Starting phenix.real_space_refine on Thu Mar 13 18:34:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ykd_33891/03_2025/7ykd_33891.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ykd_33891/03_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_33891/03_2025/7ykd_33891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ykd_33891/03_2025/7ykd_33891.map" model { file = "/net/cci-nas-00/data/ceres_data/7ykd_33891/03_2025/7ykd_33891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ykd_33891/03_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-5624/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: 6.10, per 1000 atoms: 0.68 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: 2.59 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: 1.07 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: 2.67 Time building geometry restraints manager: 2.93 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: 2.020 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.750 Find NCS groups from input model: 0.110 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.090 ------------------------------------------------------------------------------- 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 : 0.933 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: 1.5008 time to fit residues: 236.1614 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 : 0.937 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.103649 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: 0.3011 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 : 1.078 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 33 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7349 (mm-30) REVERT: C 248 LYS cc_start: 0.7801 (mmtt) cc_final: 0.7542 (mmtt) REVERT: B 13 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8465 (pp30) REVERT: B 19 ARG cc_start: 0.7593 (tmm160) cc_final: 0.7346 (ttp-110) REVERT: B 198 LEU cc_start: 0.8244 (pp) cc_final: 0.8023 (pt) REVERT: S 18 ARG cc_start: 0.8551 (tpp80) cc_final: 0.8340 (tpp80) REVERT: S 202 ARG cc_start: 0.8024 (ptt-90) cc_final: 0.7731 (ptt-90) outliers start: 15 outliers final: 4 residues processed: 134 average time/residue: 1.5032 time to fit residues: 213.9278 Evaluate side-chains 120 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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: 0.9980 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 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: 0.7580 ------------------------------------------------------------------------------- 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** B 75 GLN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.145841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.100226 restraints weight = 11714.414| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.62 r_work: 0.3117 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9170 Z= 0.218 Angle : 0.633 13.049 12449 Z= 0.314 Chirality : 0.045 0.256 1433 Planarity : 0.004 0.046 1535 Dihedral : 7.488 74.468 1539 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.88 % Allowed : 11.98 % Favored : 86.15 % 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 (0.26), residues: 1111 helix: 1.87 (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 B 82 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 148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.001 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: 0.7028 (mt-10) cc_final: 0.6544 (tt0) REVERT: C 248 LYS cc_start: 0.7632 (mmtt) cc_final: 0.7367 (mmtt) REVERT: B 19 ARG cc_start: 0.7479 (tmm160) cc_final: 0.7118 (ttp-110) REVERT: B 160 SER cc_start: 0.8527 (t) cc_final: 0.7740 (p) REVERT: B 198 LEU cc_start: 0.8014 (pp) cc_final: 0.7734 (pt) REVERT: S 6 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.6948 (mt-10) REVERT: S 18 ARG cc_start: 0.8320 (tpp80) cc_final: 0.8079 (tpp80) REVERT: S 202 ARG cc_start: 0.7767 (ptt-90) cc_final: 0.7501 (ptt-90) REVERT: S 246 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8019 (mp0) outliers start: 18 outliers final: 8 residues processed: 141 average time/residue: 1.3856 time to fit residues: 207.6433 Evaluate side-chains 133 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 215 GLU 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: 0.8980 chunk 86 optimal weight: 0.0070 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 65 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 107 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.147371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.101805 restraints weight = 11558.763| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.61 r_work: 0.3143 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9170 Z= 0.181 Angle : 0.613 13.919 12449 Z= 0.303 Chirality : 0.044 0.263 1433 Planarity : 0.004 0.044 1535 Dihedral : 6.903 57.395 1539 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.98 % Allowed : 14.06 % 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: 2.05 (0.26), residues: 385 sheet: -0.02 (0.30), residues: 273 loop : -0.77 (0.30), residues: 453 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 0.014 0.001 PHE A 52 TYR 0.011 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 153 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.037 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: 0.6959 (mt-10) cc_final: 0.6471 (tt0) REVERT: C 33 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7205 (mt-10) REVERT: C 248 LYS cc_start: 0.7639 (mmtt) cc_final: 0.7383 (mmtt) REVERT: C 263 SER cc_start: 0.9022 (m) cc_final: 0.8734 (p) REVERT: B 19 ARG cc_start: 0.7567 (tmm160) cc_final: 0.7281 (ttp-110) REVERT: B 44 