Starting phenix.real_space_refine on Sun Oct 25 10:49:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p52_71298/10_2026/9p52_71298_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p52_71298/10_2026/9p52_71298.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/9p52_71298/10_2026/9p52_71298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p52_71298/10_2026/9p52_71298.map" model { file = "/net/cci-nas-00/data/ceres_data/9p52_71298/10_2026/9p52_71298_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p52_71298/10_2026/9p52_71298_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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: 5 Type Number sf(0) Gaussians S 47 5.16 5 C 5065 2.51 5 N 1357 2.21 5 O 1410 1.98 5 H 8187 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16066 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3735 Classifications: {'peptide': 238} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "C" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 519 Classifications: {'peptide': 32} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 31} Chain: "F" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 4069 Classifications: {'peptide': 251} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 240} Chain breaks: 1 Chain: "G" Number of atoms: 3983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 3983 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 12, 'TRANS': 240} Chain breaks: 1 Chain: "H" Number of atoms: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 3760 Classifications: {'peptide': 239} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 230} Time building chain proxies: 2.25, per 1000 atoms: 0.14 Number of scatterers: 16066 At special positions: 0 Unit cell: (72.6, 94.05, 111.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 O 1410 8.00 N 1357 7.00 C 5065 6.00 H 8187 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.44 Conformation dependent library (CDL) restraints added in 432.3 milliseconds 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1876 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 67.9% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 41 through 51 Processing helix chain 'B' and resid 71 through 79 Processing helix chain 'B' and resid 94 through 104 removed outlier: 4.485A pdb=" N VAL B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 125 removed outlier: 3.726A pdb=" N GLU B 123 " --> pdb=" O ASN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 154 Processing helix chain 'B' and resid 169 through 186 removed outlier: 4.158A pdb=" N ILE B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP B 175 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'C' and resid 2 through 28 Processing helix chain 'F' and resid 2 through 41 removed outlier: 4.375A pdb=" N GLY F 36 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA F 37 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 55 Processing helix chain 'F' and resid 55 through 82 removed outlier: 3.740A pdb=" N MET F 59 " --> pdb=" O GLY F 55 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) Proline residue: F 65 - end of helix Processing helix chain 'F' and resid 83 through 91 Processing helix chain 'F' and resid 94 through 119 removed outlier: 4.359A pdb=" N LEU F 98 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL F 112 " --> pdb=" O PHE F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 137 Processing helix chain 'F' and resid 250 through 256 Processing helix chain 'F' and resid 259 through 287 removed outlier: 4.081A pdb=" N VAL F 276 " --> pdb=" O LEU F 272 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE F 277 " --> pdb=" O VAL F 273 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL F 284 " --> pdb=" O ALA F 280 " (cutoff:3.500A) Proline residue: F 285 - end of helix Processing helix chain 'F' and resid 293 through 322 removed outlier: 4.224A pdb=" N LEU F 297 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Proline residue: F 301 - end of helix removed outlier: 3.538A pdb=" N SER F 315 " --> pdb=" O LEU F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 348 Processing helix chain 'F' and resid 350 through 355 Processing helix chain 'G' and resid 6 through 40 Processing helix chain 'G' and resid 48 through 86 Proline residue: G 61 - end of helix Proline residue: G 69 - end of helix Processing helix chain 'G' and resid 87 through 95 removed outlier: 3.758A pdb=" N VAL G 