Starting phenix.real_space_refine on Tue Mar 11 19:10:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ge6_29958/03_2025/8ge6_29958.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ge6_29958/03_2025/8ge6_29958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ge6_29958/03_2025/8ge6_29958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ge6_29958/03_2025/8ge6_29958.map" model { file = "/net/cci-nas-00/data/ceres_data/8ge6_29958/03_2025/8ge6_29958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ge6_29958/03_2025/8ge6_29958.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.032 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 40 5.16 5 C 4220 2.51 5 N 1131 2.21 5 O 1169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6560 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1731 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 135 Chain: "B" Number of atoms: 2405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2405 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 109 Chain: "G" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 349 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2059 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 7, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 4.47, per 1000 atoms: 0.68 Number of scatterers: 6560 At special positions: 0 Unit cell: (69.96, 98.58, 129.32, 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 40 16.00 O 1169 8.00 N 1131 7.00 C 4220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " 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: 1.60 Conformation dependent library (CDL) restraints added in 1.0 seconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 47.5% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.524A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.946A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.639A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 12 through 22 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 36 through 61 Processing helix chain 'R' and resid 66 through 97 removed outlier: 3.701A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.401A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.530A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.684A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.801A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 327 removed outlier: 3.784A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.352A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.581A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.747A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.826A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.819A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.021A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.708A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.676A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1122 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: 1.80 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2121 1.34 - 1.46: 1429 1.46 - 1.58: 3096 1.58 - 1.69: 0 1.69 - 1.81: 55 Bond restraints: 6701 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.449 -0.052 2.00e-02 2.50e+03 6.79e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.570 -0.047 2.00e-02 2.50e+03 5.45e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.565 -0.045 2.00e-02 2.50e+03 5.02e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.439 -0.045 2.00e-02 2.50e+03 5.02e+00 bond pdb=" CAI G1I R 501 " pdb=" NAN G1I R 501 " ideal model delta sigma weight residual 1.451 1.485 -0.034 2.00e-02 2.50e+03 2.81e+00 ... (remaining 6696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 8975 1.39 - 2.78: 145 2.78 - 4.18: 25 4.18 - 5.57: 10 5.57 - 6.96: 2 Bond angle restraints: 9157 Sorted by residual: angle pdb=" N GLU R 225 " pdb=" CA GLU R 225 " pdb=" CB GLU R 225 " ideal model delta sigma weight residual 110.16 114.08 -3.92 1.48e+00 4.57e-01 7.01e+00 angle pdb=" N GLY A 329 " pdb=" CA GLY A 329 " pdb=" C GLY A 329 " ideal model delta sigma weight residual 113.18 107.04 6.14 2.37e+00 1.78e-01 6.72e+00 angle pdb=" CA GLU A 50 " pdb=" CB GLU A 50 " pdb=" CG GLU A 50 " ideal model delta sigma weight residual 114.10 118.67 -4.57 2.00e+00 2.50e-01 5.22e+00 angle pdb=" CA LEU A 46 " pdb=" CB LEU A 46 " pdb=" CG LEU A 46 " ideal model delta sigma weight residual 116.30 123.26 -6.96 3.50e+00 8.16e-02 3.96e+00 angle pdb=" C THR R 96 " pdb=" N LYS R 97 " pdb=" CA LYS R 97 " ideal model delta sigma weight residual 124.31 127.60 -3.29 1.67e+00 3.59e-01 3.88e+00 ... (remaining 9152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.94: 3459 13.94 - 27.89: 309 27.89 - 41.83: 100 41.83 - 55.77: 10 55.77 - 69.72: 6 Dihedral angle restraints: 3884 sinusoidal: 1284 harmonic: 2600 Sorted by residual: dihedral pdb=" CB CYS R 106 " pdb=" SG CYS R 106 " pdb=" SG CYS R 191 " pdb=" CB CYS R 191 " ideal model delta sinusoidal sigma weight residual -86.00 -145.70 59.70 1 1.00e+01 1.00e-02 4.76e+01 dihedral pdb=" CB MET