Starting phenix.real_space_refine on Sat Dec 28 11:18:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xjk_33230/12_2024/7xjk_33230.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xjk_33230/12_2024/7xjk_33230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xjk_33230/12_2024/7xjk_33230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xjk_33230/12_2024/7xjk_33230.map" model { file = "/net/cci-nas-00/data/ceres_data/7xjk_33230/12_2024/7xjk_33230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xjk_33230/12_2024/7xjk_33230.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.115 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 53 5.16 5 C 5478 2.51 5 N 1472 2.21 5 O 1567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8570 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 112 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 14} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1750 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2477 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 93 Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1712 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "F" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2166 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 5.16, per 1000 atoms: 0.60 Number of scatterers: 8570 At special positions: 0 Unit cell: (91.308, 119.57, 120.657, 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 53 16.00 O 1567 8.00 N 1472 7.00 C 5478 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS F 98 " - pdb=" SG CYS F 175 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.2 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 38.5% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.956A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 183 through 204 removed outlier: 3.533A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 removed outlier: 4.045A pdb=" N ARG B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.693A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.505A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.803A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.092A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.073A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 53 Processing helix chain 'F' and resid 58 through 88 Proline residue: F 80 - end of helix Processing helix chain 'F' and resid 95 through 129 removed outlier: 3.505A pdb=" N LYS F 99 " --> pdb=" O SER F 95 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N HIS F 102 " --> pdb=" O CYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 138 through 157 Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 180 through 196 Processing helix chain 'F' and resid 196 through 215 Processing helix chain 'F' and resid 225 through 262 removed outlier: 4.196A pdb=" N TRP F 249 " --> pdb=" O PHE F 245 " (cutoff:3.500A) Proline residue: F 251 - end of helix Processing helix chain 'F' and resid 267 through 293 removed outlier: 3.912A pdb=" N SER F 285 " --> pdb=" O SER F 281 " (cutoff:3.500A) Proline residue: F 289 - end of helix Processing helix chain 'F' and resid 296 through 307 Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76 removed outlier: 3.942A pdb=" N PHE B 84 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.666A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA C 328 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU C 318 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY C 330 " --> pdb=" O SER C 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 62 through 63 removed outlier: 6.546A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.702A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.756A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.844A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.403A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.950A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN C 295 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 5.156A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.463A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 4.115A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 164 through 169 459 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: 