Starting phenix.real_space_refine on Fri Aug 22 17:09:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gmu_34154/08_2025/8gmu_34154.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gmu_34154/08_2025/8gmu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gmu_34154/08_2025/8gmu_34154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gmu_34154/08_2025/8gmu_34154.map" model { file = "/net/cci-nas-00/data/ceres_data/8gmu_34154/08_2025/8gmu_34154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gmu_34154/08_2025/8gmu_34154.cif" } 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-2.0-5787/lib/python3.9/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: 1.57, per 1000 atoms: 0.25 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: 0.52 Conformation dependent library (CDL) restraints added in 320.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.15 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: 0.79 Time building geometry restraints manager: 0.65 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=" CA VAL F 246 " pdb=" CB VAL F 246 " ideal model delta sigma weight residual 1.527 1.538 -0.011 1.31e-02 5.83e+03 7.48e-01 bond pdb=" C GLU A 146 " pdb=" N GLY A 147 " ideal model delta sigma weight residual 1.331 1.318 0.012 1.46e-02 4.69e+03 7.24e-01 bond pdb=" C4' DT S 9 " pdb=" O4' DT S 9 " ideal model delta sigma weight residual 1.450 1.433 0.017 2.00e-02 2.50e+03 7.17e-01 bond pdb=" CB LYS G 198 " pdb=" CG LYS G 198 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 7.14e-01 bond pdb=" N ARG A 119 " pdb=" CA ARG A 119 " ideal model delta sigma weight residual 1.457 1.468 -0.010 1.29e-02 6.01e+03 6.31e-01 ... (remaining 6310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 8317 1.45 - 2.89: 201 2.89 - 4.34: 26 4.34 - 5.79: 6 5.79 - 7.23: 1 Bond angle restraints: 8551 Sorted by residual: angle pdb=" C LEU A 118 " pdb=" N ARG A 119 " pdb=" CA ARG A 119 " ideal model delta sigma weight residual 121.54 128.77 -7.23 1.91e+00 2.74e-01 1.43e+01 angle pdb=" CA ILE A 195 " pdb=" CB ILE A 195 " pdb=" CG1 ILE A 195 " ideal model delta sigma weight residual 110.40 115.01 -4.61 1.70e+00 3.46e-01 7.37e+00 angle pdb=" CA MET F 197 " pdb=" CB MET F 197 " pdb=" CG MET F 197 " ideal model delta sigma weight residual 114.10 119.36 -5.26 2.00e+00 2.50e-01 6.93e+00 angle pdb=" C4' DT S 9 " pdb=" O4' DT S 9 " pdb=" C1' DT S 9 " ideal model delta sigma weight residual 109.70 106.22 3.48 1.50e+00 4.44e-01 5.38e+00 angle pdb=" N ILE A 213 " pdb=" CA ILE A 213 " pdb=" C ILE A 213 " ideal model delta sigma weight residual 107.76 109.79 -2.03 1.01e+00 9.80e-01 4.05e+00 ... (remaining 8546 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.21: 3620 34.21 - 68.43: 202 68.43 - 102.64: 13 102.64 - 136.85: 0 136.85 - 171.07: 2 Dihedral angle restraints: 3837 sinusoidal: 1588 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 3834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 717 0.040 - 0.081: 171 0.081 - 0.121: 75 0.121 - 0.161: 7 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=" 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 chirality pdb=" CG LEU G 309 " pdb=" CB LEU G 309 " pdb=" CD1 LEU G 309 " pdb=" CD2 LEU G 309 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.14e-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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.990 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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= 0.140 Angle : 0.546 7.234 8551 Z= 0.311 Chirality : 0.042 0.202 971 Planarity : 0.004 0.063 1083 Dihedral : 19.468 171.067 2399 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 aren 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 covalent geometry : bond 0.00302 ( 6315) covalent geometry : angle 0.54572 ( 8551) hydrogen bonds : bond 0.15847 ( 308) hydrogen bonds : angle 5.85839 ( 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 : 0.231 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: 0.5625 time to fit residues: 55.7696 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 : 0.239 ------------------------------------------------------------------------------- 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: 0.7980 chunk 62 optimal weight: 5.9990 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: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3734 r_free = 0.3734 