91 " --> pdb=" O SER G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 123 removed outlier: 3.636A pdb=" N THR G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) Proline residue: G 112 - end of helix Processing helix chain 'G' and resid 123 through 142 Processing helix chain 'G' and resid 250 through 265 Processing helix chain 'G' and resid 268 through 298 removed outlier: 3.885A pdb=" N LYS G 278 " --> pdb=" O ASN G 274 " (cutoff:3.500A) Proline residue: G 282 - end of helix removed outlier: 3.629A pdb=" N MET G 288 " --> pdb=" O SER G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 333 Proline residue: G 328 - end of helix removed outlier: 4.017A pdb=" N LEU G 331 " --> pdb=" O GLY G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 358 Proline residue: G 344 - end of helix Processing helix chain 'H' and resid 41 through 51 Processing helix chain 'H' and resid 71 through 79 Processing helix chain 'H' and resid 94 through 106 removed outlier: 3.848A pdb=" N VAL H 102 " --> pdb=" O ASN H 98 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG H 106 " --> pdb=" O VAL H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 125 removed outlier: 3.988A pdb=" N GLU H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASP H 116 " --> pdb=" O GLU H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 131 Processing helix chain 'H' and resid 145 through 154 removed outlier: 3.509A pdb=" N ALA H 154 " --> pdb=" O ARG H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 186 removed outlier: 4.212A pdb=" N ILE H 174 " --> pdb=" O PRO H 170 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP H 175 " --> pdb=" O ILE H 171 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG H 178 " --> pdb=" O ILE H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 204 removed outlier: 3.716A pdb=" N THR H 200 " --> pdb=" O ASN H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 226 removed outlier: 3.578A pdb=" N LEU H 225 " --> pdb=" O PRO H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 234 Processing sheet with id=AA1, first strand: chain 'B' and resid 16 through 27 removed outlier: 6.885A pdb=" N LYS B 11 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU B 20 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU B 9 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL B 22 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS B 7 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 24 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N THR B 5 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL B 26 " --> pdb=" O THR B 3 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR B 3 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU B 9 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B 57 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 83 removed outlier: 6.992A pdb=" N GLY B 81 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ASP B 162 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU B 83 " --> pdb=" O ASP B 162 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N LEU B 191 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE B 159 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR B 193 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU B 161 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 31 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N TYR B 208 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY B 33 " --> pdb=" O TYR B 208 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 19 through 27 removed outlier: 5.514A pdb=" N GLU H 20 " --> pdb=" O LYS H 11 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LYS H 11 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU H 24 " --> pdb=" O LYS H 7 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS H 7 " --> pdb=" O LEU H 24 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL H 26 " --> pdb=" O THR H 5 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N THR H 5 " --> pdb=" O VAL H 26 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 80 through 83 removed outlier: 3.604A pdb=" N ARG H 206 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE H 209 " --> pdb=" O ILE H 216 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1509 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: 2.82 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.01: 8183 1.01 - 1.21: 4 1.21 - 1.41: 3139 1.41 - 1.61: 4784 1.61 - 1.81: 90 Bond