Starting phenix.real_space_refine on Fri Aug 22 23:44:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dzp_27804/08_2025/8dzp_27804.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dzp_27804/08_2025/8dzp_27804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dzp_27804/08_2025/8dzp_27804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dzp_27804/08_2025/8dzp_27804.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dzp_27804/08_2025/8dzp_27804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dzp_27804/08_2025/8dzp_27804.map" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.022 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 62 5.16 5 C 5524 2.51 5 N 1443 2.21 5 O 1628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8657 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2160 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 4, 'TYR:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1691 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 211} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2593 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 399 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'U99': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.79, per 1000 atoms: 0.21 Number of scatterers: 8657 At special positions: 0 Unit cell: (90.64, 123.2, 125.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1628 8.00 N 1443 7.00 C 5524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 210 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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: 0.47 Conformation dependent library (CDL) restraints added in 317.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 36.7% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 58 through 63 removed outlier: 4.008A pdb=" N ILE A 61 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 86 removed outlier: 4.204A pdb=" N PHE A 70 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 79 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 111 removed outlier: 3.516A pdb=" N ILE A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 121 removed outlier: 3.771A pdb=" N GLN A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 162 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 171 through 196 removed outlier: 3.588A pdb=" N SER A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 235 Processing helix chain 'A' and resid 235 through 254 Processing helix chain 'A' and resid 263 through 300 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 305 through 326 removed outlier: 3.506A pdb=" N LEU A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.796A pdb=" N ARG A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.800A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.605A pdb=" N LYS B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 282 through 286 removed outlier: 4.067A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 Processing helix chain 'B' and resid 329 through 351 removed outlier: 3.838A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 25 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.788A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.717A pdb=" N VAL E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 201 Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 191 removed outlier: 8.515A pdb=" N ALA B 220 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ALA B 226 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.763A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.908A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.987A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.545A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.469A 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=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.902A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.596A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.721A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASN C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.170A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.170A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'E' and resid 135 through 136 removed outlier: 6.536A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1251 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: 0.96 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1581 1.33 - 1.45: 2279 1.45 - 1.57: 4883 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 8833 Sorted by residual: bond pdb=" N ASP B 200 " pdb=" CA ASP B 200 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.21e-02 6.83e+03 4.16e+00 bond pdb=" N TYR E 223 " pdb=" CA TYR E 223 " ideal model delta sigma weight residual 1.456 1.478 -0.023 