2.71 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2772 1.34 - 1.46: 2196 1.46 - 1.58: 3719 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 8759 Sorted by residual: bond pdb=" CB ASN F 43 " pdb=" CG ASN F 43 " ideal model delta sigma weight residual 1.516 1.467 0.049 2.50e-02 1.60e+03 3.90e+00 bond pdb=" C VAL F 79 " pdb=" N PRO F 80 " ideal model delta sigma weight residual 1.333 1.359 -0.026 1.44e-02 4.82e+03 3.16e+00 bond pdb=" N LEU F 72 " pdb=" CA LEU F 72 " ideal model delta sigma weight residual 1.459 1.437 0.022 1.24e-02 6.50e+03 3.11e+00 bond pdb=" CA ASP F 71 " pdb=" C ASP F 71 " ideal model delta sigma weight residual 1.524 1.506 0.017 1.27e-02 6.20e+03 1.86e+00 bond pdb=" CB CYS C 103 " pdb=" SG CYS C 103 " ideal model delta sigma weight residual 1.808 1.765 0.043 3.30e-02 9.18e+02 1.67e+00 ... (remaining 8754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 11572 1.64 - 3.28: 294 3.28 - 4.92: 47 4.92 - 6.56: 13 6.56 - 8.20: 2 Bond angle restraints: 11928 Sorted by residual: angle pdb=" N ILE C 270 " pdb=" CA ILE C 270 " pdb=" C ILE C 270 " ideal model delta sigma weight residual 113.71 109.28 4.43 9.50e-01 1.11e+00 2.17e+01 angle pdb=" N HIS F 176 " pdb=" CA HIS F 176 " pdb=" C HIS F 176 " ideal model delta sigma weight residual 108.25 113.56 -5.31 1.16e+00 7.43e-01 2.10e+01 angle pdb=" CA GLU C 130 " pdb=" CB GLU C 130 " pdb=" CG GLU C 130 " ideal model delta sigma weight residual 114.10 119.22 -5.12 2.00e+00 2.50e-01 6.54e+00 angle pdb=" CA TYR F 163 " pdb=" CB TYR F 163 " pdb=" CG TYR F 163 " ideal model delta sigma weight residual 113.90 118.40 -4.50 1.80e+00 3.09e-01 6.26e+00 angle pdb=" CA ILE C 270 " pdb=" C ILE C 270 " pdb=" N CYS C 271 " ideal model delta sigma weight residual 119.87 116.52 3.35 1.34e+00 5.57e-01 6.24e+00 ... (remaining 11923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4636 17.90 - 35.80: 408 35.80 - 53.69: 62 53.69 - 71.59: 6 71.59 - 89.49: 4 Dihedral angle restraints: 5116 sinusoidal: 1824 harmonic: 3292 Sorted by residual: dihedral pdb=" CA TRP C 82 " pdb=" C TRP C 82 " pdb=" N ASP C 83 " pdb=" CA ASP C 83 " ideal model delta harmonic sigma weight residual 180.00 158.15 21.85 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ASP F 71 " pdb=" C ASP F 71 " pdb=" N LEU F 72 " pdb=" CA LEU F 72 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE B 81 " pdb=" C PHE B 81 " pdb=" N HIS B 82 " pdb=" CA HIS B 82 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 5113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1011 0.045 - 0.090: 288 0.090 - 0.134: 78 0.134 - 0.179: 5 0.179 - 0.224: 2 Chirality restraints: 1384 Sorted by residual: chirality pdb=" CG LEU F 76 " pdb=" CB LEU F 76 " pdb=" CD1 LEU F 76 " pdb=" CD2 LEU F 76 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU F 72 " pdb=" CB LEU F 72 " pdb=" CD1 LEU F 72 " pdb=" CD2 LEU F 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LEU F 76 " pdb=" N LEU F 76 " pdb=" C LEU F 76 " pdb=" CB LEU F 76 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 1381 not shown) Planarity restraints: 1510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 48 " -0.056 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO D 49 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 69 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.98e+00 pdb=" C VAL F 69 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL F 69 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA F 70 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 194 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C PHE F 194 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE F 194 " 0.015 2.00e-02 2.50e+03 pdb=" N SER F 195 " 0.014 2.00e-02 2.50e+03 ... (remaining 1507 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 385 2.72 - 3.26: 8667 3.26 - 3.81: 14226 3.81 - 4.35: 17066 4.35 - 4.90: 30039 Nonbonded interactions: 70383 Sorted by model distance: nonbonded pdb=" OD2 ASP F 188 " pdb=" NE1 TRP F 260 " model vdw 2.172 3.120 nonbonded pdb=" O SER E 31 " pdb=" OG SER E 53 " model vdw 2.175 3.040 nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 163 " model vdw 2.204 3.040 nonbonded pdb=" OE2 GLU C 260 " pdb=" OG1 THR C 263 " model