Starting phenix.real_space_refine on Sat Dec 28 01:00:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wvw_32860/12_2024/7wvw_32860.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wvw_32860/12_2024/7wvw_32860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wvw_32860/12_2024/7wvw_32860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wvw_32860/12_2024/7wvw_32860.map" model { file = "/net/cci-nas-00/data/ceres_data/7wvw_32860/12_2024/7wvw_32860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wvw_32860/12_2024/7wvw_32860.cif" } resolution = 3.1 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= 0.004 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 54 5.16 5 C 4608 2.51 5 N 1212 2.21 5 O 1295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7169 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 65 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2344 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 285} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1753 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2583 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 424 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 4.67, per 1000 atoms: 0.65 Number of scatterers: 7169 At special positions: 0 Unit cell: (114.95, 119.13, 84.645, 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 54 16.00 O 1295 8.00 N 1212 7.00 C 4608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " 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: 1.72 Conformation dependent library (CDL) restraints added in 1.1 seconds 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1734 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 10 sheets defined 48.3% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'R' and resid 20 through 55 Proline residue: R 29 - end of helix removed outlier: 3.737A pdb=" N PHE R 53 " --> pdb=" O TRP R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 87 Proline residue: R 79 - end of helix Processing helix chain 'R' and resid 94 through 129 Processing helix chain 'R' and resid 129 through 136 Processing helix chain 'R' and resid 138 through 163 removed outlier: 4.089A pdb=" N GLY R 148 " --> pdb=" O LYS R 144 " (cutoff:3.500A) Proline residue: R 149 - end of helix Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 186 through 209 Processing helix chain 'R' and resid 210 through 231 Processing helix chain 'R' and resid 237 through 267 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 267 through 274 Processing helix chain 'R' and resid 278 through 303 removed outlier: 4.388A pdb=" N ASN R 285 " --> pdb=" O ASP R 281 " (cutoff:3.500A) Proline residue: R 286 - end of helix Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 317 Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.798A pdb=" N GLU A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.888A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.700A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 4.290A pdb=" N ASP A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 257 through 261 removed outlier: 4.086A pdb=" N THR A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 removed outlier: 4.051A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N HIS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.819A pdb=" N ILE A 286 " --> pdb=" O PRO A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 312 removed outlier: 3.687A pdb=" N ASN A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.614A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 23 removed outlier: 3.653A pdb=" N LEU C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.783A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 164 through 168 removed outlier: 3.501A pdb=" N THR R 177 " --> pdb=" O THR R 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 187 Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 187 removed outlier: 6.075A pdb=" N VAL A 34 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N ALA A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.526A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.661A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.625A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.592A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.687A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.734A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.559A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1131 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: 2.35 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2294 1.35 - 1.47: 1778 1.47 - 1.59: 3168 1.59 - 1.71: 0 1.71 - 1.83: 79 Bond restraints: 7319 Sorted