1.13e-02 7.83e+03 4.03e+00 bond pdb=" CA THR B 48 " pdb=" C THR B 48 " ideal model delta sigma weight residual 1.522 1.548 -0.026 1.33e-02 5.65e+03 3.89e+00 bond pdb=" N PRO E 224 " pdb=" CA PRO E 224 " ideal model delta sigma weight residual 1.469 1.444 0.025 1.28e-02 6.10e+03 3.80e+00 bond pdb=" C PRO E 224 " pdb=" O PRO E 224 " ideal model delta sigma weight residual 1.235 1.211 0.024 1.30e-02 5.92e+03 3.34e+00 ... (remaining 8828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 11655 1.79 - 3.57: 283 3.57 - 5.36: 34 5.36 - 7.14: 17 7.14 - 8.93: 4 Bond angle restraints: 11993 Sorted by residual: angle pdb=" C TYR E 223 " pdb=" CA TYR E 223 " pdb=" CB TYR E 223 " ideal model delta sigma weight residual 110.44 105.08 5.36 9.00e-01 1.23e+00 3.55e+01 angle pdb=" N PRO E 224 " pdb=" CA PRO E 224 " pdb=" CB PRO E 224 " ideal model delta sigma weight residual 103.25 99.25 4.00 1.05e+00 9.07e-01 1.45e+01 angle pdb=" N ASP B 200 " pdb=" CA ASP B 200 " pdb=" CB ASP B 200 " ideal model delta sigma weight residual 110.57 116.19 -5.62 1.57e+00 4.06e-01 1.28e+01 angle pdb=" C ALA A 57 " pdb=" N ILE A 58 " pdb=" CA ILE A 58 " ideal model delta sigma weight residual 122.13 128.54 -6.41 1.85e+00 2.92e-01 1.20e+01 angle pdb=" CA ILE A 58 " pdb=" CB ILE A 58 " pdb=" CG2 ILE A 58 " ideal model delta sigma weight residual 110.50 115.95 -5.45 1.70e+00 3.46e-01 1.03e+01 ... (remaining 11988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 5006 24.08 - 48.16: 239 48.16 - 72.24: 25 72.24 - 96.32: 4 96.32 - 120.40: 1 Dihedral angle restraints: 5275 sinusoidal: 2021 harmonic: 3254 Sorted by residual: dihedral pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" N PRO E 224 " pdb=" CA PRO E 224 " ideal model delta harmonic sigma weight residual 180.00 59.60 120.40 0 5.00e+00 4.00e-02 5.80e+02 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 167.02 -74.02 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CA ALA E 229 " pdb=" C ALA E 229 " pdb=" N GLY E 230 " pdb=" CA GLY E 230 " ideal model delta harmonic sigma weight residual -180.00 -161.14 -18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1207 0.068 - 0.135: 176 0.135 - 0.203: 11 0.203 - 0.270: 3 0.270 - 0.338: 2 Chirality restraints: 1399 Sorted by residual: chirality pdb=" C22 U99 A 401 " pdb=" C20 U99 A 401 " pdb=" C23 U99 A 401 " pdb=" C8 U99 A 401 " both_signs ideal model delta sigma weight residual False -2.23 -1.89 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CB ILE A 58 " pdb=" CA ILE A 58 " pdb=" CG1 ILE A 58 " pdb=" CG2 ILE A 58 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CG LEU E 162 " pdb=" CB LEU E 162 " pdb=" CD1 LEU E 162 " pdb=" CD2 LEU E 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1396 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 222 " -0.017 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C GLU E 222 " 0.061 2.00e-02 2.50e+03 pdb=" O GLU E 222 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR E 223 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " -0.044 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO C 236 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 337 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C ASP B 337 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP B 337 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA B 338 " -0.014 2.00e-02 2.50e+03 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 973 2.75 - 3.29: 8030 3.29 - 3.83: 14569 3.83 - 4.36: 17170 4.36 - 4.90: 30204 Nonbonded interactions: 70946 Sorted by model distance: nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.216 3.040 nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASP C 163 " pdb=" OG1 THR C 165 " model vdw 2.283 3.040 nonbonded pdb=" OG SER B 6 " pdb=" OD1 ASP B 9 " model vdw 2.302 3.040 nonbonded pdb=" O THR A 150 " pdb=" OG SER A 153 " model vdw 2.334 3.040 ... (remaining 70941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.270 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:5.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 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 : 0.004 0.042 8835 Z= 0.176 Angle : 0.675 8.930 11997 Z= 0.372 Chirality : 0.048 0.338 1399 Planarity : 0.006 0.066 1503 Dihedral : 13.618 120.400 3165 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.11 % Allowed : 0.75 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.24), residues: 1100 helix: 0.49 (0.25), residues: 371 sheet: 0.30 (0.29), residues: 285 loop : -1.35 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 19 TYR 0.021 0.002 TYR E 178 PHE 0.015 0.002 PHE A 143 TRP 0.017 0.002 TRP C 82 HIS 0.011 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8833) covalent geometry : angle 0.67547 (11993) SS