target = 0.163085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.122444 restraints weight = 6372.553| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.93 r_work: 0.3011 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6315 Z= 0.106 Angle : 0.485 4.780 8551 Z= 0.265 Chirality : 0.042 0.148 971 Planarity : 0.004 0.050 1083 Dihedral : 13.558 164.540 954 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.64 % Favored : 98.23 % Rotamer: Outliers : 3.14 % Allowed : 21.54 % Favored : 75.31 % 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 aren not related in a simple way. whole: 1.31 (0.30), residues: 791 helix: 2.08 (0.30), residues: 292 sheet: 1.32 (0.42), residues: 144 loop : -0.35 (0.33), residues: 355 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 0.009 0.001 PHE G 260 TRP 0.012 0.001 TRP F 308 HIS 0.002 0.000 HIS F 163 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 6315) covalent geometry : angle 0.48503 ( 8551) hydrogen bonds : bond 0.03460 ( 308) hydrogen bonds : angle 4.40389 ( 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 107 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.243 Fit side-chains REVERT: A 101 TYR cc_start: 0.7230 (OUTLIER) cc_final: 0.6682 (m-80) REVERT: A 113 MET cc_start: 0.6244 (ttp) cc_final: 0.5982 (ttt) REVERT: A 114 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.5778 (t80) REVERT: A 149 SER cc_start: 0.7881 (p) cc_final: 0.7652 (t) REVERT: F 184 GLN cc_start: 0.7641 (tm-30) cc_final: 0.7427 (tm-30) REVERT: F 197 MET cc_start: 0.8302 (tmt) cc_final: 0.7954 (ppp) REVERT: F 271 TYR cc_start: 0.7985 (m-10) cc_final: 0.7593 (m-80) REVERT: G 256 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7804 (mtmt) outliers start: 20 outliers final: 6 residues processed: 100 average time/residue: 0.6215 time to fit residues: 64.8020 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 : 0.179 ------------------------------------------------------------------------------- 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: 0.3980 chunk 42 optimal weight: 0.0570 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3743 r_free = 0.3743 target = 0.163945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.122472 restraints weight = 6370.032| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.01 r_work: 0.3019 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6315 Z= 0.098 Angle : 0.459 5.813 8551 Z= 0.247 Chirality : 0.041 0.139 971 Planarity : 0.003 0.043 1083 Dihedral : 12.956 166.640 943 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.01 % Favored : 98.86 % Rotamer: Outliers : 2.67 % Allowed : 22.48 % Favored : 74.84 % 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 aren not related in a simple way. whole: 1.44 (0.30), residues: 791 helix: 2.30 (0.30), residues: 292 sheet: 1.29 (0.42), residues: 147 loop : -0.34 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 183 TYR 0.005 0.001 TYR F 103 PHE 0.007 0.001 PHE G 260 TRP 0.008 0.001 TRP F 308 HIS 0.002 0.001 HIS F 163 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 6315) covalent geometry : angle 0.45857 ( 8551) hydrogen bonds : bond 0.03134 ( 308) hydrogen bonds : angle 4.16743 ( 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 99 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.182 Fit side-chains REVERT: A 101 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6677 (m-80) REVERT: A 102 GLU cc_start: 0.7601 (pt0) cc_final: 0.7247 (pt0) REVERT: A 113 MET cc_start: 0.6142 (ttp) cc_final: 0.5918 (ttt) REVERT: A 114 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.5458 (t80) REVERT: A 149 SER cc_start: 0.7889 (p) cc_final: 0.7653 (t) REVERT: A 188 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8355 (mt-10) REVERT: A 193 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8378 (tmmm) REVERT: A 217 GLU cc_start: 0.8075 (mp0) cc_final: 0.7846 (mt-10) REVERT: F 184 GLN cc_start: 0.7624 (tm-30) cc_final: 0.7397 (tm-30) REVERT: F 271 TYR cc_start: 0.8003 (m-10) cc_final: 0.7566 (m-80) outliers start: 17 outliers final: 9 residues processed: 92 average time/residue: 0.5949 time to fit residues: 57.3373 Evaluate side-chains 90 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 144 GLU 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: 0.7980 chunk 40 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.160174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.119004 