G 38 " pdb=" CG MET G 38 " pdb=" SD MET G 38 " pdb=" CE MET G 38 " ideal model delta sinusoidal sigma weight residual 60.00 118.04 -58.04 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual -180.00 -165.04 -14.96 0 5.00e+00 4.00e-02 8.95e+00 ... (remaining 3881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 711 0.031 - 0.061: 246 0.061 - 0.092: 83 0.092 - 0.123: 48 0.123 - 0.154: 6 Chirality restraints: 1094 Sorted by residual: chirality pdb=" CA ASP B 291 " pdb=" N ASP B 291 " pdb=" C ASP B 291 " pdb=" CB ASP B 291 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 1091 not shown) Planarity restraints: 1153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO G 55 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 329 " -0.028 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO R 330 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO R 330 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 330 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.014 2.00e-02 2.50e+03 1.18e-02 2.77e+00 pdb=" CG TYR B 59 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.001 2.00e-02 2.50e+03 ... (remaining 1150 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1049 2.76 - 3.29: 6405 3.29 - 3.83: 11190 3.83 - 4.36: 12467 4.36 - 4.90: 22671 Nonbonded interactions: 53782 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.224 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.231 3.040 nonbonded pdb=" OG SER B 281 " pdb=" O HIS G 44 " model vdw 2.251 3.040 nonbonded pdb=" O PRO A 332 " pdb=" OG1 THR A 335 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.262 3.040 ... (remaining 53777 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=0.00 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: 1.160 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.830 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 : 0.003 0.052 6701 Z= 0.194 Angle : 0.495 6.961 9157 Z= 0.272 Chirality : 0.040 0.154 1094 Planarity : 0.003 0.047 1153 Dihedral : 12.286 69.718 2193 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.32 (0.28), residues: 876 helix: 2.43 (0.25), residues: 385 sheet: 0.27 (0.39), residues: 182 loop : -0.76 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 158 HIS 0.002 0.001 HIS B 183 PHE 0.010 0.001 PHE B 199 TYR 0.029 0.001 TYR B 59 ARG 0.004 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.738 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1647 time to fit residues: 22.5431 Evaluate side-chains 85 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 GLN R 318 ASN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.126035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108614 restraints weight = 10403.423| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.11 r_work: 0.3216 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6701 Z= 0.208 Angle : 0.484 5.675 9157 Z= 0.269 Chirality : 0.041 0.140 1094 Planarity : 0.004 0.046 1153 Dihedral : 4.024 17.538 964 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.97 % Allowed : 9.03 % Favored : 90.00 % 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: 1.40 (0.28), residues: 876 helix: 2.40 (0.26), residues: 396 sheet: 0.40 (0.36), residues: 180 loop : -0.76 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.012 0.001 PHE B 199 TYR 0.024 0.001 TYR B 59 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.761 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 97 average time/residue: 0.1667 time to fit residues: 22.5136 Evaluate side-chains 96 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 205 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 GLN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.125407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107915 restraints weight = 10524.173| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.11 r_work: 0.3212 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6701 Z= 0.199 Angle : 0.464 5.813 9157 Z= 0.256 Chirality : 0.041 0.135 1094 Planarity : 0.003 0.048 1153 Dihedral : 4.001 20.795 964 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.61 % Allowed : 11.29 % Favored : 87.10 % 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: 1.39 (0.28), residues: 876 helix: 2.43 (0.26), residues: 396 sheet: 0.38 (0.37), residues: 181 loop : -0.81 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.002 0.001 HIS A 220 PHE 0.013 0.001 PHE B 199 TYR 0.021 0.001 TYR B 59 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.724 Fit side-chains REVERT: A 372 ILE cc_start: 0.8700 (mp) cc_final: 0.8367 (mt) outliers start: 10 outliers final: 7 residues processed: 104 average time/residue: 0.1967 time to fit residues: 27.2277 Evaluate side-chains 96 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 205 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 178 HIS R 231 GLN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.124429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.106751 restraints weight = 10684.188| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.13 