vdw 2.225 3.040 nonbonded pdb=" OG SER F 95 " pdb=" OE1 GLN F 166 " model vdw 2.247 3.040 ... (remaining 70378 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.000 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 21.960 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 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 : 0.005 0.049 8759 Z= 0.325 Angle : 0.651 8.197 11928 Z= 0.353 Chirality : 0.044 0.224 1384 Planarity : 0.005 0.086 1510 Dihedral : 13.522 89.491 2988 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1117 helix: 1.58 (0.26), residues: 399 sheet: 0.07 (0.31), residues: 264 loop : -0.90 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 179 HIS 0.009 0.001 HIS F 176 PHE 0.016 0.002 PHE E 27 TYR 0.029 0.002 TYR F 292 ARG 0.006 0.001 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.007 Fit side-chains REVERT: A 11 LEU cc_start: 0.9083 (mm) cc_final: 0.8810 (mm) REVERT: B 179 GLU cc_start: 0.5497 (pp20) cc_final: 0.5127 (pp20) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2157 time to fit residues: 48.0126 Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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: 0.2980 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 HIS E 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8759 Z= 0.310 Angle : 0.599 8.535 11928 Z= 0.315 Chirality : 0.044 0.161 1384 Planarity : 0.005 0.057 1510 Dihedral : 4.410 28.840 1228 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.06 % Allowed : 9.85 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.25), residues: 1117 helix: 1.83 (0.26), residues: 399 sheet: 0.06 (0.32), residues: 258 loop : -0.90 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 179 HIS 0.011 0.002 HIS F 176 PHE 0.020 0.002 PHE F 81 TYR 0.024 0.002 TYR F 163 ARG 0.004 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.972 Fit side-chains REVERT: A 11 LEU cc_start: 0.8984 (mm) cc_final: 0.8705 (mm) REVERT: B 120 GLU cc_start: 0.7736 (pp20) cc_final: 0.7343 (pp20) REVERT: E 38 ARG cc_start: 0.7711 (ptp90) cc_final: 0.7330 (ptp90) REVERT: E 46 GLU cc_start: 0.7903 (pt0) cc_final: 0.7652 (mt-10) REVERT: E 202 LEU cc_start: 0.8637 (tp) cc_final: 0.8145 (tp) REVERT: F 187 MET cc_start: 0.8360 (tpp) cc_final: 0.7887 (tpp) outliers start: 18 outliers final: 15 residues processed: 158 average time/residue: 0.2015 time to fit residues: 44.4642 Evaluate side-chains 146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 120 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN E 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8759 Z= 0.348 Angle : 0.600 7.354 11928 Z= 0.318 Chirality : 0.044 0.150 1384 Planarity : 0.004 0.048 1510 Dihedral : 4.461 29.450 1228 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.09 % Allowed : 15.46 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.30 (0.25), residues: 1117 helix: 1.66 (0.25), residues: 400 sheet: -0.05 (0.32), residues: 258 loop : -0.94 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.012 0.002 HIS F 176 PHE 0.031 0.002 PHE F 156 TYR 0.026 0.002 TYR F 163 ARG 0.004 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.966 Fit side-chains REVERT: A 11 LEU cc_start: 0.8994 (mm) cc_final: 0.8725 (mm) REVERT: B 166 GLU cc_start: 0.8060 (pm20) cc_final: 0.7761 (pm20) REVERT: F 187 MET cc_start: 0.8490 (tpp) cc_final: 0.8126 (tpp) outliers start: 27 outliers final: 21 residues processed: 151 average time/residue: 0.1993 time to fit residues: 41.9418 Evaluate side-chains 151 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 60 optimal weight: 0.0970 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8759 Z= 0.192 Angle : 0.541 7.829 11928 Z= 0.283 Chirality : 0.041 0.150 1384 Planarity : 0.004 0.042 1510 Dihedral : 4.138 25.882 1228 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.52 % Allowed : 17.87 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.51 (0.25), residues: 1117 helix: 1.88 (0.26), residues: 406 sheet: 0.03 (0.32), residues: 252 loop : -0.87 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.009 0.001 HIS F 176 PHE 0.019 0.001 PHE F 194 TYR 0.018 0.001 TYR F 163 ARG 0.002 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.032 Fit side-chains REVERT: A 11 LEU