Starting phenix.real_space_refine on Tue Aug 4 19:15:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gmu_34154/08_2026/8gmu_34154.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gmu_34154/08_2026/8gmu_34154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8gmu_34154/08_2026/8gmu_34154.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gmu_34154/08_2026/8gmu_34154.cif" model { file = "/net/cci-nas-00/data/ceres_data/8gmu_34154/08_2026/8gmu_34154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gmu_34154/08_2026/8gmu_34154.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gmu_34154/08_2026/8gmu_34154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gmu_34154/08_2026/8gmu_34154.map" } resolution = 2.78 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= 0.009 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 2 5.21 5 S 33 5.16 5 C 3880 2.51 5 N 1055 2.21 5 O 1232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6214 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1014 Classifications: {'peptide': 131} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 118} Chain: "F" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2508 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "G" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2508 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.50, per 1000 atoms: 0.24 Number of scatterers: 6214 At special positions: 0 Unit cell: (99.96, 86.87, 104.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 12 15.00 Mg 2 11.99 O 1232 8.00 N 1055 7.00 C 3880 6.00 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: 0.33 Conformation dependent library (CDL) restraints added in 273.8 milliseconds 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1438 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 40.9% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'F' and resid 2 through 22 Processing helix chain 'F' and resid 30 through 36 removed outlier: 5.740A pdb=" N ARG F 33 " --> pdb=" O GLY F 30 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N SER F 34 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET F 35 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 51 Processing helix chain 'F' and resid 71 through 86 removed outlier: 3.583A pdb=" N GLU F 86 " --> pdb=" O ALA F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 108 Processing helix chain 'F' and resid 110 through 114 Processing helix chain 'F' and resid 121 through 136 removed outlier: 3.523A pdb=" N GLY F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 149 Processing helix chain 'F' and resid 151 through 157 Processing helix chain 'F' and resid 165 through 186 removed outlier: 4.691A pdb=" N GLY F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN F 181 " --> pdb=" O LYS F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 219 removed outlier: 3.534A pdb=" N PHE F 217 " --> pdb=" O ASN F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 281 Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 312 through 328 Processing helix chain 'G' and resid 2 through 22 Processing helix chain 'G' and resid 28 through 36 removed outlier: 3.599A pdb=" N ASP G 32 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ARG G 33 " --> pdb=" O GLY G 30 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N SER G 34 " --> pdb=" O GLU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 51 Processing helix chain 'G' and resid 71 through 86 removed outlier: 3.508A pdb=" N GLU G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 107 Processing helix chain 'G' and resid 121 through 136 removed outlier: 3.651A pdb=" N GLY G 136 " --> pdb=" O LEU G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 149 Processing helix chain 'G' and resid 151 through 157 Processing helix chain 'G' and resid 165 through 186 removed outlier: 4.878A pdb=" N GLY G 180 " --> pdb=" O ARG G 176 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN G 181 " --> pdb=" O LYS G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 219 Processing helix chain 'G' and resid 269 through 281 Processing helix chain 'G' and resid 301 through 312 Processing helix chain 'G' and resid 312 through 328 removed outlier: 3.602A pdb=" N LEU G 328 " --> pdb=" O ARG G 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 116 removed outlier: 7.419A pdb=" N PHE A 179 