010 0.001 HIS A 184 PHE 0.017 0.001 PHE A 190 TYR 0.013 0.001 TYR B 264 ARG 0.007 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 151 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.984 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 289 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8404 (mtp) REVERT: C 25 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6598 (tt0) REVERT: C 33 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7330 (mt-10) REVERT: C 248 LYS cc_start: 0.7703 (mmtt) cc_final: 0.7453 (mmtt) REVERT: B 19 ARG cc_start: 0.7655 (tmm160) cc_final: 0.7339 (ttp-110) REVERT: B 44 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8077 (mm-40) REVERT: B 100 VAL cc_start: 0.8946 (OUTLIER) cc_final: 0.8719 (m) REVERT: B 198 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7803 (pt) REVERT: B 217 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7153 (pmm) REVERT: B 301 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7912 (mtpp) REVERT: G 21 MET cc_start: 0.8311 (tpp) cc_final: 0.8032 (tpp) REVERT: G 42 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: S 6 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7040 (mt-10) REVERT: S 186 GLN cc_start: 0.8212 (tt0) cc_final: 0.7904 (pt0) REVERT: S 202 ARG cc_start: 0.7722 (ptt-90) cc_final: 0.7354 (ptt-90) REVERT: S 246 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8134 (mt-10) outliers start: 32 outliers final: 15 residues processed: 138 average time/residue: 1.3949 time to fit residues: 204.1458 Evaluate side-chains 140 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 38 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 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU 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 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 Chi-restraints excluded: chain S residue 246 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 101 optimal weight: 0.0270 chunk 19 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 overall best weight: 0.9440 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.145197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.099433 restraints weight = 11708.745| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.62 r_work: 0.3104 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9170 Z= 0.242 Angle : 0.633 16.491 12449 Z= 0.320 Chirality : 0.045 0.271 1433 Planarity : 0.004 0.045 1535 Dihedral : 6.292 59.204 1539 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.81 % Allowed : 16.98 % Favored : 80.21 % 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 (0.26), residues: 1111 helix: 2.06 (0.26), residues: 385 sheet: -0.11 (0.30), residues: 274 loop : -0.79 (0.30), residues: 452 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 0.018 0.001 PHE A 190 TYR 0.013 0.001 TYR B 59 ARG 0.011 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 151 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.075 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 25 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6553 (tt0) REVERT: C 33 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7297 (mt-10) REVERT: C 248 LYS cc_start: 0.7686 (mmtt) cc_final: 0.7440 (mmtt) REVERT: B 19 ARG cc_start: 0.7665 (tmm160) cc_final: 0.7225 (ttp-110) REVERT: B 44 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8063 (mm-40) REVERT: B 100 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8682 (m) REVERT: B 135 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8755 (p) REVERT: B 198 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7768 (pt) REVERT: B 217 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7210 (pmm) REVERT: B 301 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7932 (mtpp) REVERT: G 21 MET cc_start: 0.8345 (tpp) cc_final: 0.8067 (tpp) REVERT: S 186 GLN cc_start: 0.8224 (tt0) cc_final: 0.7918 (pt0) REVERT: S 202 ARG cc_start: 0.7744 (ptt-90) cc_final: 0.7351 (ptt-90) REVERT: S 246 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8142 (mt-10) outliers start: 27 outliers final: 13 residues processed: 140 average time/residue: 1.4013 time to fit residues: 207.7829 Evaluate side-chains 136 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 33 GLU 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 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET 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 Chi-restraints excluded: chain S residue 246 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.142317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.096940 restraints weight = 11773.916| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.52 r_work: 0.3068 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 9170 Z= 0.420 Angle : 0.711 17.136 12449 Z= 0.358 Chirality : 0.048 0.273 1433 Planarity : 0.004 0.046 1535 Dihedral : 6.503 56.296 1539 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % 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: 0.40 (0.25), residues: 1111 helix: 1.84 (0.26), residues: 386 sheet: -0.12 (0.30), residues: 281 loop : -0.83 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 77 HIS 0.009 0.001 HIS A 184 PHE 0.022 0.002 PHE A 190 TYR 0.017 0.002 TYR B 264 ARG 0.010 0.001 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 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 1.015 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 25 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6565 (tt0) REVERT: C 33 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7240 (mt-10) REVERT: C 248 LYS cc_start: 0.7727 (mmtt) cc_final: 0.7455 (mmtt) REVERT: B 19 ARG cc_start: 0.7647 (tmm160) cc_final: 0.7243 (ttp-110) REVERT: B 44 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8091 (mm-40) REVERT: B 100 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8611 (m) REVERT: B 198 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7697 (pt) REVERT: B 215 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8103 (mp0) REVERT: B 217 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7221 (pmm) REVERT: B 259 GLN cc_start: 0.8291 (pm20) cc_final: 0.7776 (pm20) REVERT: B 301 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7924 (mtpp) REVERT: G 21 MET cc_start: 0.8331 (tpp) cc_final: 0.8049 (tpp) REVERT: G 42 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6683 (mp0) REVERT: S 202 ARG cc_start: 0.7756 (ptt-90) cc_final: 0.7441 (ptt-90) REVERT: S 246 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8175 (mt-10) outliers start: 27 outliers final: 14 residues processed: 133 average time/residue: 1.3611 time to fit residues: 192.1297 Evaluate side-chains 132 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 