cc_start: 0.8945 (mm) cc_final: 0.8648 (mm) REVERT: B 166 GLU cc_start: 0.8073 (pm20) cc_final: 0.7827 (pm20) REVERT: E 38 ARG cc_start: 0.7813 (ptp90) cc_final: 0.7420 (ptp90) REVERT: F 187 MET cc_start: 0.8498 (tpp) cc_final: 0.8089 (tpp) outliers start: 22 outliers final: 12 residues processed: 158 average time/residue: 0.2067 time to fit residues: 46.0130 Evaluate side-chains 153 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 85 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 0.0670 chunk 91 optimal weight: 5.9990 chunk 74 optimal weight: 50.0000 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 overall best weight: 1.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8759 Z= 0.287 Angle : 0.570 7.446 11928 Z= 0.300 Chirality : 0.043 0.150 1384 Planarity : 0.004 0.046 1510 Dihedral : 4.247 26.690 1228 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.09 % Allowed : 19.93 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.51 (0.25), residues: 1117 helix: 1.90 (0.26), residues: 400 sheet: -0.09 (0.32), residues: 259 loop : -0.77 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 179 HIS 0.008 0.001 HIS F 176 PHE 0.023 0.002 PHE F 156 TYR 0.023 0.002 TYR F 163 ARG 0.003 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.923 Fit side-chains REVERT: A 11 LEU cc_start: 0.8989 (mm) cc_final: 0.8692 (mm) REVERT: B 179 GLU cc_start: 0.5917 (pp20) cc_final: 0.5425 (pp20) REVERT: E 38 ARG cc_start: 0.7894 (ptp90) cc_final: 0.7494 (ptp90) REVERT: F 187 MET cc_start: 0.8541 (tpp) cc_final: 0.8155 (tpp) outliers start: 27 outliers final: 23 residues processed: 155 average time/residue: 0.2051 time to fit residues: 44.0302 Evaluate side-chains 156 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 0.0870 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8759 Z= 0.211 Angle : 0.540 8.288 11928 Z= 0.285 Chirality : 0.042 0.147 1384 Planarity : 0.004 0.046 1510 Dihedral : 4.061 25.582 1228 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.44 % Allowed : 20.73 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.68 (0.25), residues: 1117 helix: 2.18 (0.26), residues: 394 sheet: -0.03 (0.32), residues: 260 loop : -0.76 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.008 0.001 HIS F 176 PHE 0.024 0.001 PHE F 156 TYR 0.019 0.001 TYR F 163 ARG 0.003 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.978 Fit side-chains REVERT: A 11 LEU cc_start: 0.8987 (mm) cc_final: 0.8687 (mm) REVERT: B 166 GLU cc_start: 0.8018 (pm20) cc_final: 0.7728 (pm20) REVERT: E 38 ARG cc_start: 0.7811 (ptp90) cc_final: 0.7436 (ptp90) REVERT: E 180 MET cc_start: 0.7055 (ptm) cc_final: 0.6603 (ptt) REVERT: F 187 MET cc_start: 0.8524 (tpp) cc_final: 0.8155 (tpp) outliers start: 30 outliers final: 23 residues processed: 157 average time/residue: 0.2065 time to fit residues: 45.0537 Evaluate side-chains 159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 0.0670 chunk 90 optimal weight: 0.9990 chunk 59 optimal weight: 0.2980 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS B 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8759 Z= 0.164 Angle : 0.516 7.827 11928 Z= 0.272 Chirality : 0.041 0.148 1384 Planarity : 0.004 0.039 1510 Dihedral : 3.903 23.745 1228 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.75 % Allowed : 21.76 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.83 (0.26), residues: 1117 helix: 2.36 (0.26), residues: 394 sheet: 0.08 (0.33), residues: 255 loop : -0.74 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.006 0.001 HIS F 176 PHE 0.017 0.001 PHE F 81 TYR 0.017 0.001 TYR F 163 ARG 0.004 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.932 Fit side-chains REVERT: A 11 LEU cc_start: 0.8977 (mm) cc_final: 0.8677 (mm) REVERT: B 179 GLU cc_start: 0.6016 (pp20) cc_final: 0.5605 (pp20) REVERT: E 38 ARG cc_start: 0.7783 (ptp90) cc_final: 0.7415 (ptp90) REVERT: F 187 MET cc_start: 0.8567 (tpp) cc_final: 0.8192 (tpp) outliers start: 24 outliers final: 19 residues processed: 164 average time/residue: 0.2038 time to fit residues: 46.7153 Evaluate side-chains 160 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 120 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8759 Z= 0.204 Angle : 0.539 7.779 11928 