restraints: 16200 Sorted by residual: bond pdb=" NE2 GLN G 44 " pdb="HE22 GLN G 44 " ideal model delta sigma weight residual 0.860 0.804 0.056 2.00e-02 2.50e+03 7.93e+00 bond pdb=" NE2 GLN F 248 " pdb="HE22 GLN F 248 " ideal model delta sigma weight residual 0.860 0.806 0.054 2.00e-02 2.50e+03 7.37e+00 bond pdb=" NE2 GLN H 136 " pdb="HE22 GLN H 136 " ideal model delta sigma weight residual 0.860 0.809 0.051 2.00e-02 2.50e+03 6.63e+00 bond pdb=" N GLY G 5 " pdb=" CA GLY G 5 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.50e+00 bond pdb=" NE2 GLN B 136 " pdb="HE22 GLN B 136 " ideal model delta sigma weight residual 0.860 0.822 0.038 2.00e-02 2.50e+03 3.69e+00 ... (remaining 16195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.88: 29401 6.88 - 13.76: 7 13.76 - 20.64: 0 20.64 - 27.52: 2 27.52 - 34.40: 4 Bond angle restraints: 29414 Sorted by residual: angle pdb=" CD GLN B 136 " pdb=" NE2 GLN B 136 " pdb="HE22 GLN B 136 " ideal model delta sigma weight residual 120.00 154.40 -34.40 3.00e+00 1.11e-01 1.32e+02 angle pdb="HE21 GLN B 136 " pdb=" NE2 GLN B 136 " pdb="HE22 GLN B 136 " ideal model delta sigma weight residual 120.00 89.21 30.79 3.00e+00 1.11e-01 1.05e+02 angle pdb=" CD GLN H 136 " pdb=" NE2 GLN H 136 " pdb="HE22 GLN H 136 " ideal model delta sigma weight residual 120.00 147.86 -27.86 3.00e+00 1.11e-01 8.62e+01 angle pdb=" CD GLN B 136 " pdb=" NE2 GLN B 136 " pdb="HE21 GLN B 136 " ideal model delta sigma weight residual 120.00 92.19 27.81 3.00e+00 1.11e-01 8.59e+01 angle pdb="HE21 GLN H 136 " pdb=" NE2 GLN H 136 " pdb="HE22 GLN H 136 " ideal model delta sigma weight residual 120.00 94.26 25.74 3.00e+00 1.11e-01 7.36e+01 ... (remaining 29409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.13: 6657 18.13 - 36.26: 520 36.26 - 54.39: 186 54.39 - 72.53: 119 72.53 - 90.66: 12 Dihedral angle restraints: 7494 sinusoidal: 4179 harmonic: 3315 Sorted by residual: dihedral pdb=" CA LEU H 188 " pdb=" C LEU H 188 " pdb=" N GLY H 189 " pdb=" CA GLY H 189 " ideal model delta harmonic sigma weight residual 180.00 153.82 26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ILE H 192 " pdb=" C ILE H 192 " pdb=" N THR H 193 " pdb=" CA THR H 193 " ideal model delta harmonic sigma weight residual 180.00 154.00 26.00 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA GLY B 236 " pdb=" C GLY B 236 " pdb=" N GLU B 237 " pdb=" CA GLU B 237 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 7491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 864 0.037 - 0.075: 318 0.075 - 0.112: 83 0.112 - 0.150: 22 0.150 - 0.187: 2 Chirality restraints: 1289 Sorted by residual: chirality pdb=" CA ILE H 62 " pdb=" N ILE H 62 " pdb=" C ILE H 62 " pdb=" CB ILE H 62 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CA ILE B 62 " pdb=" N ILE B 62 " pdb=" C ILE B 62 " pdb=" CB ILE B 62 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA ILE H 192 " pdb=" N ILE H 192 " pdb=" C ILE H 192 " pdb=" CB ILE H 192 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 1286 not shown) Planarity restraints: 2336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN G 44 " -0.067 2.00e-02 2.50e+03 9.32e-02 1.30e+02 pdb=" CD GLN G 44 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN G 44 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN G 44 " 0.152 2.00e-02 2.50e+03 pdb="HE21 GLN G 44 " 0.024 2.00e-02 2.50e+03 pdb="HE22 GLN G 44 " -0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 248 " 0.068 2.00e-02 2.50e+03 9.16e-02 1.26e+02 pdb=" CD GLN F 248 " -0.048 2.00e-02 2.50e+03 pdb=" OE1 GLN F 248 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN F 248 " -0.147 2.00e-02 2.50e+03 pdb="HE21 GLN F 248 " -0.020 2.00e-02 2.50e+03 pdb="HE22 GLN F 248 " 0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN H 136 " 0.045 2.00e-02 2.50e+03 8.89e-02 1.19e+02 pdb=" CD GLN H 136 " 0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN H 136 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 GLN H 136 " -0.155 2.00e-02 2.50e+03 pdb="HE21 GLN H 136 " -0.039 2.00e-02 2.50e+03 pdb="HE22 GLN H 136 " 0.141 2.00e-02 2.50e+03 ... (remaining 2333 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 751 2.16 - 2.77: 32520 2.77 - 3.38: 48207 3.38 - 3.99: 59597 3.99 - 4.60: 93686 Nonbonded interactions: 234761 Sorted by model distance: nonbonded pdb="HD21 ASN H 8 " pdb=" OD1 ASP H 21 " model vdw 1.545 2.450 nonbonded pdb=" OD2 ASP B 194 " pdb=" HG1 THR B 200 " model vdw 1.553 2.450 nonbonded