33 GLU 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 339 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU 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 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 Chi-restraints excluded: chain S residue 246 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.145214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099142 restraints weight = 11627.254| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.62 r_work: 0.3083 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9170 Z= 0.283 Angle : 0.668 17.431 12449 Z= 0.335 Chirality : 0.045 0.270 1433 Planarity : 0.004 0.045 1535 Dihedral : 6.339 55.282 1539 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.71 % Allowed : 18.02 % 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: 0.46 (0.26), residues: 1111 helix: 1.90 (0.26), residues: 387 sheet: -0.14 (0.30), residues: 274 loop : -0.79 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 77 HIS 0.009 0.001 HIS A 184 PHE 0.021 0.001 PHE A 190 TYR 0.014 0.001 TYR B 59 ARG 0.012 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 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.992 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 25 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6612 (tt0) REVERT: C 33 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: C 248 LYS cc_start: 0.7714 (mmtt) cc_final: 0.7453 (mmtt) REVERT: B 19 ARG cc_start: 0.7620 (tmm160) cc_final: 0.7213 (ttp-110) REVERT: B 44 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8065 (mt0) REVERT: B 100 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8714 (m) REVERT: B 198 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7796 (pt) REVERT: B 217 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7243 (pmm) REVERT: B 301 LYS cc_start: 0.8223 (mtpt) cc_final: 0.7936 (mtpp) REVERT: G 21 MET cc_start: 0.8354 (tpp) cc_final: 0.8076 (tpp) REVERT: G 42 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6734 (mp0) REVERT: S 186 GLN cc_start: 0.8233 (tt0) cc_final: 0.7922 (pt0) REVERT: S 202 ARG cc_start: 0.7730 (ptt-90) cc_final: 0.7406 (ptt-90) REVERT: S 246 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8138 (mt-10) outliers start: 26 outliers final: 14 residues processed: 133 average time/residue: 1.3860 time to fit residues: 195.7334 Evaluate side-chains 134 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 33 GLU 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 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 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 Chi-restraints excluded: chain S residue 246 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.146689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.100784 restraints weight = 11667.772| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.61 r_work: 0.3119 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9170 Z= 0.218 Angle : 0.637 18.224 12449 Z= 0.319 Chirality : 0.044 0.257 1433 Planarity : 0.004 0.045 1535 Dihedral : 6.121 54.261 1539 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.29 % Allowed : 18.54 % Favored : 79.17 % 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: 0.58 (0.26), residues: 1111 helix: 2.06 (0.26), residues: 386 sheet: -0.14 (0.30), residues: 278 loop : -0.72 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 77 HIS 0.009 0.001 HIS A 184 PHE 0.022 0.001 PHE A 52 TYR 0.015 0.001 TYR B 264 ARG 0.012 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 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.925 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 25 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6536 (tt0) REVERT: C 33 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: C 248 LYS cc_start: 0.7673 (mmtt) cc_final: 0.7417 (mmtt) REVERT: C 263 SER cc_start: 0.9029 (m) cc_final: 0.8747 (p) REVERT: B 19 ARG cc_start: 0.7626 (tmm160) cc_final: 0.7211 (ttp-110) REVERT: B 44 GLN cc_start: 0.8272 (mt0) cc_final: 0.8000 (mt0) REVERT: B 100 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8657 (m) REVERT: B 135 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8732 (p) REVERT: B 198 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7816 (pt) REVERT: B 217 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7226 (pmm) REVERT: B 274 THR cc_start: 0.8782 (p) cc_final: 0.8492 (p) REVERT: B 301 LYS cc_start: 0.8206 (mtpt) cc_final: 0.7923 (mtpp) REVERT: G 21 MET cc_start: 0.8380 (tpp) cc_final: 0.8096 (tpp) REVERT: G 42 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: S 186 GLN cc_start: 0.8277 (tt0) cc_final: 0.7970 (pt0) REVERT: S 202 ARG cc_start: 0.7755 (ptt-90) cc_final: 0.7342 (ptt-90) REVERT: S 246 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8117 (mt-10) outliers start: 22 outliers final: 11 residues processed: 136 average time/residue: 1.4234 time to fit residues: 205.5555 Evaluate side-chains 133 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain C residue 33 GLU 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 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 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 Chi-restraints excluded: chain S residue 246 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 80 optimal weight: 2.9990 chunk 27 optimal weight: 0.0870 chunk 35 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 21 optimal weight: 0.0670 chunk 23 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 19 optimal weight: 0.0000 chunk 46 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.2900 ------------------------------------------------------------------------------- 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** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.149363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.104355 restraints weight = 11554.444| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.60 r_work: 0.3168 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2551 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= 0.164 Angle : 0.619 16.701 12449 Z= 0.311 Chirality : 0.043 0.244 1433 Planarity : 0.004 0.044 1535 Dihedral : 5.924 55.140 1539 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.46 % Allowed : 19.79 % Favored : 78.75 % 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: 0.70 (0.26), residues: 1111 helix: 2.19 (0.27), residues: 386 sheet: -0.07 (0.30), residues: 289 loop : -0.70 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.010 0.001 HIS A 184 PHE 0.015 0.001 PHE A 190 TYR 0.012 0.001 TYR B 289 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: 7667.68 seconds wall clock time: 136 minutes 16.54 seconds (8176.54 seconds total)