BOND : bond 0.00131 ( 2) SS BOND : angle 0.55673 ( 4) hydrogen bonds : bond 0.13751 ( 442) hydrogen bonds : angle 6.51130 ( 1251) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.210 Fit side-chains REVERT: B 225 VAL cc_start: 0.8319 (t) cc_final: 0.8118 (t) REVERT: B 269 ASN cc_start: 0.8395 (m110) cc_final: 0.8058 (m110) REVERT: B 275 GLU cc_start: 0.7065 (tt0) cc_final: 0.6770 (tt0) REVERT: B 337 ASP cc_start: 0.7171 (m-30) cc_final: 0.6868 (m-30) REVERT: C 219 ARG cc_start: 0.7254 (mmt90) cc_final: 0.6935 (mmt90) REVERT: C 258 ASP cc_start: 0.6739 (t70) cc_final: 0.6498 (t70) REVERT: E 89 GLU cc_start: 0.7146 (mp0) cc_final: 0.6855 (mp0) outliers start: 1 outliers final: 2 residues processed: 192 average time/residue: 0.4482 time to fit residues: 91.8878 Evaluate side-chains 182 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 180 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN C 125 ASN C 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.131787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.109017 restraints weight = 11874.731| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.77 r_work: 0.3262 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8835 Z= 0.267 Angle : 0.627 7.495 11997 Z= 0.335 Chirality : 0.046 0.199 1399 Planarity : 0.005 0.060 1503 Dihedral : 5.633 66.660 1272 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.24 % Allowed : 7.91 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.24), residues: 1100 helix: 1.37 (0.26), residues: 377 sheet: 0.36 (0.29), residues: 279 loop : -1.20 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 197 TYR 0.029 0.002 TYR E 178 PHE 0.016 0.002 PHE C 151 TRP 0.023 0.002 TRP C 169 HIS 0.011 0.002 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00629 ( 8833) covalent geometry : angle 0.62675 (11993) SS BOND : bond 0.00079 ( 2) SS BOND : angle 0.48623 ( 4) hydrogen bonds : bond 0.05270 ( 442) hydrogen bonds : angle 4.99358 ( 1251) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.381 Fit side-chains REVERT: A 121 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.6924 (ppp) REVERT: A 151 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7834 (tmm) REVERT: A 325 LEU cc_start: 0.8223 (mm) cc_final: 0.8010 (mt) REVERT: B 186 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7206 (mm-30) REVERT: B 275 GLU cc_start: 0.7516 (tt0) cc_final: 0.7101 (tt0) REVERT: B 337 ASP cc_start: 0.7908 (m-30) cc_final: 0.7691 (m-30) REVERT: C 197 ARG cc_start: 0.8168 (mtm-85) cc_final: 0.7742 (mtm-85) REVERT: C 258 ASP cc_start: 0.7478 (t70) cc_final: 0.7126 (t70) REVERT: C 314 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7906 (ttm170) REVERT: E 89 GLU cc_start: 0.7813 (mp0) cc_final: 0.7388 (mp0) outliers start: 21 outliers final: 8 residues processed: 180 average time/residue: 0.4424 time to fit residues: 85.4975 Evaluate side-chains 183 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 43 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.132814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110241 restraints weight = 11964.835| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.77 r_work: 0.3282 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8835 Z= 0.156 Angle : 0.526 6.819 11997 Z= 0.284 Chirality : 0.042 0.175 1399 Planarity : 0.004 0.055 1503 Dihedral : 5.174 63.082 1270 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.67 % Allowed : 10.47 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.25), residues: 1100 helix: 1.87 (0.27), residues: 377 sheet: 0.29 (0.29), residues: 295 loop : -1.19 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.021 0.002 TYR E 178 PHE 0.012 0.001 PHE C 151 TRP 0.019 0.002 TRP C 169 HIS 0.003 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8833) covalent geometry : angle 0.52640 (11993) SS BOND : bond 0.00057 ( 2) SS BOND : angle 0.45185 ( 4) hydrogen bonds : bond 0.04430 ( 442) hydrogen bonds : angle 4.66600 ( 1251) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.378 Fit side-chains REVERT: A 121 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.6784 (ppp) REVERT: A 151 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7826 (tmm) REVERT: A 192 SER cc_start: 0.7633 (OUTLIER) cc_final: 0.7334 (m) REVERT: A 325 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7943 (mt) REVERT: A 329 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7655 (pp) REVERT: B 253 ILE cc_start: 0.8546 (mm) cc_final: 0.8321 (mp) REVERT: B 275 GLU cc_start: 0.7528 (tt0) cc_final: 0.7113 (tt0) REVERT: B 337 ASP cc_start: 0.7899 (m-30) cc_final: 0.7685 (m-30) REVERT: C 19 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7490 (ttp80) REVERT: C 137 ARG cc_start: 0.8451 (tpp-160) cc_final: 0.8245 (tpp-160) REVERT: C 197 ARG cc_start: 0.8184 (mtm-85) cc_final: 0.7841 (mtm-85) REVERT: C 217 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.7749 (pmt) REVERT: C 258 ASP cc_start: 0.7499 (t70) cc_final: 0.7112 (t0) REVERT: E 89 GLU cc_start: 0.7806 (mp0) cc_final: 0.7363 (mp0) outliers start: 25 outliers final: 7 residues processed: 181 average time/residue: 0.4225 time to fit residues: 82.2724 Evaluate side-chains 184 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 0.0000 chunk 73 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 chunk 11 optimal weight: 0.1980 chunk 101 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 102 optimal weight: 0.4980 chunk 64 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 overall best weight: 0.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN B 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.135450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.112960 restraints weight = 12100.709| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.79 r_work: 0.3326 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8835 Z= 0.095 Angle : 0.464 5.944 11997 Z= 0.250 Chirality : 0.040 0.168 1399 Planarity : 0.004 0.054 1503 Dihedral : 4.506 54.024 1270 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.46 % Allowed : 11.75 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.25), residues: 1100 helix: 2.25 (0.27), residues: 377 sheet: 0.45 (0.30), residues: 272 loop : -1.10 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 219 TYR 0.015 0.001 TYR B 320 PHE 0.008 0.001 PHE C 199 TRP 0.016 0.001 TRP C 82 HIS 0.002 0.000 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 8833) covalent geometry : angle 0.46393 (11993) SS BOND : bond 0.00120 ( 2) SS BOND : angle 0.45384 ( 4) hydrogen bonds : bond 0.03607 ( 442) hydrogen bonds : angle 4.27961 ( 1251) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.238 Fit side-chains REVERT: A 151 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7813 (tmm) REVERT: A 192 SER cc_start: 0.7593 (t) cc_final: 0.7316 (m) REVERT: A 329 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7653 (pp) REVERT: B 186 GLU cc_start: 0.7281 (mm-30) cc_final: 0.7037 (mm-30) REVERT: B 207 GLU cc_start: 0.7182 (tp30) cc_final: 0.6920 (tp30) REVERT: B 253 ILE cc_start: 0.8537 (mm) cc_final: 0.8298 (mp) REVERT: B 269 ASN cc_start: 0.8633 (m-40) cc_final: 0.8327 (m110) REVERT: B 275 GLU cc_start: 0.7536 (tt0) cc_final: 0.7130 (tt0) REVERT: B 337 ASP cc_start: 0.7870 (m-30) cc_final: 0.7652 (m-30) REVERT: B 350 ASP cc_start: 0.7707 (t70) cc_final: 0.7459 (t70) REVERT: C 197 ARG cc_start: 0.8183 (mtm-85) cc_final: 0.7942 (mtm-85) REVERT: C 198 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7883 (pt) REVERT: C 258 ASP cc_start: 0.7408 (t70) cc_final: 0.7114 (t0) REVERT: E 89 GLU cc_start: 0.7786 (mp0) cc_final: 0.7351 (mp0) outliers start: 23 outliers final: 6 residues processed: 193 average time/residue: 0.4466 time to fit residues: 92.7254 Evaluate side-chains 195 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 186 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain E residue 78 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 ASN E 130 GLN E 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.132426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.109716 restraints weight = 11970.946| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.76 r_work: 0.3277 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8835 Z= 0.191 Angle : 0.543 6.276 11997 Z= 0.290 Chirality : 0.043 0.202 1399 Planarity : 0.004 0.059 1503 Dihedral : 4.608 57.780 1267 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.46 % Allowed : 13.57 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.25), residues: 1100 helix: 2.18 (0.27), residues: 378 sheet: 0.27 (0.28), residues: 296 loop : -1.05 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 219 TYR 0.025 0.002 TYR E 178 PHE 0.015 0.002 PHE C 151 TRP 0.015 0.002 TRP C 169 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8833) covalent geometry : angle 0.54328 (11993) SS BOND : bond 0.00022 ( 2) SS BOND : angle 0.49020 ( 4) hydrogen bonds : bond 0.04442 ( 442) hydrogen bonds : angle 4.52606 ( 1251) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.339 Fit side-chains REVERT: A 121 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.6855 (ppp) REVERT: A 151 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7793 (tmm) REVERT: A 192 SER cc_start: 0.7627 (OUTLIER) cc_final: 0.7355 (m) REVERT: A 329 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7681 (pp) REVERT: B 186 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7127 (mm-30) REVERT: B 253 ILE cc_start: 0.8548 (mm) cc_final: 0.8315 (mp) REVERT: B 269 