restraints weight = 6368.372| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.95 r_work: 0.2940 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6315 Z= 0.164 Angle : 0.523 5.474 8551 Z= 0.277 Chirality : 0.044 0.172 971 Planarity : 0.004 0.041 1083 Dihedral : 13.188 171.975 943 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.39 % Favored : 98.48 % Rotamer: Outliers : 3.46 % Allowed : 22.01 % 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 aren not related in a simple way. whole: 1.21 (0.30), residues: 791 helix: 2.03 (0.29), residues: 292 sheet: 0.89 (0.41), residues: 155 loop : -0.28 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 226 TYR 0.006 0.001 TYR F 103 PHE 0.013 0.001 PHE G 203 TRP 0.007 0.001 TRP F 308 HIS 0.003 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 6315) covalent geometry : angle 0.52292 ( 8551) hydrogen bonds : bond 0.03537 ( 308) hydrogen bonds : angle 4.15668 ( 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 105 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.285 Fit side-chains REVERT: A 101 TYR cc_start: 0.7457 (OUTLIER) cc_final: 0.6900 (m-80) REVERT: A 113 MET cc_start: 0.6330 (ttp) cc_final: 0.6061 (ttt) REVERT: A 134 LYS cc_start: 0.7891 (tptm) cc_final: 0.7654 (tptt) REVERT: A 149 SER cc_start: 0.8102 (p) cc_final: 0.7877 (t) REVERT: A 193 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8519 (tmmm) REVERT: A 217 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: F 184 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7458 (tm-30) REVERT: F 271 TYR cc_start: 0.7951 (m-10) cc_final: 0.7603 (m-80) outliers start: 22 outliers final: 10 residues processed: 95 average time/residue: 0.6672 time to fit residues: 66.3346 Evaluate side-chains 94 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 144 GLU 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: 10.0000 chunk 11 optimal weight: 7.9990 chunk 67 optimal weight: 0.0870 chunk 62 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 46 optimal weight: 0.4980 chunk 72 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3709 r_free = 0.3709 target = 0.160674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.119441 restraints weight = 6459.557| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.96 r_work: 0.2954 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1202 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= 0.153 Angle : 0.506 5.125 8551 Z= 0.269 Chirality : 0.043 0.184 971 Planarity : 0.004 0.039 1083 Dihedral : 13.217 171.906 943 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.39 % Favored : 98.48 % 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 aren not related in a simple way. whole: 1.16 (0.30), residues: 791 helix: 2.12 (0.30), residues: 280 sheet: 0.82 (0.41), residues: 155 loop : -0.33 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 226 TYR 0.008 0.001 TYR F 103 PHE 0.011 0.001 PHE G 203 TRP 0.009 0.001 TRP A 129 HIS 0.002 0.001 HIS F 163 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 6315) covalent geometry : angle 0.50556 ( 8551) hydrogen bonds : bond 0.03381 ( 308) hydrogen bonds : angle 4.12420 ( 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 105 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.258 Fit side-chains REVERT: A 101 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.7072 (m-80) REVERT: A 102 GLU cc_start: 0.7657 (pt0) cc_final: 0.7382 (pt0) REVERT: A 113 MET cc_start: 0.6343 (ttp) cc_final: 0.6092 (ttt) REVERT: A 134 LYS cc_start: 0.7875 (tptm) cc_final: 0.7526 (tptt) REVERT: A 204 GLN cc_start: 0.8385 (pt0) cc_final: 0.8141 (pt0) REVERT: A 212 MET cc_start: 0.7934 (mtm) cc_final: 0.7359 (mmm) REVERT: A 217 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7870 (mt-10) REVERT: F 111 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7810 (pt) REVERT: F 184 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7440 (tm-30) REVERT: F 271 TYR cc_start: 0.7933 (m-10) cc_final: 0.7607 (m-80) outliers start: 21 outliers final: 10 residues processed: 94 average time/residue: 0.6849 time to fit residues: 67.2339 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 : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 144 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 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 Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 