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7998 (mm-40) REVERT: B 160 SER cc_start: 0.8479 (t) cc_final: 0.7883 (p) REVERT: S 6 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6985 (mt-10) REVERT: S 18 ARG cc_start: 0.8287 (tpp80) cc_final: 0.8000 (tpp80) REVERT: S 186 GLN cc_start: 0.8228 (tt0) cc_final: 0.8004 (pt0) REVERT: S 202 ARG cc_start: 0.7731 (ptt-90) cc_final: 0.7401 (ptt-90) REVERT: S 246 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8036 (mt-10) outliers start: 19 outliers final: 8 residues processed: 146 average time/residue: 1.4938 time to fit residues: 232.2372 Evaluate side-chains 132 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 198 MET 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 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: 0.9980 chunk 18 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 31 optimal weight: 0.0370 overall best weight: 1.6064 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.143749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.097645 restraints weight = 11598.475| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.61 r_work: 0.3065 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9170 Z= 0.355 Angle : 0.679 14.956 12449 Z= 0.340 Chirality : 0.047 0.269 1433 Planarity : 0.004 0.046 1535 Dihedral : 7.068 58.830 1539 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.81 % Allowed : 14.38 % Favored : 82.81 % 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 (0.25), residues: 1111 helix: 2.02 (0.26), residues: 385 sheet: -0.19 (0.29), residues: 279 loop : -0.82 (0.30), residues: 447 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 0.017 0.002 PHE A 124 TYR 0.015 0.002 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 150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 1.635 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 25 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6561 (tt0) REVERT: C 33 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: C 53 MET cc_start: 0.6495 (mpp) cc_final: 0.6275 (mtt) REVERT: C 248 LYS cc_start: 0.7682 (mmtt) cc_final: 0.7428 (mmtt) REVERT: B 19 ARG cc_start: 0.7520 (tmm160) cc_final: 0.7072 (ttp-110) REVERT: B 44 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8015 (mm-40) REVERT: B 198 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7709 (pt) REVERT: B 217 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7091 (pmm) REVERT: G 42 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: S 6 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.6947 (mt-10) REVERT: S 18 ARG cc_start: 0.8275 (tpp80) cc_final: 0.7942 (tpp80) REVERT: S 202 ARG cc_start: 0.7730 (ptt-90) cc_final: 0.7388 (ptt-90) REVERT: S 246 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8063 (mt-10) outliers start: 27 outliers final: 9 residues processed: 138 average time/residue: 1.6558 time to fit residues: 244.5806 Evaluate side-chains 135 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 339 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL 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 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: 6.9990 chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3795 r_free = 0.3795 target = 0.146502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.100577 restraints weight = 11524.342| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.63 r_work: 0.3100 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9170 Z= 0.231 Angle : 0.622 15.674 12449 Z= 0.312 Chirality : 0.044 0.271 1433 Planarity : 0.004 0.045 1535 Dihedral : 6.387 59.661 1539 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.81 % Allowed : 15.21 % Favored : 81.98 % 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: 2.07 (0.26), residues: 385 sheet: -0.17 (0.30), residues: 274 loop : -0.75 (0.30), residues: 452 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 0.017 0.001 PHE A 52 TYR 0.013 0.001 TYR B 264 ARG 0.006 0.000 ARG B 197 *********************** 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 148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.943 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 25 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6617 (tt0) REVERT: C 33 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7337 (mt-10) REVERT: C 248 LYS cc_start: 0.7710 (mmtt) cc_final: 0.7464 (mmtt) REVERT: B 19 ARG cc_start: 0.7656 (tmm160) cc_final: 0.7210 (ttp-110) REVERT: B 44 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8071 (mm-40) REVERT: B 198 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7776 (pt) REVERT: B 217 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7167 (pmm) REVERT: B 301 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7909 (mtpp) REVERT: G 21 MET cc_start: 0.8324 (tpp) cc_final: 0.8037 (tpp) REVERT: G 42 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: S 6 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.6984 (mt-10) REVERT: S 18 ARG cc_start: 0.8307 (tpp80) cc_final: 0.8045 (tpp80) REVERT: S 186 GLN cc_start: 0.8261 (tt0) cc_final: 0.7942 (pt0) REVERT: S 202 ARG cc_start: 0.7735 (ptt-90) cc_final: 0.7362 (ptt-90) REVERT: S 246 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8136 (mt-10) outliers start: 27 outliers final: 9 residues processed: 138 average time/residue: 1.4830 time to fit residues: 216.8809 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 : 1.329 ------------------------------------------------------------------------------- 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 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 198 LEU 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 246 