ASN cc_start: 0.8546 (m-40) cc_final: 0.8301 (m110) REVERT: B 275 GLU cc_start: 0.7538 (tt0) cc_final: 0.7139 (tt0) REVERT: B 337 ASP cc_start: 0.7932 (m-30) cc_final: 0.7674 (m-30) REVERT: B 350 ASP cc_start: 0.7713 (t70) cc_final: 0.7447 (t70) REVERT: C 197 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.7965 (mtm-85) REVERT: C 198 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7918 (pt) REVERT: C 217 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7755 (pmt) REVERT: C 258 ASP cc_start: 0.7442 (t70) cc_final: 0.7086 (t0) REVERT: E 89 GLU cc_start: 0.7820 (mp0) cc_final: 0.7378 (mp0) outliers start: 23 outliers final: 9 residues processed: 196 average time/residue: 0.4163 time to fit residues: 87.4318 Evaluate side-chains 200 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 HIS E 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.132962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110226 restraints weight = 11967.751| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.76 r_work: 0.3281 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8835 Z= 0.172 Angle : 0.531 8.582 11997 Z= 0.283 Chirality : 0.042 0.179 1399 Planarity : 0.004 0.056 1503 Dihedral : 4.612 56.845 1267 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.67 % Allowed : 14.00 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.25), residues: 1100 helix: 2.21 (0.27), residues: 378 sheet: 0.29 (0.28), residues: 295 loop : -1.04 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 219 TYR 0.022 0.002 TYR E 178 PHE 0.014 0.001 PHE C 151 TRP 0.018 0.001 TRP C 169 HIS 0.003 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8833) covalent geometry : angle 0.53137 (11993) SS BOND : bond 0.00026 ( 2) SS BOND : angle 0.56888 ( 4) hydrogen bonds : bond 0.04328 ( 442) hydrogen bonds : angle 4.48777 ( 1251) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.208 Fit side-chains REVERT: A 121 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.6838 (ppp) REVERT: A 151 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7727 (tmm) REVERT: A 192 SER cc_start: 0.7676 (OUTLIER) cc_final: 0.7376 (m) REVERT: A 329 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7773 (pp) REVERT: B 186 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7124 (mm-30) REVERT: B 269 ASN cc_start: 0.8538 (m-40) cc_final: 0.8297 (m110) REVERT: B 275 GLU cc_start: 0.7528 (tt0) cc_final: 0.7129 (tt0) REVERT: B 337 ASP cc_start: 0.7932 (m-30) cc_final: 0.7678 (m-30) REVERT: B 350 ASP cc_start: 0.7697 (t70) cc_final: 0.7484 (t70) REVERT: C 197 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.7959 (mtm-85) REVERT: C 198 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7899 (pt) REVERT: C 258 ASP cc_start: 0.7457 (t70) cc_final: 0.7099 (OUTLIER) REVERT: E 89 GLU cc_start: 0.7853 (mp0) cc_final: 0.7406 (mp0) outliers start: 25 outliers final: 12 residues processed: 193 average time/residue: 0.4599 time to fit residues: 95.1044 Evaluate side-chains 198 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 223 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 8 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 104 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.132251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109693 restraints weight = 11915.925| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.75 r_work: 0.3277 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8835 Z= 0.211 Angle : 0.565 8.907 11997 Z= 0.300 Chirality : 0.044 0.188 1399 Planarity : 0.004 0.059 1503 Dihedral : 4.775 58.636 1267 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.56 % Allowed : 14.64 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.25), residues: 1100 helix: 2.11 (0.27), residues: 379 sheet: 0.29 (0.29), residues: 295 loop : -1.06 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.026 0.002 TYR E 178 PHE 0.016 0.002 PHE C 151 TRP 0.018 0.002 TRP C 169 HIS 0.004 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 8833) covalent geometry : angle 0.56461 (11993) SS BOND : bond 0.00023 ( 2) SS BOND : angle 1.00923 ( 4) hydrogen bonds : bond 0.04615 ( 442) hydrogen bonds : angle 4.57221 ( 1251) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.267 Fit side-chains REVERT: A 118 VAL cc_start: 0.6344 (t) cc_final: 0.5855 (t) REVERT: A 121 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.6876 (ppp) REVERT: A 151 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7708 (tmm) REVERT: A 192 SER cc_start: 0.7689 (OUTLIER) cc_final: 0.7401 (m) REVERT: A 329 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7658 (pp) REVERT: B 186 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7176 (mm-30) REVERT: B 269 ASN cc_start: 0.8538 (m-40) cc_final: 0.8308 (m110) REVERT: B 275 GLU cc_start: 0.7560 (tt0) cc_final: 0.7148 (tt0) REVERT: B 337 ASP cc_start: 0.7949 (m-30) cc_final: 0.7692 (m-30) REVERT: B 350 ASP cc_start: 0.7693 (t70) cc_final: 0.7490 (t70) REVERT: C 197 ARG cc_start: 0.8205 (mtm-85) cc_final: 0.7979 (mtm-85) REVERT: C 198 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7937 (pt) REVERT: C 258 ASP cc_start: 0.7531 (t70) cc_final: 0.7132 (OUTLIER) REVERT: E 89 GLU cc_start: 0.7849 (mp0) cc_final: 0.7400 (mp0) outliers start: 24 outliers final: 14 residues processed: 194 average time/residue: 0.4537 time to fit residues: 94.2820 Evaluate side-chains 202 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 223 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 93 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 HIS C 295 ASN E 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.132766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110326 restraints weight = 11777.249| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.74 r_work: 0.3285 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8835 Z= 0.178 Angle : 0.545 8.441 11997 Z= 0.290 Chirality : 0.043 0.178 1399 Planarity : 0.004 0.055 1503 Dihedral : 4.706 57.251 1267 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.56 % Allowed : 15.71 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.25), residues: 1100 helix: 2.18 (0.27), residues: 379 sheet: 0.36 (0.29), residues: 293 loop : -1.07 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.023 0.002 TYR E 178 PHE 0.014 0.001 PHE C 151 TRP 0.018 0.001 TRP C 169 HIS 0.003 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 8833) covalent geometry : angle 0.54522 (11993) SS BOND : bond 0.00042 ( 2) SS BOND : angle 1.04837 ( 4) hydrogen bonds : bond 0.04392 ( 442) hydrogen bonds : angle 4.50441 ( 1251) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.310 Fit side-chains REVERT: A 118 VAL cc_start: 0.6348 (t) cc_final: 0.5880 (t) REVERT: A 121 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.6820 (ppp) REVERT: A 151 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7740 (tmm) REVERT: A 192 SER cc_start: 0.7651 (OUTLIER) cc_final: 0.7373 (m) REVERT: A 329 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7763 (pp) REVERT: B 186 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7179 (mm-30) REVERT: B 269 ASN cc_start: 0.8554 (m-40) cc_final: 0.8323 (m110) REVERT: B 275 GLU cc_start: 0.7548 (tt0) cc_final: 0.7153 (tt0) REVERT: B 337 ASP cc_start: 0.7955 (m-30) cc_final: 0.7703 (m-30) REVERT: B 350 ASP cc_start: 0.7675 (t70) cc_final: 0.7468 (t70) REVERT: C 197 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7985 (mtm-85) REVERT: C 198 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7915 (pt) REVERT: C 258 ASP cc_start: 0.7500 (t70) cc_final: 0.7129 (OUTLIER) REVERT: C 303 ASP cc_start: 0.7801 (m-30) cc_final: 0.7392 (m-30) REVERT: E 89 GLU cc_start: 0.7855 (mp0) cc_final: 0.7409 (mp0) REVERT: E 167 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7950 (tt0) outliers start: 24 outliers final: 13 residues processed: 192 average time/residue: 0.4485 time to fit residues: 92.3498 Evaluate side-chains 199 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain E residue 223 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 103 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 0.0770 chunk 48 optimal weight: 0.7980 chunk 11 optimal weight: 0.0770 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 HIS E 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.134019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.111674 restraints weight = 11797.199| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.75 r_work: 0.3322 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8835 Z= 0.124 Angle : 0.506 7.931 11997 Z= 0.269 Chirality : 0.041 0.172 1399 Planarity : 0.004 0.056 1503 Dihedral : 4.474 54.759 1267 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.46 % Allowed : 15.60 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.26), residues: 1100 helix: 2.33 (0.27), residues: 379 sheet: 0.32 (0.30), residues: 285 loop : -0.94 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 219 TYR 0.017 0.001 TYR E 178 PHE 0.011 0.001 PHE C 151 TRP 0.017 0.001 TRP C 169 HIS 0.003 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8833) covalent geometry : angle 0.50599 (11993) SS BOND : bond 0.00071 ( 2) SS BOND : angle 0.93114 ( 4) hydrogen bonds : bond 0.03931 ( 442) hydrogen bonds : angle 4.33840 ( 1251) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.223 Fit side-chains REVERT: A 118 VAL cc_start: 0.6280 (t) cc_final: 0.5827 (t) REVERT: A 121 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.6764 (ppp) REVERT: A 151 