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LYS A 224 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE A 181 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL A 225 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASP A 169 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A 227 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N TRP A 142 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N GLU A 144 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N PHE A 106 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N GLU A 146 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N HIS A 108 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 122 Processing sheet with id=AA4, first strand: chain 'F' and resid 27 through 28 removed outlier: 6.539A pdb=" N ILE G 141 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE G 192 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL G 143 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL G 62 " --> pdb=" O PHE G 191 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASN G 193 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE G 64 " --> pdb=" O ASN G 193 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE G 61 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N LEU G 223 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU G 63 " --> pdb=" O LEU G 223 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE G 225 " --> pdb=" O GLU G 63 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR G 65 " --> pdb=" O ILE G 225 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG G 227 " --> pdb=" O TYR G 65 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG G 222 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLU G 241 " --> pdb=" O ILE G 228 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ALA G 230 " --> pdb=" O GLY G 239 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLY G 239 " --> pdb=" O ALA G 230 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS G 232 " --> pdb=" O VAL G 237 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL G 237 " --> pdb=" O LYS G 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AA6, first strand: chain 'F' and resid 115 through 117 removed outlier: 6.379A pdb=" N VAL F 62 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ASN F 193 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE F 64 " --> pdb=" O ASN F 193 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE F 61 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU F 223 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU F 63 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE F 225 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR F 65 " --> pdb=" O ILE F 225 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ARG F 227 " --> pdb=" O TYR F 65 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG F 222 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLU F 241 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ALA F 230 " --> pdb=" O GLY F 239 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY F 239 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS F 232 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL F 237 " --> pdb=" O LYS F 232 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 195 through 197 Processing sheet with id=AA8, first strand: chain 'F' and resid 284 through 287 removed outlier: 6.118A pdb=" N TYR F 293 " --> pdb=" O LYS F 297 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS F 297 " --> pdb=" O TYR F 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 39 through 40 Processing sheet with id=AB1, first strand: chain 'G' and resid 195 through 197 Processing sheet with id=AB2, first strand: chain 'G' and resid 285 through 287 removed outlier: 6.971A pdb=" N TYR G 291 " --> pdb=" O ILE G 298 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.64 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 2062 1.36 - 1.51: 1584 1.51 - 1.65: 2614 1.65 - 1.80: 30 1.80 - 1.95: 25 Bond restraints: 6315 Sorted by residual: bond pdb=" C3' DT S 9 " pdb=" C2' DT S 9 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.53e+00 bond pdb=" C3' DT S 8 " pdb=" O3' DT S 8 " ideal model delta sigma weight residual 1.435 1.406 0.029 1.30e-02 5.92e+03 4.89e+00 bond pdb=" C3' DT S 8 " pdb=" C2' DT S 8 