by residual: bond pdb=" SD FME L 1 " pdb=" CE FME L 1 " ideal model delta sigma weight residual 1.805 1.752 0.053 2.00e-02 2.50e+03 6.95e+00 bond pdb=" CG FME L 1 " pdb=" SD FME L 1 " ideal model delta sigma weight residual 1.817 1.770 0.047 2.00e-02 2.50e+03 5.50e+00 bond pdb=" N FME L 1 " pdb=" CN FME L 1 " ideal model delta sigma weight residual 1.335 1.376 -0.041 2.00e-02 2.50e+03 4.24e+00 bond pdb=" N FME L 1 " pdb=" CA FME L 1 " ideal model delta sigma weight residual 1.458 1.437 0.021 1.90e-02 2.77e+03 1.26e+00 bond pdb=" CN FME L 1 " pdb=" O1 FME L 1 " ideal model delta sigma weight residual 1.221 1.241 -0.020 2.00e-02 2.50e+03 9.75e-01 ... (remaining 7314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 9792 1.65 - 3.31: 103 3.31 - 4.96: 25 4.96 - 6.62: 7 6.62 - 8.27: 1 Bond angle restraints: 9928 Sorted by residual: angle pdb=" C TYR R 175 " pdb=" N CYS R 176 " pdb=" CA CYS R 176 " ideal model delta sigma weight residual 122.84 118.55 4.29 1.30e+00 5.92e-01 1.09e+01 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.71 111.03 2.68 9.50e-01 1.11e+00 7.95e+00 angle pdb=" CA CYS R 176 " pdb=" CB CYS R 176 " pdb=" SG CYS R 176 " ideal model delta sigma weight residual 114.40 120.09 -5.69 2.30e+00 1.89e-01 6.12e+00 angle pdb=" CA LEU R 162 " pdb=" CB LEU R 162 " pdb=" CG LEU R 162 " ideal model delta sigma weight residual 116.30 124.57 -8.27 3.50e+00 8.16e-02 5.58e+00 angle pdb=" C ASP A 329 " pdb=" N THR A 330 " pdb=" CA THR A 330 " ideal model delta sigma weight residual 122.08 125.17 -3.09 1.47e+00 4.63e-01 4.41e+00 ... (remaining 9923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 3850 16.27 - 32.54: 361 32.54 - 48.81: 88 48.81 - 65.08: 9 65.08 - 81.35: 7 Dihedral angle restraints: 4315 sinusoidal: 1641 harmonic: 2674 Sorted by residual: dihedral pdb=" CA PHE R 161 " pdb=" C PHE R 161 " pdb=" N LEU R 162 " pdb=" CA LEU R 162 " ideal model delta harmonic sigma weight residual -180.00 -162.92 -17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASN A 348 " pdb=" CB ASN A 348 " pdb=" CG ASN A 348 " pdb=" OD1 ASN A 348 " ideal model delta sinusoidal sigma weight residual 120.00 -177.28 -62.72 2 2.00e+01 2.50e-03 9.48e+00 dihedral pdb=" CB MET R 214 " pdb=" CG MET R 214 " pdb=" SD MET R 214 " pdb=" CE MET R 214 " ideal model delta sinusoidal sigma weight residual -180.00 -122.29 -57.71 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 4312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 686 0.027 - 0.053: 280 0.053 - 0.080: 110 0.080 - 0.107: 55 0.107 - 0.133: 28 Chirality restraints: 1159 Sorted by residual: chirality pdb=" CA LEU R 162 " pdb=" N LEU R 162 " pdb=" C LEU R 162 " pdb=" CB LEU R 162 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA VAL C 54 " pdb=" N VAL C 54 " pdb=" C VAL C 54 " pdb=" CB VAL C 54 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 1156 not shown) Planarity restraints: 1243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 148 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.14e+00 pdb=" N PRO R 149 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO R 149 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 149 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO B 236 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 95 " -0.012 2.00e-02 2.50e+03 8.74e-03 1.91e+00 pdb=" CG TRP R 95 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP R 95 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP R 95 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 95 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 95 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 95 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 95 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 95 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 95 " -0.001 2.00e-02 2.50e+03 ... (remaining 1240 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 448 2.74 - 3.28: 7244 3.28 - 3.82: 12448 3.82 - 4.36: 14507 4.36 - 4.90: 25386 Nonbonded interactions: 60033 Sorted by model distance: nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASN A 270 " pdb=" OG1 THR A 325 " model vdw 2.221 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.239 3.040 nonbonded pdb=" OH TYR A 231 " pdb=" OG SER A 282 " model vdw 2.290 3.040 nonbonded pdb=" NH2 ARG B 256 " pdb=" OD2 ASP C 36 " model vdw 2.309 3.120 ... (remaining 60028 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.260 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 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 : 0.002 0.053 7319 Z= 0.137 Angle : 0.496 8.271 9928 Z= 0.266 Chirality : 0.040 0.133 1159 Planarity : 0.003 0.051 1243 Dihedral : 13.512 81.345 