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7765 (tmm) REVERT: A 192 SER cc_start: 0.7652 (OUTLIER) cc_final: 0.7383 (m) REVERT: A 329 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7736 (pp) REVERT: B 186 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7199 (mm-30) REVERT: B 269 ASN cc_start: 0.8565 (m-40) cc_final: 0.8327 (m110) REVERT: B 275 GLU cc_start: 0.7550 (tt0) cc_final: 0.7154 (tt0) REVERT: B 337 ASP cc_start: 0.7937 (m-30) cc_final: 0.7677 (m-30) REVERT: B 350 ASP cc_start: 0.7722 (t70) cc_final: 0.7499 (t70) REVERT: C 197 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7935 (mtm-85) REVERT: C 198 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7896 (pt) REVERT: C 217 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7745 (pmt) REVERT: C 258 ASP cc_start: 0.7501 (t70) cc_final: 0.7171 (t0) REVERT: C 303 ASP cc_start: 0.7765 (m-30) cc_final: 0.7471 (m-30) REVERT: E 89 GLU cc_start: 0.7856 (mp0) cc_final: 0.7410 (mp0) outliers start: 23 outliers final: 12 residues processed: 195 average time/residue: 0.4195 time to fit residues: 87.6880 Evaluate side-chains 204 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 103 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.133390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110920 restraints weight = 11868.784| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.75 r_work: 0.3293 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8835 Z= 0.162 Angle : 0.537 8.100 11997 Z= 0.284 Chirality : 0.042 0.178 1399 Planarity : 0.004 0.055 1503 Dihedral : 4.586 55.846 1267 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.14 % Allowed : 16.03 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.26), residues: 1100 helix: 2.29 (0.27), residues: 379 sheet: 0.31 (0.30), residues: 285 loop : -0.94 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 219 TYR 0.023 0.002 TYR E 178 PHE 0.013 0.001 PHE C 151 TRP 0.015 0.001 TRP C 169 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8833) covalent geometry : angle 0.53677 (11993) SS BOND : bond 0.00044 ( 2) SS BOND : angle 1.01577 ( 4) hydrogen bonds : bond 0.04229 ( 442) hydrogen bonds : angle 4.42580 ( 1251) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.346 Fit side-chains REVERT: A 118 VAL cc_start: 0.6331 (t) cc_final: 0.5860 (t) REVERT: A 121 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.6831 (ppp) REVERT: A 151 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7740 (tmm) REVERT: A 192 SER cc_start: 0.7640 (OUTLIER) cc_final: 0.7370 (m) REVERT: A 329 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7772 (pp) REVERT: B 269 ASN cc_start: 0.8573 (m-40) cc_final: 0.8336 (m110) REVERT: B 275 GLU cc_start: 0.7559 (tt0) cc_final: 0.7164 (tt0) REVERT: B 337 ASP cc_start: 0.7941 (m-30) cc_final: 0.7690 (m-30) REVERT: B 350 ASP cc_start: 0.7703 (t70) cc_final: 0.7499 (t70) REVERT: C 197 ARG cc_start: 0.8196 (mtm-85) cc_final: 0.7973 (mtm-85) REVERT: C 198 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7921 (pt) REVERT: C 258 ASP cc_start: 0.7507 (t70) cc_final: 0.7136 (t0) REVERT: C 303 ASP cc_start: 0.7795 (m-30) cc_final: 0.7400 (m-30) REVERT: E 89 GLU cc_start: 0.7873 (mp0) cc_final: 0.7434 (mp0) REVERT: E 130 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7910 (pt0) REVERT: E 167 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7927 (tt0) outliers start: 20 outliers final: 11 residues processed: 190 average time/residue: 0.4650 time to fit residues: 94.8473 Evaluate side-chains 200 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 167 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 41 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.133051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.110638 restraints weight = 11754.210| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.74 r_work: 0.3295 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8835 Z= 0.179 Angle : 0.561 8.172 11997 Z= 0.296 Chirality : 0.043 0.182 1399 Planarity : 0.004 0.055 1503 Dihedral : 4.645 56.662 1267 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.14 % Allowed : 16.03 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.25), residues: 1100 helix: 2.26 (0.27), residues: 379 sheet: 0.34 (0.29), residues: 283 loop : -1.02 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.023 0.002 TYR E 178 PHE 0.014 0.001 PHE C 151 TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 8833) covalent geometry : angle 0.55724 (11993) SS BOND : bond 0.00105 ( 2) SS BOND : angle 3.71814 ( 4) hydrogen bonds : bond 0.04343 ( 442) hydrogen bonds : angle 4.46872 ( 1251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3080.39 seconds wall clock time: 53 minutes 5.61 seconds (3185.61 seconds total)