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 4.80e+00 bond pdb=" C2' DT S 12 " pdb=" C1' DT S 12 " ideal model delta sigma weight residual 1.518 1.539 -0.021 1.00e-02 1.00e+04 4.26e+00 bond pdb=" C3' DT S 11 " pdb=" C2' DT S 11 " ideal model delta sigma weight residual 1.516 1.533 -0.017 8.00e-03 1.56e+04 4.26e+00 ... (remaining 6310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 8298 1.45 - 2.89: 220 2.89 - 4.34: 26 4.34 - 5.79: 6 5.79 - 7.23: 1 Bond angle restraints: 8551 Sorted by residual: angle pdb=" N3 DT S 8 " pdb=" C4 DT S 8 " pdb=" O4 DT S 8 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT S 11 " pdb=" C4 DT S 11 " pdb=" O4 DT S 11 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT S 7 " pdb=" C4 DT S 7 " pdb=" O4 DT S 7 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 angle pdb=" N3 DT S 9 " pdb=" C4 DT S 9 " pdb=" O4 DT S 9 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 angle pdb=" O4' DT S 12 " pdb=" C4' DT S 12 " pdb=" C3' DT S 12 " ideal model delta sigma weight residual 106.00 103.60 2.40 6.00e-01 2.78e+00 1.60e+01 ... (remaining 8546 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.21: 3607 34.21 - 68.43: 193 68.43 - 102.64: 13 102.64 - 136.85: 0 136.85 - 171.07: 2 Dihedral angle restraints: 3815 sinusoidal: 1566 harmonic: 2249 Sorted by residual: dihedral pdb=" O1A AGS G 402 " pdb=" O3A AGS G 402 " pdb=" PA AGS G 402 " pdb=" PB AGS G 402 " ideal model delta sinusoidal sigma weight residual -67.73 103.34 -171.07 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O1A AGS F 402 " pdb=" O3A AGS F 402 " pdb=" PA AGS F 402 " pdb=" PB AGS F 402 " ideal model delta sinusoidal sigma weight residual -67.73 80.51 -148.24 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" CA VAL A 145 " pdb=" C VAL A 145 " pdb=" N GLU A 146 " pdb=" CA GLU A 146 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 3812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 714 0.040 - 0.081: 171 0.081 - 0.121: 77 0.121 - 0.161: 8 0.161 - 0.202: 1 Chirality restraints: 971 Sorted by residual: chirality pdb=" CB THR G 208 " pdb=" CA THR G 208 " pdb=" OG1 THR G 208 " pdb=" CG2 THR G 208 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C3' DT S 8 " pdb=" C4' DT S 8 " pdb=" O3' DT S 8 " pdb=" C2' DT S 8 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CG LEU F 309 " pdb=" CB LEU F 309 " pdb=" CD1 LEU F 309 " pdb=" CD2 LEU F 309 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.32e-01 ... (remaining 968 not shown) Planarity restraints: 1083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 207 " 0.041 5.00e-02 4.00e+02 6.34e-02 6.42e+00 pdb=" N PRO A 208 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 195 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C ILE A 195 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE A 195 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG A 196 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY F 66 " -0.017 5.00e-02 4.00e+02 2.50e-02 1.00e+00 pdb=" N PRO F 67 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO F 67 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO F 67 " -0.014 5.00e-02 4.00e+02 ... (remaining 1080 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 39 2.53 - 3.12: 4410 3.12 - 3.72: 9774 3.72 - 4.31: 14137 4.31 - 4.90: 23511 Nonbonded interactions: 51871 Sorted by model distance: nonbonded pdb="MG MG G 401 " pdb=" O2G AGS G 402 " model vdw 1.941 2.170 nonbonded pdb=" OG1 THR G 73 " pdb="MG MG G 401 " model vdw 1.954 2.170 nonbonded pdb="MG MG F 401 " pdb=" O2G AGS F 402 " model vdw 1.957 2.170 nonbonded pdb="MG MG G 401 " pdb=" O1B AGS G 402 " model vdw 1.969 2.170 nonbonded pdb=" OG1 THR F 73 " pdb="MG MG F 401 " model vdw 1.970 2.170 ... (remaining 51866 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 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.920 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 0.039 6315 Z= 0.179 Angle : 0.559 7.234 8551 Z= 0.357 Chirality : 0.043 0.202 971 Planarity : 0.004 0.063 1083 Dihedral : 19.275 171.067 2377 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.25 % Allowed : 1.77 % Favored : 97.98 % Rotamer: Outliers : 1.73 % Allowed : 23.58 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.01 (0.29), residues: 791 helix: 1.71 (0.29), residues: 292 sheet: 1.71 (0.43), residues: 132 loop : -0.59 