2578 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.28), residues: 911 helix: 1.80 (0.26), residues: 413 sheet: 0.56 (0.45), residues: 152 loop : -1.09 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 95 HIS 0.004 0.000 HIS R 102 PHE 0.016 0.001 PHE R 161 TYR 0.009 0.001 TYR R 175 ARG 0.013 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.805 Fit side-chains REVERT: R 106 ASP cc_start: 0.7299 (t70) cc_final: 0.7097 (t70) REVERT: R 204 ILE cc_start: 0.7547 (mt) cc_final: 0.6928 (mt) REVERT: A 325 THR cc_start: 0.7395 (m) cc_final: 0.7172 (m) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2058 time to fit residues: 46.8941 Evaluate side-chains 125 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 0.0270 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 220 GLN B 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7319 Z= 0.272 Angle : 0.575 8.192 9928 Z= 0.300 Chirality : 0.044 0.151 1159 Planarity : 0.004 0.048 1243 Dihedral : 4.111 53.587 984 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.17 % Allowed : 11.72 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.28), residues: 911 helix: 1.76 (0.25), residues: 424 sheet: 0.67 (0.41), residues: 170 loop : -1.10 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.004 0.001 HIS B 225 PHE 0.016 0.002 PHE B 199 TYR 0.013 0.002 TYR R 175 ARG 0.006 0.000 ARG R 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 0.832 Fit side-chains REVERT: R 103 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8168 (mp) REVERT: R 278 LYS cc_start: 0.7829 (mtmt) cc_final: 0.7451 (mttm) outliers start: 9 outliers final: 7 residues processed: 172 average time/residue: 0.2036 time to fit residues: 46.5285 Evaluate side-chains 147 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 103 ILE Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain B residue 173 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.0470 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 0.0570 chunk 22 optimal weight: 0.0570 chunk 81 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.3514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 102 HIS R 294 ASN A 245 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7319 Z= 0.152 Angle : 0.508 7.977 9928 Z= 0.262 Chirality : 0.041 0.134 1159 Planarity : 0.004 0.049 1243 Dihedral : 3.986 53.465 984 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.17 % Allowed : 15.23 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.05 (0.28), residues: 911 helix: 1.95 (0.25), residues: 424 sheet: 0.49 (0.40), residues: 177 loop : -0.95 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.004 0.001 HIS R 102 PHE 0.017 0.001 PHE B 199 TYR 0.011 0.001 TYR R 175 ARG 0.005 0.000 ARG R 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 153 time to evaluate : 0.872 Fit side-chains REVERT: R 103 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8184 (mp) REVERT: R 273 PHE cc_start: 0.7659 (m-10) cc_final: 0.7442 (m-80) REVERT: R 278 LYS cc_start: 0.7829 (mtmt) cc_final: 0.7399 (mttm) REVERT: B 36 ASN cc_start: 0.7547 (p0) cc_final: 0.7222 (p0) outliers start: 9 outliers final: 7 residues processed: 156 average time/residue: 0.2341 time to fit residues: 48.0513 Evaluate side-chains 150 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 ILE Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 72 optimal weight: 0.0870 chunk 49 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7319 Z= 0.195 Angle : 0.510 9.001 9928 Z= 0.264 Chirality : 0.041 0.131 1159 Planarity : 0.004 0.048 1243 Dihedral : 4.053 54.409 984 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.08 % Allowed : 15.76 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.29), residues: 911 helix: 1.96 (0.26), residues: 426 sheet: 0.28 (0.40), residues: 183 loop : -0.88 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.001 PHE B 199 TYR 0.013 0.001 TYR B 59 ARG 0.008 0.000 ARG R 238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.914 Fit side-chains REVERT: R 27 ILE cc_start: 0.7352 (mm) cc_final: 0.7029 (mt) REVERT: R 143 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.6365 (mpt) REVERT: R 273 PHE cc_start: 0.7706 (m-10) cc_final: 0.7480 (m-80) REVERT: R 278 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7497 (mttm) REVERT: C 31 SER cc_start: 0.8140 (m) cc_final: 0.7806 (p) outliers start: 16 outliers final: 10 residues processed: 160 average time/residue: 0.2112 time to fit residues: 45.2631 Evaluate side-chains 150 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 0.0970 chunk 17 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7764 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7319 