Z= 0.282 Chirality : 0.042 0.150 1384 Planarity : 0.004 0.056 1510 Dihedral : 3.919 24.245 1228 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.55 % Allowed : 22.34 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.25), residues: 1117 helix: 2.23 (0.26), residues: 400 sheet: 0.04 (0.33), residues: 255 loop : -0.80 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 260 HIS 0.007 0.001 HIS F 176 PHE 0.018 0.001 PHE F 81 TYR 0.019 0.001 TYR F 163 ARG 0.003 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.908 Fit side-chains REVERT: A 11 LEU cc_start: 0.9037 (mm) cc_final: 0.8749 (mm) REVERT: B 179 GLU cc_start: 0.6000 (pp20) cc_final: 0.5536 (pp20) REVERT: E 38 ARG cc_start: 0.7766 (ptp90) cc_final: 0.7473 (ptp90) REVERT: F 187 MET cc_start: 0.8513 (tpp) cc_final: 0.8151 (tpp) outliers start: 31 outliers final: 22 residues processed: 158 average time/residue: 0.1981 time to fit residues: 43.5545 Evaluate side-chains 160 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 120 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8759 Z= 0.233 Angle : 0.558 7.632 11928 Z= 0.291 Chirality : 0.042 0.158 1384 Planarity : 0.004 0.047 1510 Dihedral : 3.996 24.817 1228 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.55 % Allowed : 22.34 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.68 (0.26), residues: 1117 helix: 2.15 (0.26), residues: 399 sheet: -0.04 (0.32), residues: 266 loop : -0.77 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 260 HIS 0.007 0.001 HIS F 176 PHE 0.021 0.001 PHE F 81 TYR 0.020 0.002 TYR F 163 ARG 0.004 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.909 Fit side-chains REVERT: A 11 LEU cc_start: 0.9066 (mm) cc_final: 0.8763 (mm) REVERT: B 179 GLU cc_start: 0.6050 (pp20) cc_final: 0.5626 (pp20) REVERT: E 38 ARG cc_start: 0.7814 (ptp90) cc_final: 0.7507 (ptp90) REVERT: F 187 MET cc_start: 0.8532 (tpp) cc_final: 0.8206 (tpp) outliers start: 31 outliers final: 25 residues processed: 159 average time/residue: 0.2040 time to fit residues: 45.0998 Evaluate side-chains 165 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 161 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 69 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8759 Z= 0.177 Angle : 0.538 7.518 11928 Z= 0.280 Chirality : 0.041 0.157 1384 Planarity : 0.004 0.084 1510 Dihedral : 3.884 23.802 1228 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.98 % Allowed : 22.91 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.77 (0.26), residues: 1117 helix: 2.27 (0.26), residues: 398 sheet: 0.05 (0.33), residues: 261 loop : -0.78 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 260 HIS 0.007 0.001 HIS F 176 PHE 0.019 0.001 PHE F 81 TYR 0.017 0.001 TYR F 163 ARG 0.004 0.000 ARG E 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.984 Fit side-chains REVERT: B 120 GLU cc_start: 0.7740 (pp20) cc_final: 0.7349 (pp20) REVERT: B 179 GLU cc_start: 0.5994 (pp20) cc_final: 0.5571 (pp20) REVERT: E 38 ARG cc_start: 0.7781 (ptp90) cc_final: 0.7482 (ptp90) REVERT: F 187 MET cc_start: 0.8551 (tpp) cc_final: 0.8152 (tpp) outliers start: 26 outliers final: 24 residues processed: 160 average time/residue: 0.1918 time to fit residues: 43.5364 Evaluate side-chains 166 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 161 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.182443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.144176 restraints weight = 10529.497| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.04 r_work: 0.3518 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8759 Z= 0.188 Angle : 0.551 7.449 11928 Z= 0.284 Chirality : 0.041 0.147 1384 Planarity : 0.004 0.073 1510 Dihedral : 3.865 23.668 1228 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.86 % Allowed : 23.25 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.76 (0.26), residues: 1117 helix: 2.28 (0.26), residues: 398 sheet: 0.05 (0.32), residues: 264 loop : -0.81 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 260 HIS 0.007 0.001 HIS F 176 PHE 0.019 0.001 PHE F 81 TYR 0.019 0.001 TYR F 129 ARG 0.003 0.000 ARG E 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1963.23 seconds wall clock time: 37 minutes 0.68 seconds (2220.68 seconds total)