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 85 TYR 0.005 0.001 TYR F 271 PHE 0.008 0.001 PHE A 114 TRP 0.017 0.002 TRP F 308 HIS 0.003 0.001 HIS F 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.18 ( 6315) covalent geometry : angle 0.55926 / 0.36 ( 8551) hydrogen bonds : bond 0.15847 / 10.23 ( 308) hydrogen bonds : angle 5.85839 / 4.03 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.130 Fit side-chains REVERT: A 113 MET cc_start: 0.6090 (ttp) cc_final: 0.5857 (ttt) REVERT: F 184 GLN cc_start: 0.7516 (tm-30) cc_final: 0.7303 (tm-30) outliers start: 11 outliers final: 8 residues processed: 95 average time/residue: 0.5118 time to fit residues: 50.5965 Evaluate side-chains 92 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 196 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain G residue 195 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.0370 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.0870 chunk 74 optimal weight: 9.9990 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN G 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.163374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.124461 restraints weight = 6370.214| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.68 r_work: 0.2979 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6315 Z= 0.101 Angle : 0.481 5.385 8551 Z= 0.266 Chirality : 0.042 0.148 971 Planarity : 0.004 0.050 1083 Dihedral : 13.101 163.989 932 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.52 % Favored : 98.36 % Rotamer: Outliers : 2.83 % Allowed : 22.01 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.32 (0.30), residues: 791 helix: 2.11 (0.30), residues: 292 sheet: 1.27 (0.42), residues: 145 loop : -0.33 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 196 TYR 0.006 0.001 TYR F 65 PHE 0.008 0.001 PHE G 260 TRP 0.012 0.001 TRP F 308 HIS 0.002 0.001 HIS F 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 6315) covalent geometry : angle 0.48090 / 0.27 ( 8551) hydrogen bonds : bond 0.03447 / 2.28 ( 308) hydrogen bonds : angle 4.43369 / 3.06 ( 846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.136 Fit side-chains REVERT: A 101 TYR cc_start: 0.7166 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: A 113 MET cc_start: 0.6295 (ttp) cc_final: 0.6019 (ttt) REVERT: A 114 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.5640 (t80) REVERT: F 184 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7490 (tm-30) REVERT: F 197 MET cc_start: 0.8233 (tmt) cc_final: 0.7919 (ppp) REVERT: F 271 TYR cc_start: 0.8003 (m-10) cc_final: 0.7609 (m-80) REVERT: G 256 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7846 (mtmt) outliers start: 18 outliers final: 6 residues processed: 98 average time/residue: 0.5159 time to fit residues: 52.6999 Evaluate side-chains 90 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 256 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 12 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 37 optimal weight: 10.0000 chunk 13 optimal weight: 0.0270 chunk 57 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN G 118 GLN G 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.162664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.121292 restraints weight = 6359.022| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.00 r_work: 0.2999 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6315 Z= 0.110 Angle : 0.466 5.235 8551 Z= 0.254 Chirality : 0.042 0.139 971 Planarity : 0.003 0.043 1083 Dihedral : 12.871 165.984 921 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.26 % Favored : 98.61 % Rotamer: Outliers : 2.36 % Allowed : 23.11 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.38 (0.30), residues: 791 helix: 2.24 (0.30), residues: 292 sheet: 1.22 (0.42), residues: 147 loop : -0.35 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 183 TYR 0.006 0.001 TYR F 103 PHE 0.008 0.001 PHE G 203 TRP 0.008 0.001 TRP F 308 HIS 0.002 0.001 HIS F 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 6315) covalent geometry : angle 0.46610 / 0.25 ( 8551) hydrogen bonds : bond 0.03277 / 2.15 ( 308) hydrogen bonds : angle 4.18615 / 2.90 ( 846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.141 Fit side-chains REVERT: A 101 TYR cc_start: 0.7306 (OUTLIER) cc_final: 0.6710 (m-80) REVERT: A 102 GLU cc_start: 0.7686 (pt0) cc_final: 