Z= 0.226 Angle : 0.510 8.774 9928 Z= 0.265 Chirality : 0.042 0.133 1159 Planarity : 0.004 0.049 1243 Dihedral : 4.141 54.761 984 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.34 % Allowed : 16.28 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.28), residues: 911 helix: 1.86 (0.25), residues: 426 sheet: 0.15 (0.38), residues: 191 loop : -0.99 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.001 PHE R 178 TYR 0.014 0.001 TYR B 59 ARG 0.003 0.000 ARG R 238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.871 Fit side-chains REVERT: R 27 ILE cc_start: 0.7273 (mm) cc_final: 0.6908 (mt) REVERT: R 99 LYS cc_start: 0.8209 (tptm) cc_final: 0.7879 (mmtt) REVERT: R 143 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.6447 (mpt) REVERT: R 192 LYS cc_start: 0.7683 (tptp) cc_final: 0.7421 (mttp) REVERT: R 273 PHE cc_start: 0.7717 (m-10) cc_final: 0.7508 (m-80) REVERT: B 188 MET cc_start: 0.7476 (mmm) cc_final: 0.7037 (mmm) REVERT: C 31 SER cc_start: 0.8260 (m) cc_final: 0.7931 (p) outliers start: 18 outliers final: 13 residues processed: 149 average time/residue: 0.1870 time to fit residues: 38.0098 Evaluate side-chains 147 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 303 VAL Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.1980 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 0.0670 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7319 Z= 0.175 Angle : 0.498 9.018 9928 Z= 0.258 Chirality : 0.041 0.137 1159 Planarity : 0.004 0.049 1243 Dihedral : 4.089 54.159 984 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.21 % Allowed : 17.71 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.91 (0.28), residues: 911 helix: 1.88 (0.25), residues: 427 sheet: 0.06 (0.38), residues: 191 loop : -0.89 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS B 225 PHE 0.013 0.001 PHE B 199 TYR 0.013 0.001 TYR B 59 ARG 0.004 0.000 ARG R 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.898 Fit side-chains REVERT: R 27 ILE cc_start: 0.7249 (mm) cc_final: 0.6894 (mt) REVERT: R 99 LYS cc_start: 0.8278 (tptm) cc_final: 0.8040 (mmtt) REVERT: R 143 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.6373 (mpt) REVERT: R 192 LYS cc_start: 0.7617 (tptp) cc_final: 0.7415 (mttp) REVERT: R 273 PHE cc_start: 0.7733 (m-10) cc_final: 0.7469 (m-80) REVERT: B 188 MET cc_start: 0.7415 (mmm) cc_final: 0.7050 (mmm) REVERT: C 31 SER cc_start: 0.8251 (m) cc_final: 0.7972 (p) outliers start: 17 outliers final: 13 residues processed: 154 average time/residue: 0.1916 time to fit residues: 40.3640 Evaluate side-chains 143 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 303 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 40 optimal weight: 0.2980 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 0.0040 chunk 51 optimal weight: 0.6980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7319 Z= 0.169 Angle : 0.499 9.254 9928 Z= 0.258 Chirality : 0.041 0.130 1159 Planarity : 0.004 0.049 1243 Dihedral : 4.073 53.834 984 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.08 % Allowed : 18.88 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.90 (0.28), residues: 911 helix: 1.88 (0.25), residues: 427 sheet: -0.04 (0.38), residues: 191 loop : -0.85 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS B 225 PHE 0.012 0.001 PHE B 199 TYR 0.012 0.001 TYR B 59 ARG 0.003 0.000 ARG R 238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 1.094 Fit side-chains REVERT: R 27 ILE cc_start: 0.7217 (mm) cc_final: 0.6838 (mt) REVERT: R 99 LYS cc_start: 0.8287 (tptm) cc_final: 0.8045 (mmtt) REVERT: R 143 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.6371 (mpt) REVERT: R 273 PHE cc_start: 0.7738 (m-10) cc_final: 0.7468 (m-80) REVERT: B 188 MET cc_start: 0.7349 (mmm) cc_final: 0.6968 (mmm) REVERT: C 31 SER cc_start: 0.8232 (m) cc_final: 0.7952 (p) outliers start: 16 outliers final: 12 residues processed: 138 average time/residue: 0.1938 time to fit residues: 36.2700 Evaluate side-chains 140 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 0.0000 chunk 59 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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: 0.7750 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7319 Z= 0.184 Angle : 0.507 9.602 9928 Z= 0.262 Chirality : 0.041 0.131 1159 Planarity : 0.004 0.049 1243 Dihedral : 4.081 54.179 984 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.21 % Allowed : 18.88 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.29), residues: 911 helix: 1.91 (0.25), residues: 427 sheet: -0.10 (0.38), residues: 191 loop : -0.86 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.002 0.001 HIS B 54 PHE 0.011 0.001 PHE