r_work: 0.3192 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6701 Z= 0.218 Angle : 0.466 5.798 9157 Z= 0.257 Chirality : 0.041 0.132 1094 Planarity : 0.003 0.048 1153 Dihedral : 4.031 23.442 964 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.45 % Allowed : 11.94 % Favored : 86.61 % 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: 1.37 (0.28), residues: 876 helix: 2.42 (0.26), residues: 397 sheet: 0.46 (0.38), residues: 174 loop : -0.90 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.002 0.001 HIS B 183 PHE 0.013 0.001 PHE B 199 TYR 0.018 0.002 TYR B 59 ARG 0.002 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.806 Fit side-chains REVERT: A 372 ILE cc_start: 0.8695 (mp) cc_final: 0.8375 (mt) outliers start: 9 outliers final: 7 residues processed: 98 average time/residue: 0.1662 time to fit residues: 22.6831 Evaluate side-chains 92 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 205 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 GLN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.105249 restraints weight = 10653.642| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.09 r_work: 0.3166 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6701 Z= 0.274 Angle : 0.494 6.271 9157 Z= 0.270 Chirality : 0.042 0.136 1094 Planarity : 0.003 0.049 1153 Dihedral : 4.173 25.604 964 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.26 % Allowed : 12.42 % Favored : 85.32 % 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: 1.26 (0.28), residues: 876 helix: 2.44 (0.26), residues: 390 sheet: 0.10 (0.37), residues: 186 loop : -0.86 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.006 0.001 HIS B 183 PHE 0.014 0.001 PHE B 199 TYR 0.020 0.002 TYR B 59 ARG 0.002 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: A 372 ILE cc_start: 0.8722 (mp) cc_final: 0.8393 (mt) REVERT: B 59 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.8425 (m-80) REVERT: B 228 ASP cc_start: 0.8233 (m-30) cc_final: 0.7934 (m-30) outliers start: 14 outliers final: 11 residues processed: 101 average time/residue: 0.1745 time to fit residues: 24.1323 Evaluate side-chains 101 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 37 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 46 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 GLN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.124360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107077 restraints weight = 10402.143| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.07 r_work: 0.3195 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6701 Z= 0.181 Angle : 0.461 10.102 9157 Z= 0.251 Chirality : 0.040 0.130 1094 Planarity : 0.003 0.049 1153 Dihedral : 4.031 24.925 964 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.77 % Allowed : 13.55 % Favored : 84.68 % 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: 1.32 (0.29), residues: 876 helix: 2.53 (0.26), residues: 390 sheet: 0.14 (0.37), residues: 184 loop : -0.89 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.012 0.001 PHE B 199 TYR 0.015 0.001 TYR B 59 ARG 0.002 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.743 Fit side-chains REVERT: A 372 ILE cc_start: 0.8713 (mp) cc_final: 0.8383 (mt) REVERT: B 59 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8360 (m-80) REVERT: B 228 ASP cc_start: 0.8194 (m-30) cc_final: 0.7867 (m-30) outliers start: 11 outliers final: 7 residues processed: 103 average time/residue: 0.1744 time to fit residues: 24.7406 Evaluate side-chains 98 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 68 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.0670 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 51 ASN R 231 GLN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.123352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105906 restraints weight = 10571.959| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.10 r_work: 0.3179 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6701 Z= 0.228 Angle : 0.492 12.845 9157 Z= 0.263 Chirality : 0.041 0.153 1094 Planarity : 0.003 0.049 1153 Dihedral : 4.110 25.607 964 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.58 % Allowed : 13.71 % Favored : 83.71 % 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: 1.24 (0.29), residues: 876 helix: 2.49 (0.26), residues: 390 sheet: -0.04 (0.37), residues: 186 loop : -0.87 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.013 0.001 PHE B 199 TYR 0.018 0.001 TYR B 59 ARG 0.002 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.798 Fit side-chains REVERT: A 372 ILE cc_start: 0.8755 (mp) cc_final: 0.8452 (mt) REVERT: B 59 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.8451 (m-80) REVERT: B 228 ASP cc_start: 0.8211 (m-30) cc_final: 0.7904 (m-30) REVERT: R 51 ASN cc_start: 0.7871 (m-40) cc_final: 0.7394 (m110) outliers start: 16 outliers final: 13 residues processed: 102 average time/residue: 0.1699 time to fit residues: 24.0400 Evaluate side-chains 104 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 