0.7334 (pt0) REVERT: A 113 MET cc_start: 0.6163 (ttp) cc_final: 0.5922 (ttt) REVERT: A 149 SER cc_start: 0.7907 (p) cc_final: 0.7679 (t) REVERT: A 193 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8313 (tmmm) REVERT: F 184 GLN cc_start: 0.7654 (tm-30) cc_final: 0.7415 (tm-30) REVERT: F 271 TYR cc_start: 0.7969 (m-10) cc_final: 0.7534 (m-80) outliers start: 15 outliers final: 8 residues processed: 91 average time/residue: 0.4744 time to fit residues: 45.2034 Evaluate side-chains 89 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.0570 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 213 ASN G 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.160073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.118947 restraints weight = 6373.334| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.37 r_work: 0.3062 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6315 Z= 0.159 Angle : 0.515 5.355 8551 Z= 0.276 Chirality : 0.044 0.173 971 Planarity : 0.004 0.041 1083 Dihedral : 13.133 171.302 921 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.52 % Favored : 98.36 % Rotamer: Outliers : 3.30 % Allowed : 22.64 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.18 (0.30), residues: 791 helix: 2.02 (0.29), residues: 292 sheet: 0.86 (0.41), residues: 155 loop : -0.29 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 226 TYR 0.006 0.001 TYR F 103 PHE 0.012 0.001 PHE G 203 TRP 0.007 0.001 TRP F 308 HIS 0.002 0.001 HIS F 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 6315) covalent geometry : angle 0.51485 / 0.28 ( 8551) hydrogen bonds : bond 0.03507 / 2.31 ( 308) hydrogen bonds : angle 4.15343 / 2.87 ( 846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.177 Fit side-chains REVERT: A 101 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.6882 (m-80) REVERT: A 113 MET cc_start: 0.6264 (ttp) cc_final: 0.5994 (ttt) REVERT: A 131 SER cc_start: 0.7926 (OUTLIER) cc_final: 0.7453 (m) REVERT: A 134 LYS cc_start: 0.7852 (tptm) cc_final: 0.7620 (tptt) REVERT: A 149 SER cc_start: 0.8105 (p) cc_final: 0.7881 (t) REVERT: A 193 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8421 (tmmm) REVERT: A 212 MET cc_start: 0.7694 (mtm) cc_final: 0.7210 (mmm) REVERT: A 217 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.6836 (mp0) REVERT: F 27 MET cc_start: 0.7903 (ptm) cc_final: 0.7695 (ptm) REVERT: F 184 GLN cc_start: 0.7680 (tm-30) cc_final: 0.7404 (tm-30) REVERT: F 271 TYR cc_start: 0.7925 (m-10) cc_final: 0.7576 (m-80) outliers start: 21 outliers final: 9 residues processed: 94 average time/residue: 0.4707 time to fit residues: 46.3279 Evaluate side-chains 95 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 172 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 GLN F 213 ASN G 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.159002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.112872 restraints weight = 6485.412| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.36 r_work: 0.3035 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6315 Z= 0.178 Angle : 0.536 6.009 8551 Z= 0.285 Chirality : 0.045 0.198 971 Planarity : 0.004 0.040 1083 Dihedral : 13.407 173.644 921 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.77 % Favored : 98.10 % Rotamer: Outliers : 3.46 % Allowed : 23.11 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.06 (0.30), residues: 791 helix: 2.03 (0.30), residues: 280 sheet: 0.72 (0.41), residues: 155 loop : -0.35 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 226 TYR 0.007 0.001 TYR F 103 PHE 0.012 0.002 PHE G 203 TRP 0.009 0.001 TRP A 129 HIS 0.002 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 6315) covalent geometry : angle 0.53600 / 0.28 ( 8551) hydrogen bonds : bond 0.03598 / 2.37 ( 308) hydrogen bonds : angle 4.16621 / 2.89 ( 846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.215 Fit side-chains REVERT: A 101 TYR cc_start: 0.7515 (OUTLIER) cc_final: 0.6868 (m-80) REVERT: A 103 TYR cc_start: 0.8508 (m-80) cc_final: 0.8280 (m-80) REVERT: A 113 MET cc_start: 0.6339 (ttp) cc_final: 0.6074 (ttt) REVERT: A 131 SER cc_start: 0.7881 (OUTLIER) cc_final: 0.7447 (m) REVERT: A 134 LYS cc_start: 0.7739 (tptm) cc_final: 0.7395 (tptt) REVERT: A 146 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6834 (mt-10) REVERT: A 212 MET cc_start: 0.7844 (mtm) cc_final: 0.7266 (mmm) REVERT: A 217 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7868 (mt-10) REVERT: F 27 MET cc_start: 0.7921 (ptm) cc_final: 0.7676 (ptm) REVERT: F 111 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7735 (pt) REVERT: F 184 GLN cc_start: 0.7685 (tm-30) cc_final: 0.7360 (tm-30) REVERT: F 271 TYR cc_start: 0.7852 (m-10) cc_final: 0.7516 (m-80) outliers start: 22 outliers final: 7 residues processed: 97 average time/residue: 0.5005 time to fit residues: 50.7633 Evaluate side-chains 94 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 172 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 54 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 GLN F 213 ASN G 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.159251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.113156 restraints weight = 6347.325| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.38 r_work: 0.3027 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6315 Z= 0.164 Angle : 0.523 7.422 8551 Z= 0.279 Chirality : 0.044 0.203 971 Planarity : 0.004 0.039 1083 Dihedral : 13.558 174.238 921 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.52 % Favored : 98.36 % Rotamer: Outliers : 3.62 % Allowed : 23.27 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.98 (0.30), residues: 791 helix: 1.97 (0.30), residues: 280 sheet: 0.68 (0.41), residues: 155 loop : -0.40 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 226 TYR 0.007 0.001 TYR F 103 PHE 0.012 0.001 PHE G 203 TRP 0.008 0.001 TRP A 129 HIS 0.002 0.001 HIS F 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 6315) covalent geometry : angle 0.52345 / 0.28 ( 8551) hydrogen bonds : bond 0.03477 / 2.29 ( 308) hydrogen bonds : angle 4.14114 / 2.87 ( 846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.218 Fit side-chains REVERT: A 101 TYR cc_start: 0.7474 (OUTLIER) cc_final: 0.6874 (m-80) REVERT: A 113 MET cc_start: 0.6144 (ttp) cc_final: 0.5908 (ttt) REVERT: A 131 SER cc_start: 0.7919 (OUTLIER) cc_final: 0.7516 (m) REVERT: A 134 LYS cc_start: 0.7691 (tptm) cc_final: 0.7372 (tptt) REVERT: A 212 MET cc_start: 0.7808 (mtm) cc_final: 0.7265 (mmm) REVERT: A 217 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7870 (mt-10) REVERT: F 27 MET cc_start: 0.7954 (ptm) cc_final: 0.7711 (ptm) REVERT: F 111 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7692 (pt) REVERT: F 184 GLN cc_start: 0.7656 (tm-30) cc_final: 0.7294 (tm-30) REVERT: F 226 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8369 (mtt-85) REVERT: F 271 TYR cc_start: 0.7846 (m-10) cc_final: 0.7526 (m-80) outliers start: 23 outliers final: 11 residues processed: 95 average time/residue: 0.5219 time to fit residues: 51.7154 Evaluate side-chains 99 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 226 ARG Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 67 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 213 ASN G 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.157916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.111517 restraints weight = 6395.697| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.41 r_work: 0.3012 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 6315 Z= 0.200 Angle : 0.571 8.285 8551 Z= 0.300 Chirality : 0.046 0.239 971 Planarity : 0.004 0.040 1083 Dihedral : 13.776 174.564 921 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.90 % Favored : 97.98 % Rotamer: Outliers : 3.46 % Allowed : 23.58 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.82 (0.30), residues: 791 helix: 1.85 (0.30), residues: 280 sheet: 0.54 (0.41), residues: 155 loop : -0.47 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 243 TYR 0.006 0.001 TYR F 103 PHE 0.013 0.002 PHE G 203 TRP 0.009 0.001 TRP A 129 HIS 0.003 0.001 HIS F 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 ( 6315) covalent geometry : angle 0.57133 / 0.30 ( 8551) hydrogen bonds : bond 0.03730 / 2.46 ( 308) hydrogen bonds : angle 4.20617 / 2.91 ( 846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.130 Fit side-chains REVERT: A 101 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.6762 (m-80) REVERT: A 113 MET cc_start: 0.6159 (ttp) cc_final: 0.5913 (ttt) REVERT: A 131 SER cc_start: 0.7889 (OUTLIER) cc_final: 0.7447 (m) REVERT: A 212 MET cc_start: 0.7815 (mtm) cc_final: 0.7287 (mmm) REVERT: A 217 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: F 27 MET cc_start: 0.7974 (ptm) cc_final: 0.7716 (ptm) REVERT: F 111 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7748 (pt) REVERT: F 226 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8435 (mtt-85) REVERT: F 271 TYR cc_start: 0.7795 (m-10) cc_final: 0.7517 (m-80) REVERT: G 332 ASN cc_start: 0.0091 (OUTLIER) cc_final: -0.0834 (p0) outliers start: 22 outliers final: 9 residues processed: 92 average time/residue: 0.5214 time to fit residues: 50.0566 Evaluate side-chains 96 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 226 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 332 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 5 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 43 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 213 ASN G 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.159777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.113744 restraints weight = 6388.786| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.40 r_work: 0.3044 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6315 Z= 0.132 Angle : 0.502 8.305 8551 Z= 0.269 Chirality : 0.043 0.200 971 Planarity : 0.003 0.036 1083 Dihedral : 13.706 174.708 921 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.14 % Favored : 98.74 % Rotamer: Outliers : 3.62 % Allowed : 23.27 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.94 (0.30), residues: 791 helix: 1.97 (0.30), residues: 280 sheet: 0.65 (0.41), residues: 155 loop : -0.45 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 183 TYR 0.008 0.001 TYR F 103 PHE 0.010 0.001 PHE G 203 TRP 0.010 0.001 TRP A 129 HIS 0.003 0.001 HIS F 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 6315) covalent geometry : angle 0.50235 / 0.27 ( 8551) hydrogen bonds : bond 0.03232 / 2.12 ( 308) hydrogen bonds : angle 4.10960 / 2.85 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.138 Fit side-chains REVERT: A 101 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.7213 (m-80) REVERT: A 102 GLU cc_start: 0.7561 (pt0) cc_final: 0.7152 (pt0) REVERT: A 113 MET cc_start: 0.5970 (ttp) cc_final: 0.5751 (ttt) REVERT: A 131 SER cc_start: 0.7893 (OUTLIER) cc_final: 0.7449 (m) REVERT: A 212 MET cc_start: 0.7819 (mtm) cc_final: 0.7300 (mmm) REVERT: A 217 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7849 (mt-10) REVERT: F 27 MET cc_start: 0.7927 (ptm) cc_final: 0.7662 (ptm) REVERT: F 111 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7819 (pt) REVERT: F 226 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8296 (mtt-85) REVERT: F 271 TYR cc_start: 0.7798 (m-10) cc_final: 0.7532 (m-80) REVERT: G 332 ASN cc_start: -0.0386 (OUTLIER) cc_final: -0.1040 (t0) outliers start: 23 outliers final: 11 residues processed: 98 average time/residue: 0.4975 time to fit residues: 50.9154 Evaluate side-chains 98 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 226 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 332 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 33 optimal weight: 0.2980 chunk 77 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 GLN F 213 ASN G 113 ASN G 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.160681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.114675 restraints weight = 6383.983| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.41 r_work: 0.3055 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6315 Z= 0.125 Angle : 0.491 7.332 8551 Z= 0.262 Chirality : 0.043 0.189 971 Planarity : 0.003 0.036 1083 Dihedral : 13.672 174.293 921 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.26 % Favored : 98.61 % Rotamer: Outliers : 3.30 % Allowed : 22.96 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.01 (0.30), residues: 791 helix: 1.97 (0.29), residues: 292 sheet: 0.71 (0.41), residues: 155 loop : -0.46 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 85 TYR 0.007 0.001 TYR F 103 PHE 0.009 0.001 PHE G 203 TRP 0.010 0.001 TRP A 129 HIS 0.004 0.001 HIS F 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 6315) covalent geometry : angle 0.49099 / 0.26 ( 8551) hydrogen bonds : bond 0.03125 / 2.05 ( 308) hydrogen bonds : angle 4.06039 / 2.82 ( 846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.186 Fit side-chains REVERT: A 101 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.7173 (m-80) REVERT: A 103 TYR cc_start: 0.8535 (m-80) cc_final: 