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 15 optimal weight: 0.1980 chunk 87 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 101 optimal weight: 0.0060 chunk 19 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.148105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.102694 restraints weight = 11665.013| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.62 r_work: 0.3145 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2327 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= 0.178 Angle : 0.602 16.682 12449 Z= 0.300 Chirality : 0.044 0.267 1433 Planarity : 0.004 0.043 1535 Dihedral : 6.060 57.777 1539 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.50 % Allowed : 16.88 % Favored : 80.62 % 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: 0.75 (0.26), residues: 1111 helix: 2.21 (0.26), residues: 385 sheet: -0.01 (0.30), residues: 287 loop : -0.66 (0.31), residues: 439 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 0.016 0.001 PHE A 190 TYR 0.013 0.001 TYR B 59 ARG 0.005 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 150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.889 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 25 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6524 (tt0) REVERT: C 33 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7272 (mt-10) REVERT: C 230 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.7169 (p90) REVERT: C 248 LYS cc_start: 0.7683 (mmtt) cc_final: 0.7434 (mmtt) REVERT: C 263 SER cc_start: 0.9038 (m) cc_final: 0.8765 (p) REVERT: B 19 ARG cc_start: 0.7633 (tmm160) cc_final: 0.7180 (ttp-110) REVERT: B 44 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8035 (mm-40) REVERT: B 135 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8736 (p) REVERT: B 198 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7595 (pp) REVERT: B 217 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7206 (pmm) REVERT: B 274 THR cc_start: 0.8743 (p) cc_final: 0.8455 (p) REVERT: B 301 LYS cc_start: 0.8207 (mtpt) cc_final: 0.7913 (mtpp) REVERT: G 21 MET cc_start: 0.8350 (tpp) cc_final: 0.8069 (tpp) REVERT: G 42 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: S 18 ARG cc_start: 0.8335 (tpp80) cc_final: 0.8088 (tpp80) REVERT: S 186 GLN cc_start: 0.8272 (tt0) cc_final: 0.7831 (pt0) REVERT: S 202 ARG cc_start: 0.7773 (ptt-90) cc_final: 0.7392 (ptt-90) REVERT: S 246 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8096 (mt-10) outliers start: 24 outliers final: 10 residues processed: 142 average time/residue: 1.2877 time to fit residues: 194.6141 Evaluate side-chains 135 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 230 TYR 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 198 LEU 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 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 246 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.146707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.100751 restraints weight = 11761.958| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.62 r_work: 0.3115 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2292 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= 0.246 Angle : 0.631 17.313 12449 Z= 0.315 Chirality : 0.044 0.264 1433 Planarity : 0.004 0.044 1535 Dihedral : 6.091 58.805 1539 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.71 % Allowed : 17.19 % Favored : 80.10 % 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: 0.75 (0.26), residues: 1111 helix: 2.20 (0.26), residues: 385 sheet: -0.07 (0.30), residues: 278 loop : -0.61 (0.30), residues: 448 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 0.019 0.001 PHE A 52 TYR 0.011 0.001 TYR B 59 ARG 0.005 0.000 ARG B 197 *********************** 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: 26 poor density : 119 time to evaluate : 0.902 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 25 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6534 (tt0) REVERT: C 33 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: C 248 LYS cc_start: 0.7688 (mmtt) cc_final: 0.7432 (mmtt) REVERT: C 263 SER cc_start: 0.9038 (m) cc_final: 0.8753 (p) REVERT: B 19 ARG cc_start: 0.7633 (tmm160) cc_final: 0.7176 (ttp-110) REVERT: B 44 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8071 (mm-40) REVERT: B 198 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7573 (pp) REVERT: B 217 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7184 (pmm) REVERT: B 274 THR cc_start: 0.8812 (p) cc_final: 0.8531 (p) REVERT: B 301 LYS cc_start: 0.8202 (mtpt) cc_final: 0.7922 (mtpp) REVERT: G 21 MET cc_start: 0.8339 (tpp) cc_final: 0.8054 (tpp) REVERT: G 42 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: S 18 ARG cc_start: 0.8362 (tpp80) cc_final: 0.8078 (tpp80) REVERT: S 186 GLN cc_start: 0.8258 (tt0) cc_final: 0.7912 (pt0) REVERT: S 202 ARG cc_start: 0.7756 (ptt-90) cc_final: 0.7367 (ptt-90) REVERT: S 246 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8110 (mt-10) outliers start: 26 outliers final: 10 residues processed: 136 average time/residue: 1.3058 time to fit residues: 188.5534 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 : 0.917 ------------------------------------------------------------------------------- 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 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 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 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: 0.4980 chunk 40 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 53 optimal weight: 0.0870 overall best weight: 0.9164 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.146712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.100878 restraints weight = 11590.127| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.61 r_work: 0.3119 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9170 Z= 0.240 Angle : 0.642 17.863 12449 Z= 0.321 Chirality : 0.044 0.258 1433 Planarity : 0.004 0.043 1535 Dihedral : 6.052 58.300 1539 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.98 % Allowed : 18.12 % Favored : 79.90 % 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: 2.20 (0.26), residues: 385 sheet: -0.08 (0.30), residues: 278 loop : -0.62 (0.30), residues: 448 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 0.016 0.001 PHE A 190 TYR 0.012 0.001 TYR B 59 ARG 0.005 0.000 ARG B 197 *********************** 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 141 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.913 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 25 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6536 (tt0) REVERT: C 33 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: C 248 LYS cc_start: 0.7667 (mmtt) cc_final: 0.7434 (mmtt) REVERT: B 19 ARG cc_start: 0.7655 (tmm160) cc_final: 0.7190 (ttp-110) REVERT: B 44 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8083 (mm-40) REVERT: B 198 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7587 (pp) REVERT: B 217 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7188 (pmm) REVERT: B 274 THR cc_start: 0.8818 (p) cc_final: 0.8530 (p) REVERT: B 301 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7937 (mtpp) REVERT: G 21 MET cc_start: 0.8351 (tpp) cc_final: 0.8057 (tpp) REVERT: G 42 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6763 (mp0) REVERT: S 18 ARG cc_start: 0.8361 (tpp80) cc_final: 0.8059 (tpp80) REVERT: S 186 GLN cc_start: 0.8249 (tt0) cc_final: 0.7898 (pt0) REVERT: S 189 ILE cc_start: 0.8472 (mt) cc_final: 0.8243 (mp) REVERT: S 202 ARG cc_start: 0.7747 (ptt-90) cc_final: 0.7352 (ptt-90) REVERT: S 246 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8099 (mt-10) outliers start: 19 outliers final: 11 residues processed: 136 average time/residue: 1.3863 time to fit residues: 199.7320 Evaluate side-chains 132 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 44 GLN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.146699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.100626 restraints weight = 11678.330| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.65 r_work: 0.3117 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9170 Z= 0.246 Angle : 0.651 18.088 12449 Z= 0.325 Chirality : 0.044 0.251 1433 Planarity : 0.004 0.046 1535 Dihedral : 6.024 56.072 1539 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.98 % Allowed : 18.65 % Favored : 79.38 % 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: 0.73 (0.26), residues: 1111 helix: 2.20 (0.26), residues: 385 sheet: -0.09 (0.30), residues: 278 loop : -0.63 (0.30), residues: 448 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 0.022 0.001 PHE A 52 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 136 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 1.016 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 25 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6534 (tt0) REVERT: C 33 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: C 248 LYS cc_start: 0.7661 (mmtt) cc_final: 0.7433 (mmtt) REVERT: C 263 SER cc_start: 0.9032 (m) cc_final: 0.8745 (p) REVERT: B 19 ARG cc_start: 0.7644 (tmm160) cc_final: 0.7204 (ttp-110) REVERT: B 44 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8007 (mm-40) REVERT: B 135 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8739 (p) REVERT: B 198 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7583 (pp) REVERT: B 217 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7197 (pmm) REVERT: B 274 THR cc_start: 0.8817 (p) cc_final: 0.8529 (p) REVERT: B 301 LYS cc_start: 0.8219 (mtpt) cc_final: 0.7940 (mtpp) REVERT: G 21 MET cc_start: 0.8318 (tpp) cc_final: 0.8022 (tpp) REVERT: G 42 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: S 18 ARG cc_start: 0.8363 (tpp80) cc_final: 0.8055 (tpp80) REVERT: S 46 GLU cc_start: 0.7874 (tt0) cc_final: 0.7222 (pt0) REVERT: S 87 ARG cc_start: 0.6919 (mtt90) cc_final: 0.6691 (mtt90) REVERT: S 186 GLN cc_start: 0.8238 (tt0) cc_final: 0.7883 (pt0) REVERT: S 189 ILE cc_start: 0.8502 (mt) cc_final: 0.8283 (mp) REVERT: S 202 ARG cc_start: 0.7725 (ptt-90) cc_final: 0.7329 (ptt-90) REVERT: S 246 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8118 (mt-10) outliers start: 19 outliers final: 11 residues processed: 130 average time/residue: 1.4432 time to fit residues: 200.1393 Evaluate side-chains 131 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 44 GLN 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 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: 3.9990 chunk 27 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.146829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.100692 restraints weight = 11575.051| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.63 r_work: 0.3110 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9170 Z= 0.258 Angle : 0.654 18.214 12449 Z= 0.327 Chirality : 0.044 0.237 1433 Planarity : 0.004 0.046 1535 Dihedral : 6.003 53.255 1539 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.40 % Allowed : 18.23 % Favored : 79.38 % 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: 2.16 (0.26), residues: 386 sheet: -0.08 (0.30), residues: 277 loop : -0.66 (0.30), residues: 448 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 0.018 0.001 PHE A 190 TYR 0.012 0.001 TYR B 59 ARG 0.013 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7894.14 seconds wall clock time: 138 minutes 37.89 seconds (8317.89 seconds total)