11 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 20.0000 chunk 54 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3710 r_free = 0.3710 target = 0.160909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.119699 restraints weight = 6346.341| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.44 r_work: 0.3078 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6315 Z= 0.131 Angle : 0.480 4.910 8551 Z= 0.257 Chirality : 0.042 0.177 971 Planarity : 0.003 0.037 1083 Dihedral : 13.148 172.288 943 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.26 % Favored : 98.61 % Rotamer: Outliers : 3.14 % Allowed : 23.58 % Favored : 73.27 % 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 aren not related in a simple way. whole: 1.20 (0.30), residues: 791 helix: 2.18 (0.30), residues: 280 sheet: 0.82 (0.41), residues: 155 loop : -0.32 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 226 TYR 0.007 0.001 TYR F 103 PHE 0.010 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 covalent geometry : bond 0.00303 ( 6315) covalent geometry : angle 0.47969 ( 8551) hydrogen bonds : bond 0.03183 ( 308) hydrogen bonds : angle 4.07737 ( 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 105 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.254 Fit side-chains REVERT: A 101 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.7095 (m-80) REVERT: A 102 GLU cc_start: 0.7630 (pt0) cc_final: 0.7370 (pt0) REVERT: A 113 MET cc_start: 0.6011 (ttp) cc_final: 0.5787 (ttt) REVERT: A 134 LYS cc_start: 0.7864 (tptm) cc_final: 0.7625 (tptt) REVERT: A 204 GLN cc_start: 0.8322 (pt0) cc_final: 0.8114 (pt0) REVERT: A 212 MET cc_start: 0.7901 (mtm) cc_final: 0.7375 (mmm) REVERT: A 217 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7855 (mt-10) REVERT: F 111 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7782 (pt) REVERT: F 184 GLN cc_start: 0.7699 (tm-30) cc_final: 0.7380 (tm-30) REVERT: F 226 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8329 (mtt-85) REVERT: F 271 TYR cc_start: 0.7896 (m-10) cc_final: 0.7577 (m-80) REVERT: G 183 LYS cc_start: 0.8423 (tppp) cc_final: 0.7707 (tptp) outliers start: 20 outliers final: 11 residues processed: 94 average time/residue: 0.7476 time to fit residues: 73.1902 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 : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 144 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 96 GLU 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 236 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 71 optimal weight: 0.4980 chunk 12 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 67 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3715 r_free = 0.3715 target = 0.161322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.120327 restraints weight = 6369.767| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.44 r_work: 0.3082 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1354 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= 0.122 Angle : 0.468 4.943 8551 Z= 0.251 Chirality : 0.042 0.167 971 Planarity : 0.003 0.036 1083 Dihedral : 13.084 172.895 943 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.14 % Favored : 98.74 % Rotamer: Outliers : 3.62 % Allowed : 23.58 % Favored : 72.80 % 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 aren not related in a simple way. whole: 1.25 (0.30), residues: 791 helix: 2.26 (0.30), residues: 280 sheet: 0.86 (0.41), residues: 155 loop : -0.33 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 243 TYR 0.007 0.001 TYR F 103 PHE 0.009 0.001 PHE G 203 TRP 0.008 0.001 TRP A 129 HIS 0.003 0.001 HIS F 163 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6315) covalent geometry : angle 0.46778 ( 8551) hydrogen bonds : bond 0.03071 ( 308) hydrogen bonds : angle 4.05320 ( 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 105 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.244 Fit side-chains REVERT: A 101 TYR cc_start: 0.7561 (OUTLIER) cc_final: 0.7224 (m-80) REVERT: A 102 GLU cc_start: 0.7610 (pt0) cc_final: 0.7335 (pt0) REVERT: A 113 MET cc_start: 0.5919 (ttp) cc_final: 0.5688 (ttt) REVERT: A 134 LYS cc_start: 0.7866 (tptm) cc_final: 0.7623 (tptt) REVERT: A 204 GLN cc_start: 0.8300 (pt0) cc_final: 0.8099 (pt0) REVERT: A 212 MET cc_start: 0.7923 (mtm) cc_final: 0.7400 (mmm) REVERT: A 217 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7857 (mt-10) REVERT: F 111 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7861 (pt) REVERT: F 184 GLN cc_start: 0.7709 (tm-30) cc_final: 0.7376 (tm-30) REVERT: F 226 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8323 (mtt-85) REVERT: F 271 TYR cc_start: 0.7905 (m-10) cc_final: 0.7595 (m-80) REVERT: G 58 MET cc_start: 0.8817 (mmp) cc_final: 0.8607 (mmt) outliers start: 23 outliers final: 12 residues processed: 94 average time/residue: 0.7283 time to fit residues: 71.2818 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 : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 144 GLU 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 F residue 202 MET Chi-restraints excluded: chain F residue 226 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 5 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 24 optimal weight: 0.0030 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 118 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 = 0.3730 r_free = 0.3730 target = 0.162754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.121510 restraints weight = 6370.327| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.44 r_work: 0.3096 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1436 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= 0.102 Angle : 0.450 4.816 8551 Z= 0.244 Chirality : 0.041 0.153 971 Planarity : 0.003 0.034 1083 Dihedral : 13.014 173.582 943 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.14 % Favored : 98.74 % Rotamer: Outliers : 2.83 % Allowed : 24.06 % 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 aren not related in a simple way. whole: 1.29 (0.30), residues: 791 helix: 2.22 (0.30), residues: 292 sheet: 0.82 (0.42), residues: 157 loop : -0.30 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 169 TYR 0.006 0.001 TYR F 103 PHE 0.008 0.001 PHE G 260 TRP 0.009 0.001 TRP A 129 HIS 0.003 0.001 HIS F 163 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 6315) covalent geometry : angle 0.45007 ( 8551) hydrogen bonds : bond 0.02857 ( 308) hydrogen bonds : angle 4.00861 ( 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 98 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.257 Fit side-chains REVERT: A 103 TYR cc_start: 0.8559 (m-80) cc_final: 0.8329 (m-80) REVERT: A 113 MET cc_start: 0.5869 (ttp) cc_final: 0.5634 (ttt) REVERT: A 134 LYS cc_start: 0.7872 (tptm) cc_final: 0.7529 (tptt) REVERT: A 204 GLN cc_start: 0.8266 (pt0) cc_final: 0.8027 (pt0) REVERT: A 212 MET cc_start: 0.7926 (mtm) cc_final: 0.7394 (mmm) REVERT: A 217 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: F 111 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7862 (pt) REVERT: F 184 GLN cc_start: 0.7717 (tm-30) cc_final: 0.7389 (tm-30) REVERT: F 271 TYR cc_start: 0.7904 (m-10) cc_final: 0.7601 (m-80) REVERT: G 332 ASN cc_start: -0.0422 (OUTLIER) cc_final: -0.1104 (p0) outliers start: 18 outliers final: 9 residues processed: 90 average time/residue: 0.7041 time to fit residues: 66.1293 Evaluate side-chains 90 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU 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 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 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: 0.6980 chunk 77 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 2 optimal weight: 0.0060 chunk 52 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3718 r_free = 0.3718 target = 0.161594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.120266 restraints weight = 6375.585| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.45 r_work: 0.3086 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1442 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 : 0.480 5.156 8551 Z= 0.257 Chirality : 0.043 0.181 971 Planarity : 0.003 0.035 1083 Dihedral : 13.074 174.437 943 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.52 % Favored : 98.36 % Rotamer: Outliers : 2.36 % Allowed : 24.37 % Favored : 73.27 % 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 aren not related in a simple way. whole: 1.28 (0.30), residues: 791 helix: 2.30 (0.30), residues: 280 sheet: 0.91 (0.42), residues: 155 loop : -0.34 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 226 TYR 0.007 0.001 TYR F 103 PHE 0.010 0.001 PHE G 203 TRP 0.009 0.001 TRP A 129 HIS 0.004 0.001 HIS F 163 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6315) covalent