pdb=" HE ARG H 178 " pdb=" OE2 GLU H 181 " model vdw 1.562 2.450 nonbonded pdb=" HZ3 LYS B 11 " pdb=" OD1 ASP B 56 " model vdw 1.566 2.450 nonbonded pdb=" OE1 GLU H 115 " pdb=" H GLU H 115 " model vdw 1.581 2.450 ... (remaining 234756 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 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'H' and resid 2 through 239) } 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: 8.120 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: 0.030 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.240 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8013 Z= 0.223 Angle : 0.693 7.299 10851 Z= 0.382 Chirality : 0.042 0.187 1289 Planarity : 0.010 0.108 1367 Dihedral : 14.952 90.656 2969 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 15.06 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.24), residues: 999 helix: -0.80 (0.18), residues: 650 sheet: 0.30 (0.58), residues: 76 loop : -1.42 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.003 ARG F 269 TYR 0.015 0.003 TYR B 234 PHE 0.014 0.002 PHE G 348 TRP 0.012 0.003 TRP F 119 HIS 0.006 0.001 HIS G 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 ( 8013) covalent geometry : angle 0.69269 / 0.38 (10851) hydrogen bonds : bond 0.13099 / 8.93 ( 510) hydrogen bonds : angle 6.40230 / 4.49 ( 1509) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 58 GLU cc_start: 0.8306 (tp30) cc_final: 0.8023 (tp30) REVERT: F 82 GLU cc_start: 0.7716 (tp30) cc_final: 0.7282 (mt-10) REVERT: F 247 ASP cc_start: 0.8334 (m-30) cc_final: 0.7432 (p0) REVERT: F 260 ASP cc_start: 0.7713 (m-30) cc_final: 0.7369 (t70) REVERT: G 86 ARG cc_start: 0.7161 (mmt180) cc_final: 0.6950 (mtm180) REVERT: G 122 GLU cc_start: 0.7400 (tt0) cc_final: 0.7145 (tp30) REVERT: G 257 TYR cc_start: 0.7791 (t80) cc_final: 0.7243 (t80) REVERT: G 262 LYS cc_start: 0.8874 (pptt) cc_final: 0.8618 (ptmt) REVERT: H 52 ILE cc_start: 0.8930 (tt) cc_final: 0.8636 (pt) REVERT: H 100 MET cc_start: 0.7935 (tpp) cc_final: 0.7495 (tpt) REVERT: H 174 ILE cc_start: 0.9102 (tt) cc_final: 0.8875 (pt) REVERT: H 228 GLU cc_start: 0.8023 (pp20) cc_final: 0.7646 (pm20) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2496 time to fit residues: 48.5494 Evaluate side-chains 87 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 38, 61, 45] chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 248 GLN F 346 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 218 HIS H 229 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.091858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.074633 restraints weight = 51247.683| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.72 r_work: 0.3102 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8013 Z= 0.168 Angle : 0.654 6.841 10851 Z= 0.349 Chirality : 0.041 0.164 1289 Planarity : 0.005 0.043 1367 Dihedral : 5.325 29.077 1099 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.00 % Allowed : 16.00 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.25), residues: 999 helix: 0.12 (0.19), residues: 651 sheet: -0.12 (0.54), residues: 76 loop : -1.32 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 131 TYR 0.016 0.001 TYR G 260 PHE 0.011 0.001 PHE F 274 TRP 0.011 0.001 TRP G 354 HIS 0.007 0.001 HIS H 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 ( 8013) covalent geometry : angle 0.65438 / 0.35 (10851) hydrogen bonds : bond 0.05115 / 3.47 ( 510) hydrogen bonds : angle 5.24196 / 3.68 ( 1509) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 58 GLU cc_start: 0.8338 (tp30) cc_final: 0.8069 (tp30) REVERT: F 82 GLU cc_start: 0.7980 (tp30) cc_final: 0.7614 (mt-10) REVERT: F 247 ASP cc_start: 0.8532 (m-30) cc_final: 0.7613 (p0) REVERT: F 260 ASP cc_start: 0.7707 (m-30) cc_final: 0.7466 (t70) REVERT: G 107 MET cc_start: 0.8251 (mmp) cc_final: 0.7823 (mmp) REVERT: G 257 TYR cc_start: 0.7931 (t80) cc_final: 0.7327 (t80) REVERT: G 262 LYS cc_start: 0.8920 (pptt) cc_final: 0.8636 (ptmt) REVERT: H 52 ILE cc_start: 0.9013 (tt) cc_final: 0.8738 (pt) REVERT: H 100 MET cc_start: 0.8487 (tpp) cc_final: 0.8053 (tpt) REVERT: H 174 ILE cc_start: 0.9172 (tt) cc_final: 0.8951 (pt) REVERT: H 228 GLU cc_start: 0.8255 (pp20) cc_final: 0.7981 (pm20) outliers start: 17 outliers final: 8 residues processed: 104 average time/residue: 0.1847 time to fit residues: 26.6744 Evaluate side-chains 86 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 346 ASN Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain H residue 218 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: [93, 61, 67, 39, 84, 64, 63, 2, 49, 71, 37] chunk 93 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 346 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.089519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.072901 restraints weight = 52120.729| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.68 r_work: 0.3080 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8013 Z= 0.176 Angle : 0.619 6.374 10851 Z= 0.332 Chirality : 0.041 0.192 1289 Planarity : 0.005 0.045 1367 Dihedral : 4.992 23.724 1099 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.65 % Allowed : 16.24 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.25), residues: 999 helix: 0.42 (0.19), residues: 661 sheet: -0.34 (0.53), residues: 78 loop : -1.52 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 17 TYR 0.011 0.001 TYR G 135 PHE 0.022 0.001 PHE G 68 TRP 0.008 0.001 TRP G 354 HIS 0.015 0.001 HIS H 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 ( 8013) covalent geometry : angle 0.61864 / 0.33 (10851) hydrogen bonds : bond 0.04630 / 3.16 ( 510) hydrogen bonds : angle 4.92301 / 3.49 ( 1509) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 58 GLU cc_start: 0.8385 (tp30) cc_final: 0.8031 (tm-30) REVERT: F 82 GLU cc_start: 0.8029 (tp30) cc_final: 0.7713 (mt-10) REVERT: F 260 ASP cc_start: 0.7729 (m-30) cc_final: 0.7502 (t70) REVERT: G 107 MET cc_start: 0.8333 (mmp) cc_final: 0.7773 (mmp) REVERT: G 257 TYR cc_start: 0.8051 (t80) cc_final: 0.7463 (t80) REVERT: G 262 LYS cc_start: 0.8925 (pptt) cc_final: 0.8651 (ptmt) REVERT: H 100 MET cc_start: 0.8509 (tpp) cc_final: 0.8184 (tpt) REVERT: H 174 ILE cc_start: 0.9182 (tt) cc_final: 0.8958 (pt) REVERT: H 218 HIS cc_start: 0.8327 (p-80) cc_final: 0.7978 (p90) outliers start: 14 outliers final: 9 residues processed: 95 average time/residue: 0.1734 time to fit residues: 23.2267 Evaluate side-chains 84 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 342 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: [54, 45, 62, 21, 16, 3, 18, 44, 23, 60, 95] chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 16 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 ASN G 38 GLN ** H 229 HIS ** 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 = 0.3526 r_free = 0.3526 target = 0.090318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.072830 restraints weight = 51263.598| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.82 r_work: 0.3064 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8013 Z= 0.133 Angle : 0.579 6.117 10851 Z= 0.303 Chirality : 0.039 0.156 1289 Planarity : 0.004 0.039 1367 Dihedral : 4.634 22.932 1099 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.00 % Allowed : 16.12 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.25), residues: 999 helix: 0.64 (0.19), residues: 666 sheet: -0.58 (0.52), residues: 78 loop : -1.48 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 17 TYR 0.012 0.001 TYR G 260 PHE 0.010 0.001 PHE F 274 TRP 0.007 0.001 TRP F 119 HIS 0.006 0.001 HIS H 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 8013) covalent geometry : angle 0.57864 / 0.30 (10851) hydrogen bonds : bond 0.04150 / 2.81 ( 510) hydrogen bonds : angle 4.71248 / 3.32 ( 1509) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 58 GLU cc_start: 0.8388 (tp30) cc_final: 0.8042 (tm-30) REVERT: F 282 MET cc_start: 0.8993 (ttm) cc_final: 0.8700 (ttp) REVERT: G 107 MET cc_start: 0.8356 (mmp) cc_final: 0.7743 (mmp) REVERT: G 262 LYS cc_start: 0.8913 (pptt) cc_final: 0.8657 (ptmt) REVERT: H 100 MET cc_start: 0.8516 (tpp) cc_final: 0.8201 (tpt) REVERT: H 174 ILE cc_start: 0.9180 (tt) cc_final: 0.8955 (pt) REVERT: H 218 HIS cc_start: 0.8278 (p-80) cc_final: 0.8061 (p-80) outliers start: 17 outliers final: 13 residues processed: 90 average time/residue: 0.1801 time to fit residues: 22.5377 Evaluate side-chains 86 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 346 ASN Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 355 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: [0, 88, 30, 93, 73, 96, 50, 48, 90, 24, 45] chunk 0 optimal weight: 1.9990 chunk 88 optimal weight: 0.0570 chunk 30 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 73 optimal weight: 0.0670 chunk 96 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 ASN ** H 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.089205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.072736 