R 180 TYR 0.012 0.001 TYR B 59 ARG 0.003 0.000 ARG R 238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.734 Fit side-chains REVERT: R 27 ILE cc_start: 0.7252 (mm) cc_final: 0.6866 (mt) REVERT: R 99 LYS cc_start: 0.8274 (tptm) cc_final: 0.8023 (mmtt) REVERT: R 143 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.6723 (mpp) REVERT: R 273 PHE cc_start: 0.7694 (m-10) cc_final: 0.7428 (m-80) REVERT: A 25 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6244 (mp0) REVERT: B 188 MET cc_start: 0.7373 (mmm) cc_final: 0.6986 (mmm) REVERT: C 31 SER cc_start: 0.8253 (m) cc_final: 0.7976 (p) outliers start: 17 outliers final: 12 residues processed: 144 average time/residue: 0.2037 time to fit residues: 39.6944 Evaluate side-chains 144 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 48 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7759 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7319 Z= 0.191 Angle : 0.519 9.770 9928 Z= 0.265 Chirality : 0.041 0.136 1159 Planarity : 0.004 0.049 1243 Dihedral : 4.120 54.042 984 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.95 % Allowed : 19.14 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.28), residues: 911 helix: 1.93 (0.25), residues: 427 sheet: -0.16 (0.39), residues: 181 loop : -0.84 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS B 54 PHE 0.011 0.001 PHE B 199 TYR 0.012 0.001 TYR B 59 ARG 0.003 0.000 ARG R 238 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.809 Fit side-chains REVERT: R 27 ILE cc_start: 0.7126 (mm) cc_final: 0.6767 (mt) REVERT: R 99 LYS cc_start: 0.8251 (tptm) cc_final: 0.8003 (mmtt) REVERT: R 143 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.6732 (mpp) REVERT: R 273 PHE cc_start: 0.7690 (m-10) cc_final: 0.7390 (m-80) REVERT: A 25 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6192 (mp0) REVERT: B 188 MET cc_start: 0.7397 (mmm) cc_final: 0.7042 (mmm) REVERT: C 31 SER cc_start: 0.8277 (m) cc_final: 0.8007 (p) outliers start: 15 outliers final: 12 residues processed: 144 average time/residue: 0.2006 time to fit residues: 39.1461 Evaluate side-chains 145 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 71 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 55 optimal weight: 0.0870 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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: 0.7743 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7319 Z= 0.169 Angle : 0.515 9.880 9928 Z= 0.262 Chirality : 0.041 0.128 1159 Planarity : 0.004 0.049 1243 Dihedral : 4.093 53.716 984 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.08 % Allowed : 18.88 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.28), residues: 911 helix: 1.93 (0.25), residues: 427 sheet: -0.18 (0.38), residues: 181 loop : -0.83 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS B 54 PHE 0.011 0.001 PHE B 199 TYR 0.011 0.001 TYR B 59 ARG 0.004 0.000 ARG C 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.813 Fit side-chains REVERT: R 27 ILE cc_start: 0.7116 (mm) cc_final: 0.6752 (mt) REVERT: R 99 LYS cc_start: 0.8288 (tptm) cc_final: 0.8020 (mmtt) REVERT: R 143 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.6724 (mpp) REVERT: R 273 PHE cc_start: 0.7669 (m-10) cc_final: 0.7382 (m-80) REVERT: A 25 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6176 (mp0) REVERT: A 277 GLU cc_start: 0.7729 (pt0) cc_final: 0.7516 (pt0) REVERT: B 188 MET cc_start: 0.7361 (mmm) cc_final: 0.7014 (mmm) REVERT: C 31 SER cc_start: 0.8277 (m) cc_final: 0.8032 (p) outliers start: 16 outliers final: 12 residues processed: 147 average time/residue: 0.2087 time to fit residues: 41.6232 Evaluate side-chains 147 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 173 ASP Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 chunk 73 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.148018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.113174 restraints weight = 8603.993| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.01 r_work: 0.3213 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7319 Z= 0.180 Angle : 0.514 9.801 9928 Z= 0.262 Chirality : 0.041 0.136 1159 Planarity : 0.004 0.049 1243 Dihedral : 4.095 54.000 984 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.34 % Allowed : 18.88 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.92 (0.29), residues: 911 helix: 1.94 (0.25), residues: 427 sheet: -0.09 (0.38), residues: 191 loop : -0.85 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE B 199 TYR 0.011 0.001 TYR B 59 ARG 0.003 0.000 ARG C 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1905.03 seconds wall clock time: 36 minutes 5.10 seconds (2165.10 seconds total)