61 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 45 optimal weight: 0.0870 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 GLN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.122315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.105207 restraints weight = 10285.499| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.99 r_work: 0.3196 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6701 Z= 0.191 Angle : 0.478 13.281 9157 Z= 0.256 Chirality : 0.041 0.150 1094 Planarity : 0.003 0.049 1153 Dihedral : 4.035 25.415 964 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.42 % Allowed : 14.35 % Favored : 83.23 % 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: 1.25 (0.29), residues: 876 helix: 2.52 (0.26), residues: 390 sheet: 0.00 (0.38), residues: 181 loop : -0.92 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS B 183 PHE 0.013 0.001 PHE B 199 TYR 0.015 0.001 TYR B 59 ARG 0.002 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.808 Fit side-chains REVERT: A 372 ILE cc_start: 0.8747 (mp) cc_final: 0.8449 (mt) REVERT: B 59 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8402 (m-80) REVERT: B 228 ASP cc_start: 0.8187 (m-30) cc_final: 0.7808 (m-30) REVERT: R 51 ASN cc_start: 0.7987 (m-40) cc_final: 0.7750 (m-40) outliers start: 15 outliers final: 12 residues processed: 106 average time/residue: 0.1765 time to fit residues: 25.7096 Evaluate side-chains 105 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 231 GLN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.123592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.106547 restraints weight = 10619.199| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.08 r_work: 0.3187 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6701 Z= 0.209 Angle : 0.489 13.261 9157 Z= 0.262 Chirality : 0.041 0.145 1094 Planarity : 0.003 0.049 1153 Dihedral : 4.077 25.582 964 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.42 % Allowed : 14.35 % Favored : 83.23 % 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: 1.22 (0.29), residues: 876 helix: 2.50 (0.26), residues: 390 sheet: -0.07 (0.38), residues: 186 loop : -0.89 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.005 0.001 HIS B 183 PHE 0.013 0.001 PHE B 199 TYR 0.022 0.001 TYR A 318 ARG 0.002 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.726 Fit side-chains REVERT: A 372 ILE cc_start: 0.8759 (mp) cc_final: 0.8465 (mt) REVERT: B 59 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.8442 (m-80) REVERT: B 228 ASP cc_start: 0.8194 (m-30) cc_final: 0.7812 (m-30) outliers start: 15 outliers final: 12 residues processed: 104 average time/residue: 0.1660 time to fit residues: 24.0400 Evaluate side-chains 104 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 15 optimal weight: 0.2980 chunk 74 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106492 restraints weight = 10364.068| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.00 r_work: 0.3221 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6701 Z= 0.169 Angle : 0.478 13.252 9157 Z= 0.256 Chirality : 0.041 0.157 1094 Planarity : 0.003 0.049 1153 Dihedral : 4.013 24.815 964 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.94 % Allowed : 15.48 % Favored : 82.58 % 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: 1.27 (0.29), residues: 876 helix: 2.54 (0.26), residues: 391 sheet: -0.05 (0.38), residues: 186 loop : -0.88 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.012 0.001 PHE B 199 TYR 0.021 0.001 TYR A 318 ARG 0.002 0.000 ARG B 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.758 Fit side-chains REVERT: A 372 ILE cc_start: 0.8755 (mp) cc_final: 0.8462 (mt) REVERT: B 59 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.8409 (m-80) REVERT: B 228 ASP cc_start: 0.8134 (m-30) cc_final: 0.7839 (m-30) outliers start: 12 outliers final: 10 residues processed: 103 average time/residue: 0.1770 time to fit residues: 24.7421 Evaluate side-chains 98 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 80 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 19 optimal weight: 0.0970 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.125677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108142 restraints weight = 10703.019| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.13 r_work: 0.3213 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6701 Z= 0.178 Angle : 0.481 13.724 9157 Z= 0.258 Chirality : 0.041 0.147 1094 Planarity : 0.003 0.049 1153 Dihedral : 3.992 25.077 964 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.10 % Allowed : 15.65 % Favored : 82.26 % 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: 1.26 (0.29), residues: 876 helix: 2.52 (0.26), residues: 391 sheet: -0.05 (0.37), residues: 186 loop : -0.86 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 PHE 0.012 0.001 PHE B 199 TYR 0.021 0.001 TYR A 318 ARG 0.002 0.000 ARG B 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3548.50 seconds wall clock time: 61 minutes 27.08 seconds (3687.08 seconds total)