restraints weight = 51563.806| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.62 r_work: 0.3073 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8013 Z= 0.139 Angle : 0.559 6.040 10851 Z= 0.295 Chirality : 0.039 0.154 1289 Planarity : 0.004 0.040 1367 Dihedral : 4.512 22.156 1099 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.00 % Allowed : 16.59 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.26), residues: 999 helix: 0.87 (0.20), residues: 660 sheet: -0.66 (0.51), residues: 78 loop : -1.28 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 75 TYR 0.010 0.001 TYR G 260 PHE 0.010 0.001 PHE F 274 TRP 0.007 0.001 TRP F 330 HIS 0.005 0.001 HIS H 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 8013) covalent geometry : angle 0.55860 / 0.29 (10851) hydrogen bonds : bond 0.04036 / 2.74 ( 510) hydrogen bonds : angle 4.61495 / 3.26 ( 1509) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 58 GLU cc_start: 0.8408 (tp30) cc_final: 0.8059 (tm-30) REVERT: F 95 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8281 (mppt) REVERT: F 260 ASP cc_start: 0.7648 (m-30) cc_final: 0.7393 (t70) REVERT: F 282 MET cc_start: 0.9081 (ttm) cc_final: 0.8833 (ttp) REVERT: G 107 MET cc_start: 0.8317 (mmp) cc_final: 0.7672 (mmp) REVERT: G 257 TYR cc_start: 0.8333 (t80) cc_final: 0.7679 (t80) REVERT: G 262 LYS cc_start: 0.8938 (pptt) cc_final: 0.8686 (ptmt) REVERT: H 100 MET cc_start: 0.8436 (tpp) cc_final: 0.8120 (tpt) REVERT: H 174 ILE cc_start: 0.9182 (tt) cc_final: 0.8933 (pt) REVERT: H 218 HIS cc_start: 0.8326 (p-80) cc_final: 0.8076 (p-80) outliers start: 17 outliers final: 12 residues processed: 90 average time/residue: 0.1886 time to fit residues: 23.6558 Evaluate side-chains 84 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 342 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: [60, 53, 46, 22, 25, 50, 87, 64, 24, 92, 90] chunk 60 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.0870 chunk 87 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 267 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.089234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.072465 restraints weight = 51582.874| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.69 r_work: 0.3070 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8013 Z= 0.134 Angle : 0.555 5.968 10851 Z= 0.292 Chirality : 0.038 0.156 1289 Planarity : 0.004 0.043 1367 Dihedral : 4.397 19.209 1099 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.88 % Allowed : 16.94 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.26), residues: 999 helix: 0.97 (0.20), residues: 660 sheet: -0.68 (0.51), residues: 78 loop : -1.26 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 16 TYR 0.009 0.001 TYR G 260 PHE 0.010 0.001 PHE F 274 TRP 0.006 0.001 TRP F 330 HIS 0.005 0.001 HIS H 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 8013) covalent geometry : angle 0.55507 / 0.29 (10851) hydrogen bonds : bond 0.03949 / 2.69 ( 510) hydrogen bonds : angle 4.53956 / 3.21 ( 1509) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 48 MET cc_start: 0.8268 (mmm) cc_final: 0.8058 (mtt) REVERT: F 58 GLU cc_start: 0.8414 (tp30) cc_final: 0.8110 (tm-30) REVERT: F 95 LYS cc_start: 0.8830 (mmmt) cc_final: 0.8321 (mppt) REVERT: F 282 MET cc_start: 0.9087 (ttm) cc_final: 0.8871 (ttp) REVERT: G 107 MET cc_start: 0.8347 (mmp) cc_final: 0.7704 (mmp) REVERT: G 257 TYR cc_start: 0.8369 (t80) cc_final: 0.7837 (t80) REVERT: G 262 LYS cc_start: 0.8956 (pptt) cc_final: 0.8712 (ptmt) REVERT: H 100 MET cc_start: 0.8453 (tpp) cc_final: 0.8150 (tpt) REVERT: H 174 ILE cc_start: 0.9193 (tt) cc_final: 0.8938 (pt) REVERT: H 218 HIS cc_start: 0.8310 (p-80) cc_final: 0.8067 (p-80) outliers start: 16 outliers final: 13 residues processed: 88 average time/residue: 0.1720 time to fit residues: 21.6139 Evaluate side-chains 83 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 355 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: [25, 45, 32, 2, 70, 87, 7, 9, 53, 18, 52] chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 70 optimal weight: 0.1980 chunk 87 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 52 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.088594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.071908 restraints weight = 51480.915| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.63 r_work: 0.3054 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8013 