geometry : angle 0.47989 ( 8551) hydrogen bonds : bond 0.03119 ( 308) hydrogen bonds : angle 4.02634 ( 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 94 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.248 Fit side-chains REVERT: A 113 MET cc_start: 0.5862 (ttp) cc_final: 0.5619 (ttt) REVERT: A 144 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6918 (pp20) REVERT: A 204 GLN cc_start: 0.8269 (pt0) cc_final: 0.8064 (pt0) REVERT: A 212 MET cc_start: 0.7881 (mtm) cc_final: 0.7375 (mmm) REVERT: A 217 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: F 111 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7875 (pt) REVERT: F 226 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8322 (mtt-85) REVERT: F 271 TYR cc_start: 0.7890 (m-10) cc_final: 0.7583 (m-80) REVERT: G 332 ASN cc_start: -0.0149 (OUTLIER) cc_final: -0.1017 (p0) outliers start: 15 outliers final: 9 residues processed: 90 average time/residue: 0.7192 time to fit residues: 67.5062 Evaluate side-chains 92 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU 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 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 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 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: 2.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.160721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.114415 restraints weight = 6390.495| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.41 r_work: 0.3045 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: 0.7960 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6315 Z= 0.157 Angle : 0.508 5.238 8551 Z= 0.271 Chirality : 0.044 0.211 971 Planarity : 0.004 0.036 1083 Dihedral : 13.206 174.288 943 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.52 % Favored : 98.36 % Rotamer: Outliers : 2.52 % Allowed : 24.53 % 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 aren not related in a simple way. whole: 1.16 (0.30), residues: 791 helix: 2.16 (0.30), residues: 280 sheet: 0.84 (0.41), residues: 155 loop : -0.37 (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 0.011 0.001 TRP A 129 HIS 0.005 0.001 HIS F 163 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 6315) covalent geometry : angle 0.50811 ( 8551) hydrogen bonds : bond 0.03326 ( 308) hydrogen bonds : angle 4.07871 ( 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: 16 poor density : 78 time to evaluate : 0.257 Fit side-chains REVERT: A 113 MET cc_start: 0.5854 (ttp) cc_final: 0.5623 (ttt) REVERT: A 217 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: F 111 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7788 (pt) REVERT: F 184 GLN cc_start: 0.7958 (tp40) cc_final: 0.7751 (tm-30) REVERT: F 226 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8360 (mtt-85) REVERT: F 271 TYR cc_start: 0.7801 (m-10) cc_final: 0.7516 (m-80) REVERT: G 332 ASN cc_start: -0.0466 (OUTLIER) cc_final: -0.1325 (p0) outliers start: 16 outliers final: 8 residues processed: 89 average time/residue: 0.7232 time to fit residues: 67.0068 Evaluate side-chains 90 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 51 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.161597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.120375 restraints weight = 6345.237| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.42 r_work: 0.3088 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1529 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= 0.126 Angle : 0.480 6.984 8551 Z= 0.257 Chirality : 0.042 0.179 971 Planarity : 0.003 0.035 1083 Dihedral : 13.173 174.429 943 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.39 % Favored : 98.48 % Rotamer: Outliers : 2.52 % Allowed : 24.21 % Favored : 73.27 % 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 aren not related in a simple way. whole: 1.24 (0.30), residues: 791 helix: 2.27 (0.30), residues: 280 sheet: 0.90 (0.42), residues: 155 loop : -0.37 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 243 TYR 0.007 0.001 TYR F 103 PHE 0.010 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 covalent geometry : bond 0.00293 ( 6315) covalent geometry : angle 0.47980 ( 8551) hydrogen bonds : bond 0.03094 ( 308) hydrogen bonds : angle 4.03585 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2495.05 seconds wall clock time: 43 minutes 22.15 seconds (2602.15 seconds total)