0.8319 (m-80) REVERT: A 113 MET cc_start: 0.5972 (ttp) cc_final: 0.5743 (ttt) REVERT: A 131 SER cc_start: 0.7925 (OUTLIER) cc_final: 0.7522 (m) REVERT: A 193 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8332 (tmmm) REVERT: A 217 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: F 27 MET cc_start: 0.7908 (ptm) cc_final: 0.7640 (ptm) REVERT: F 111 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7815 (pt) REVERT: F 226 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8324 (mtt-85) REVERT: F 271 TYR cc_start: 0.7727 (m-10) cc_final: 0.7501 (m-80) REVERT: G 332 ASN cc_start: -0.0591 (OUTLIER) cc_final: -0.1226 (t0) outliers start: 21 outliers final: 9 residues processed: 94 average time/residue: 0.5423 time to fit residues: 53.2175 Evaluate side-chains 97 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 226 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 332 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.0060 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 213 ASN G 118 GLN G 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.163014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.122404 restraints weight = 6423.055| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.00 r_work: 0.2993 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6315 Z= 0.105 Angle : 0.471 6.872 8551 Z= 0.253 Chirality : 0.042 0.167 971 Planarity : 0.003 0.035 1083 Dihedral : 13.583 173.201 921 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.26 % Favored : 98.61 % Rotamer: Outliers : 2.36 % Allowed : 23.74 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.12 (0.30), residues: 791 helix: 2.08 (0.30), residues: 292 sheet: 0.70 (0.42), residues: 157 loop : -0.39 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 85 TYR 0.006 0.001 TYR F 103 PHE 0.008 0.001 PHE G 260 TRP 0.011 0.001 TRP A 129 HIS 0.004 0.001 HIS F 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 6315) covalent geometry : angle 0.47133 / 0.25 ( 8551) hydrogen bonds : bond 0.02915 / 1.91 ( 308) hydrogen bonds : angle 4.01756 / 2.79 ( 846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.133 Fit side-chains REVERT: A 103 TYR cc_start: 0.8553 (m-80) cc_final: 0.8315 (m-80) REVERT: A 113 MET cc_start: 0.5963 (ttp) cc_final: 0.5753 (ttt) REVERT: A 131 SER cc_start: 0.7912 (OUTLIER) cc_final: 0.7540 (m) REVERT: A 193 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8392 (tmmm) REVERT: A 217 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: F 27 MET cc_start: 0.7914 (ptm) cc_final: 0.7625 (ptm) REVERT: F 111 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7932 (pt) REVERT: F 226 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8256 (mtt-85) REVERT: F 271 TYR cc_start: 0.7802 (m-10) cc_final: 0.7590 (m-80) REVERT: G 332 ASN cc_start: -0.0626 (OUTLIER) cc_final: -0.1318 (t0) outliers start: 15 outliers final: 7 residues processed: 89 average time/residue: 0.5522 time to fit residues: 51.2601 Evaluate side-chains 92 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 226 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 332 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.0970 chunk 50 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.159872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.113865 restraints weight = 6376.435| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.39 r_work: 0.3039 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6315 Z= 0.155 Angle : 0.520 7.393 8551 Z= 0.275 Chirality : 0.044 0.211 971 Planarity : 0.004 0.037 1083 Dihedral : 13.689 172.516 921 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.64 % Favored : 98.23 % Rotamer: Outliers : 2.67 % Allowed : 23.43 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.04 (0.30), residues: 791 helix: 2.08 (0.30), residues: 280 sheet: 0.70 (0.41), residues: 155 loop : -0.43 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 226 TYR 0.006 0.001 TYR F 103 PHE 0.012 0.001 PHE G 203 TRP 0.011 0.001 TRP A 129 HIS 0.005 0.001 HIS F 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 6315) covalent geometry : angle 0.52008 / 0.27 ( 8551) hydrogen bonds : bond 0.03326 / 2.18 ( 308) hydrogen bonds : angle 4.07073 / 2.82 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1960.89 seconds wall clock time: 33 minutes 59.44 seconds (2039.44 seconds total)