Z= 0.149 Angle : 0.556 5.954 10851 Z= 0.294 Chirality : 0.039 0.151 1289 Planarity : 0.004 0.041 1367 Dihedral : 4.365 19.237 1099 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.76 % Allowed : 16.82 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.26), residues: 999 helix: 0.97 (0.20), residues: 667 sheet: -0.71 (0.52), residues: 78 loop : -1.29 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 17 TYR 0.010 0.001 TYR H 13 PHE 0.011 0.001 PHE F 274 TRP 0.007 0.001 TRP F 330 HIS 0.005 0.001 HIS H 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 8013) covalent geometry : angle 0.55583 / 0.29 (10851) hydrogen bonds : bond 0.03920 / 2.67 ( 510) hydrogen bonds : angle 4.48955 / 3.16 ( 1509) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 58 GLU cc_start: 0.8405 (tp30) cc_final: 0.8103 (tm-30) REVERT: F 95 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8323 (mppt) REVERT: F 260 ASP cc_start: 0.7658 (m-30) cc_final: 0.7417 (t70) REVERT: G 107 MET cc_start: 0.8346 (mmp) cc_final: 0.7791 (mmp) REVERT: G 257 TYR cc_start: 0.8375 (t80) cc_final: 0.7870 (t80) REVERT: G 262 LYS cc_start: 0.8962 (pptt) cc_final: 0.8738 (ptmt) REVERT: H 100 MET cc_start: 0.8423 (tpp) cc_final: 0.8125 (tpt) REVERT: H 174 ILE cc_start: 0.9196 (tt) cc_final: 0.8938 (pt) REVERT: H 218 HIS cc_start: 0.8310 (p-80) cc_final: 0.8074 (p-80) outliers start: 15 outliers final: 13 residues processed: 86 average time/residue: 0.1687 time to fit residues: 20.7112 Evaluate side-chains 83 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 355 LEU Chi-restraints excluded: chain H residue 146 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: [80, 37, 52, 39, 65, 73, 44, 2, 50, 34, 22] chunk 80 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 39 optimal weight: 0.0670 chunk 65 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.088807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.071923 restraints weight = 52019.098| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.69 r_work: 0.3052 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8013 Z= 0.131 Angle : 0.550 5.904 10851 Z= 0.289 Chirality : 0.038 0.155 1289 Planarity : 0.004 0.041 1367 Dihedral : 4.318 20.166 1099 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.53 % Allowed : 17.29 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.26), residues: 999 helix: 1.08 (0.20), residues: 660 sheet: -0.72 (0.53), residues: 78 loop : -1.30 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 17 TYR 0.009 0.001 TYR B 82 PHE 0.010 0.001 PHE F 274 TRP 0.007 0.001 TRP F 330 HIS 0.005 0.001 HIS H 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8013) covalent geometry : angle 0.54964 / 0.29 (10851) hydrogen bonds : bond 0.03863 / 2.63 ( 510) hydrogen bonds : angle 4.44661 / 3.13 ( 1509) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 95 LYS cc_start: 0.8838 (mmmt) cc_final: 0.8385 (mppt) REVERT: F 260 ASP cc_start: 0.7626 (m-30) cc_final: 0.7393 (t70) REVERT: G 107 MET cc_start: 0.8379 (mmp) cc_final: 0.7748 (mmp) REVERT: G 257 TYR cc_start: 0.8414 (t80) cc_final: 0.7833 (t80) REVERT: G 262 LYS cc_start: 0.8950 (pptt) cc_final: 0.8715 (ptmt) REVERT: H 100 MET cc_start: 0.8450 (tpp) cc_final: 0.8109 (tpt) REVERT: H 174 ILE cc_start: 0.9200 (tt) cc_final: 0.8946 (pt) REVERT: H 218 HIS cc_start: 0.8304 (p-80) cc_final: 0.8083 (p-80) outliers start: 13 outliers final: 13 residues processed: 84 average time/residue: 0.1670 time to fit residues: 20.1932 Evaluate side-chains 84 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 355 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: [27, 80, 67, 56, 12, 77, 36, 21, 73, 51, 8] chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.087874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.071017 restraints weight = 51879.952| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.67 r_work: 0.3035 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8013 Z= 0.158 Angle : 0.558 5.952 10851 Z= 0.296 Chirality : 0.040 0.269 1289 Planarity : 0.004 0.041 1367 Dihedral : 4.347 20.699 1099 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.76 % Allowed : 16.82 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.26), residues: 999 helix: 1.02 (0.20), residues: 668 sheet: -0.76 (0.53), residues: 78 loop : -1.32 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 17 TYR 0.012 0.001 TYR H 13 PHE 0.012 0.001 PHE F 274 TRP 0.007 0.001 TRP F 330 HIS 0.006 0.001 HIS H 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 8013) covalent geometry : angle 0.55800 / 0.30 (10851) hydrogen bonds : bond 0.03895 / 2.66 ( 510) hydrogen bonds : angle 4.46360 / 3.14 ( 1509) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 95 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8445 (mppt) REVERT: F 260 ASP cc_start: 0.7674 (m-30) cc_final: 0.7472 (t70) REVERT: G 107 MET cc_start: 0.8407 (mmp) cc_final: 0.7877 (mmp) REVERT: G 257 TYR cc_start: 0.8431 (t80) cc_final: 0.7916 (t80) REVERT: G 262 LYS cc_start: 0.8970 (pptt) cc_final: 0.8738 (ptmt) REVERT: H 100 MET cc_start: 0.8472 (tpp) cc_final: 0.8182 (tpt) REVERT: H 174 ILE cc_start: 0.9217 (tt) cc_final: 0.8964 (pt) REVERT: H 218 HIS cc_start: 0.8335 (p-80) cc_final: 0.8113 (p-80) outliers start: 15 outliers final: 15 residues processed: 83 average time/residue: 0.1766 time to fit residues: 21.0526 Evaluate side-chains 85 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 118 MET Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 355 LEU Chi-restraints excluded: chain H residue 146 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: [84, 55, 66, 78, 44, 54, 76, 67, 45, 77, 88] chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 78 optimal weight: 0.0060 chunk 44 optimal weight: 0.0980 chunk 54 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.088610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.071979 restraints weight = 51737.800| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.65 r_work: 0.3054 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8013 Z= 0.124 Angle : 0.542 5.905 10851 Z= 0.285 Chirality : 0.038 0.161 1289 Planarity : 0.004 0.043 1367 Dihedral : 4.262 20.691 1099 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.53 % Allowed : 17.29 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.26), residues: 999 helix: 1.16 (0.20), residues: 661 sheet: -0.74 (0.55), residues: 78 loop : -1.30 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 17 TYR 0.010 0.001 TYR B 82 PHE 0.009 0.001 PHE F 274 TRP 0.007 0.001 TRP F 330 HIS 0.005 0.001 HIS H 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 8013) covalent geometry : angle 0.54184 / 0.28 (10851) hydrogen bonds : bond 0.03755 / 2.56 ( 510) hydrogen bonds : angle 4.41087 / 3.10 ( 1509) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 95 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8435 (mppt) REVERT: G 107 MET cc_start: 0.8405 (mmp) cc_final: 0.7800 (mmp) REVERT: G 257 TYR cc_start: 0.8441 (t80) cc_final: 0.7905 (t80) REVERT: G 262 LYS cc_start: 0.8974 (pptt) cc_final: 0.8746 (ptmt) REVERT: H 100 MET cc_start: 0.8439 (tpp) cc_final: 0.8119 (tpt) REVERT: H 174 ILE cc_start: 0.9207 (tt) cc_final: 0.8953 (pt) REVERT: H 218 HIS cc_start: 0.8338 (p-80) cc_final: 0.8123 (p-80) outliers start: 13 outliers final: 13 residues processed: 83 average time/residue: 0.1675 time to fit residues: 19.9276 Evaluate side-chains 83 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 355 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: [35, 40, 44, 75, 41, 63, 67, 3, 53, 4, 73] chunk 35 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 3 optimal weight: 0.0570 chunk 53 optimal weight: 0.3980 chunk 4 optimal weight: 0.1980 chunk 73 optimal weight: 0.0170 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.089454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.072868 restraints weight = 51273.449| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.64 r_work: 0.3072 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8013 Z= 0.110 Angle : 0.526 5.868 10851 Z= 0.275 Chirality : 0.038 0.163 1289 Planarity : 0.004 0.045 1367 Dihedral : 4.159 20.493 1099 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.65 % Allowed : 17.29 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.26), residues: 999 helix: 1.27 (0.20), residues: 661 sheet: -0.68 (0.55), residues: 78 loop : -1.26 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 17 TYR 0.014 0.001 TYR H 13 PHE 0.007 0.001 PHE F 69 TRP 0.006 0.001 TRP F 330 HIS 0.005 0.001 HIS H 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 8013) covalent geometry : angle 0.52585 / 0.27 (10851) hydrogen bonds : bond 0.03631 / 2.47 ( 510) hydrogen bonds : angle 4.32570 / 3.04 ( 1509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3234.61 seconds wall clock time: 55 minutes 36.55 seconds (3336.55 seconds total)